--- /srv/reproducible-results/rbuild-debian/r-b-build.PxhV4VLr/b1/apbs_3.0.0+dfsg1-3_armhf.changes +++ /srv/reproducible-results/rbuild-debian/r-b-build.PxhV4VLr/b2/apbs_3.0.0+dfsg1-3_armhf.changes ├── Files │ @@ -1,9 +1,9 @@ │ │ - efe39fb66072236bbd44b855bd6adfd1 226054036 science optional apbs-data_3.0.0+dfsg1-3_all.deb │ + 8e0bd964794838aabf020cad9382382f 226051632 science optional apbs-data_3.0.0+dfsg1-3_all.deb │ aec9e52af137eebf716292f3f873b8e1 150680 debug optional apbs-dbgsym_3.0.0+dfsg1-3_armhf.deb │ f6b368384fdb2d7a36d6154b5e846a86 78452 science optional apbs_3.0.0+dfsg1-3_armhf.deb │ 686fd59d452b8837e34a0f61fa49a2c4 66312 libdevel optional libapbs-dev_3.0.0+dfsg1-3_armhf.deb │ 1c0731a6357931f15ddde136c32d8a01 517500 debug optional libapbs3-dbgsym_3.0.0+dfsg1-3_armhf.deb │ c5f7e47c9c4fc893e4306febf64268d2 215104 libs optional libapbs3_3.0.0+dfsg1-3_armhf.deb │ acca7639e805699d8399027302dac4e4 157116 debug optional python3-apbslib-dbgsym_3.0.0+dfsg1-3_armhf.deb │ 4770e2f8ce8b8319254161c605116a44 98876 python optional python3-apbslib_3.0.0+dfsg1-3_armhf.deb ├── apbs-data_3.0.0+dfsg1-3_all.deb │ ├── file list │ │ @@ -1,3 +1,3 @@ │ │ -rw-r--r-- 0 0 0 4 2020-07-23 09:35:23.000000 debian-binary │ │ -rw-r--r-- 0 0 0 13240 2020-07-23 09:35:23.000000 control.tar.xz │ │ --rw-r--r-- 0 0 0 226040604 2020-07-23 09:35:23.000000 data.tar.xz │ │ +-rw-r--r-- 0 0 0 226038200 2020-07-23 09:35:23.000000 data.tar.xz │ ├── control.tar.xz │ │ ├── control.tar │ │ │ ├── ./md5sums │ │ │ │ ├── ./md5sums │ │ │ │ │┄ Files differ │ ├── data.tar.xz │ │ ├── data.tar │ │ │ ├── ./usr/share/apbs/examples/FKBP/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:31:41 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:06:15 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr │ │ │ │ @@ -637,32 +637,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.747532 │ │ │ │ +Vacc_SASA: Time elapsed: 2.800800 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.440030e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.495752e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.120000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.139600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.212330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.427620e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.778378e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.866708e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.211746e-02 │ │ │ │ Vprtstp: contraction number = 6.211746e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -736,32 +736,32 @@ │ │ │ │ Vprtstp: contraction number = 6.956346e-01 │ │ │ │ Vprtstp: iteration = 25 │ │ │ │ Vprtstp: relative residual = 1.302234e-06 │ │ │ │ Vprtstp: contraction number = 6.974500e-01 │ │ │ │ Vprtstp: iteration = 26 │ │ │ │ Vprtstp: relative residual = 9.101840e-07 │ │ │ │ Vprtstp: contraction number = 6.989406e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.359739e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.557417e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.945705e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.164739e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.506409949028E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.660000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.600000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -807,30 +807,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 7766.58 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 3755.14 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.679923 │ │ │ │ +Vacc_SASA: Time elapsed: 2.753520 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.006659e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.073444e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.197400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.934000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.248410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.304250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.635267e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.821158e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.221522e-01 │ │ │ │ Vprtstp: contraction number = 1.221522e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -862,32 +862,32 @@ │ │ │ │ Vprtstp: contraction number = 4.471936e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.248629e-06 │ │ │ │ Vprtstp: contraction number = 4.746468e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 6.237535e-07 │ │ │ │ Vprtstp: contraction number = 4.995506e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.965273e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.163964e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.851445e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.166334e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.428963535142E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.930000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.470000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -908,32 +908,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.715463 │ │ │ │ +Vacc_SASA: Time elapsed: 2.779524 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.447688e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.447611e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.087200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.837500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.233180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.847760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.597480e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.878936e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.215755e-02 │ │ │ │ Vprtstp: contraction number = 2.215755e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -947,30 +947,30 @@ │ │ │ │ Vprtstp: contraction number = 9.587608e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.603412e-06 │ │ │ │ Vprtstp: contraction number = 9.909475e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.626039e-07 │ │ │ │ Vprtstp: contraction number = 1.014112e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.437317e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.637238e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.871542e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.140878e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.121921918409E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.360000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.560000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ @@ -1018,30 +1018,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 10309.9 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4985.22 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.675139 │ │ │ │ +Vacc_SASA: Time elapsed: 2.759214 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.983108e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.080852e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.989300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.990500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.235550e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.771010e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.060038e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.401032e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.329182e-01 │ │ │ │ Vprtstp: contraction number = 1.329182e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1058,32 +1058,32 @@ │ │ │ │ Vprtstp: contraction number = 1.009933e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.280625e-06 │ │ │ │ Vprtstp: contraction number = 1.024328e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.326631e-07 │ │ │ │ Vprtstp: contraction number = 1.035924e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.751563e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.947250e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.192909e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.451687e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.696401888033E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.890000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.250000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -1104,32 +1104,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.006950 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005318 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.045500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.289100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.146600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.430800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.232980e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.768080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.265268e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.655746e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.503042e-01 │ │ │ │ Vprtstp: contraction number = 1.503042e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1146,32 +1146,32 @@ │ │ │ │ Vprtstp: contraction number = 1.186135e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 3.304907e-06 │ │ │ │ Vprtstp: contraction number = 1.191339e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.951730e-07 │ │ │ │ Vprtstp: contraction number = 1.195716e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.734707e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.935923e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.298442e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.549411e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.176059394103E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.340000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -1217,30 +1217,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00535489 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.007765 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005071 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.106900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.463900e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.901700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.593200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.237240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.766730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.467327e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.920897e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.268584e-01 │ │ │ │ Vprtstp: contraction number = 2.268584e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1269,32 +1269,32 @@ │ │ │ │ Vprtstp: contraction number = 3.027355e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.523815e-06 │ │ │ │ Vprtstp: contraction number = 3.032958e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.666858e-07 │ │ │ │ Vprtstp: contraction number = 3.037805e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.721900e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.917852e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.573185e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.832734e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.709734790786E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.280000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.940000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -1315,32 +1315,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.006885 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005501 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.931100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.703100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.206000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.653900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.230070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.713950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.766567e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.309767e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.197218e-01 │ │ │ │ Vprtstp: contraction number = 1.197218e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1357,32 +1357,32 @@ │ │ │ │ Vprtstp: contraction number = 1.080232e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.668171e-06 │ │ │ │ Vprtstp: contraction number = 1.086670e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.821545e-07 │ │ │ │ Vprtstp: contraction number = 1.091941e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.695785e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.898237e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.192993e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.442059e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.413483938867E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.090000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.900000e-05 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -1428,30 +1428,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0422608 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.007160 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005107 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.293600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.488300e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.983200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.501800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.252580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.767300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.966039e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.563855e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.511608e-01 │ │ │ │ Vprtstp: contraction number = 1.511608e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1468,32 +1468,32 @@ │ │ │ │ Vprtstp: contraction number = 1.062405e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.836009e-06 │ │ │ │ Vprtstp: contraction number = 1.072929e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.984242e-07 │ │ │ │ Vprtstp: contraction number = 1.080737e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.737756e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.934949e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.287057e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.541223e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.884571864356E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.230000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.120000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -1514,32 +1514,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.700821 │ │ │ │ +Vacc_SASA: Time elapsed: 2.705796 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.357048e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.359203e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.071800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.876400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.221000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.802860e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.795902e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.455775e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.148454e-02 │ │ │ │ Vprtstp: contraction number = 6.148454e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1613,32 +1613,32 @@ │ │ │ │ Vprtstp: contraction number = 7.027151e-01 │ │ │ │ Vprtstp: iteration = 25 │ │ │ │ Vprtstp: relative residual = 1.401142e-06 │ │ │ │ Vprtstp: contraction number = 7.044026e-01 │ │ │ │ Vprtstp: iteration = 26 │ │ │ │ Vprtstp: relative residual = 9.889238e-07 │ │ │ │ Vprtstp: contraction number = 7.057985e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.299320e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.494359e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.353405e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.616908e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.486452023042E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.580000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.620000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -1684,30 +1684,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 7766.05 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 3755.1 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.647924 │ │ │ │ +Vacc_SASA: Time elapsed: 2.707145 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.972797e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.030852e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.970100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.991600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.248150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.707840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.743723e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.620775e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.211906e-01 │ │ │ │ Vprtstp: contraction number = 1.211906e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1739,32 +1739,32 @@ │ │ │ │ Vprtstp: contraction number = 4.581101e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.399352e-06 │ │ │ │ Vprtstp: contraction number = 4.836226e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.075712e-07 │ │ │ │ Vprtstp: contraction number = 5.056422e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.910975e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.107597e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.771436e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.027405e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.371923967456E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.220000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.840000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -1785,32 +1785,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.668756 │ │ │ │ +Vacc_SASA: Time elapsed: 2.789521 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.356887e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.453843e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.176300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.285800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.236760e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.913240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.691235e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.672242e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.219671e-02 │ │ │ │ Vprtstp: contraction number = 2.219671e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1824,32 +1824,32 @@ │ │ │ │ Vprtstp: contraction number = 9.588702e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.611478e-06 │ │ │ │ Vprtstp: contraction number = 9.903019e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.632204e-07 │ │ │ │ Vprtstp: contraction number = 1.012861e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.496976e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.695065e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.840147e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.118588e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.119297547416E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.730000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.700000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -1895,30 +1895,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 10305.9 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4984.29 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.663986 │ │ │ │ +Vacc_SASA: Time elapsed: 2.693024 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.968244e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.990050e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.078200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.863500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.276350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.776370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.158769e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.182276e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.325279e-01 │ │ │ │ Vprtstp: contraction number = 1.325279e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1935,44 +1935,44 @@ │ │ │ │ Vprtstp: contraction number = 1.009444e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.272261e-06 │ │ │ │ Vprtstp: contraction number = 1.024006e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.317723e-07 │ │ │ │ Vprtstp: contraction number = 1.035733e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.712624e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.913432e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.095333e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.354743e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.638817315582E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.880000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.710000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.335138e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.396491e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:32:25 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:07:46 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr │ │ │ │ @@ -2605,32 +2605,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.742750 │ │ │ │ +Vacc_SASA: Time elapsed: 2.748428 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.559322e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.578715e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.213800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.433500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.243840e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.740710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.889126e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.970687e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.251961e-02 │ │ │ │ Vprtstp: contraction number = 3.251961e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2647,32 +2647,32 @@ │ │ │ │ Vprtstp: contraction number = 1.569967e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.728368e-06 │ │ │ │ Vprtstp: contraction number = 1.692265e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.127259e-07 │ │ │ │ Vprtstp: contraction number = 1.809371e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.762916e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.956620e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.289894e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.538052e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.619056487019E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.500000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.780000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -2718,30 +2718,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 7853.47 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 3800.32 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.686109 │ │ │ │ +Vacc_SASA: Time elapsed: 2.725510 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.142735e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.172412e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.156600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.276700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.230340e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.661510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.199279e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.268351e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.054672e-01 │ │ │ │ Vprtstp: contraction number = 1.054672e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2758,32 +2758,32 @@ │ │ │ │ Vprtstp: contraction number = 1.551340e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 4.573968e-06 │ │ │ │ Vprtstp: contraction number = 1.730130e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.440650e-07 │ │ │ │ Vprtstp: contraction number = 1.845367e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.742974e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.931640e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.193555e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.432729e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.439357878013E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.010000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.560000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -2804,32 +2804,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.693639 │ │ │ │ +Vacc_SASA: Time elapsed: 2.699720 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.554179e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.512144e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.086500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.550200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.247860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.644050e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048754e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.164041e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.215755e-02 │ │ │ │ Vprtstp: contraction number = 2.215755e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2843,32 +2843,32 @@ │ │ │ │ Vprtstp: contraction number = 9.587608e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.603412e-06 │ │ │ │ Vprtstp: contraction number = 9.909475e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.626039e-07 │ │ │ │ Vprtstp: contraction number = 1.014112e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.512954e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.701492e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.836088e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.077270e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.121921918409E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.240000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.710000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -2914,30 +2914,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 10309.9 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4985.22 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.687004 │ │ │ │ +Vacc_SASA: Time elapsed: 2.719775 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.119267e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.177240e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.896400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.583100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.235670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.712550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.531646e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.691148e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.329182e-01 │ │ │ │ Vprtstp: contraction number = 1.329182e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2954,32 +2954,32 @@ │ │ │ │ Vprtstp: contraction number = 1.009933e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.280625e-06 │ │ │ │ Vprtstp: contraction number = 1.024328e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.326631e-07 │ │ │ │ Vprtstp: contraction number = 1.035924e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.708906e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.896408e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.138541e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.385942e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.696401888033E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.790000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.760000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -3000,32 +3000,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.006864 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005621 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.096070e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.175820e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.162900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.519400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.234440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.659850e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.743042e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.951930e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.464441e-01 │ │ │ │ Vprtstp: contraction number = 1.464441e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3042,32 +3042,32 @@ │ │ │ │ Vprtstp: contraction number = 1.083801e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.974607e-06 │ │ │ │ Vprtstp: contraction number = 1.096829e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.183173e-07 │ │ │ │ Vprtstp: contraction number = 1.105624e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.720216e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.906613e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.122483e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.364162e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.982504155807E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.200000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -3113,30 +3113,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0085798 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.007911 │ │ │ │ +Vacc_SASA: Time elapsed: 0.006907 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.141690e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.056550e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.947200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.222300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.252640e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.496580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.956137e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.207988e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.791557e-01 │ │ │ │ Vprtstp: contraction number = 1.791557e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3156,32 +3156,32 @@ │ │ │ │ Vprtstp: contraction number = 1.764760e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.223991e-06 │ │ │ │ Vprtstp: contraction number = 1.794914e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.841505e-07 │ │ │ │ Vprtstp: contraction number = 1.811887e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.986887e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.174688e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.514954e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.737952e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.713502079454E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.090000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.170000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -3202,32 +3202,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.006841 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005409 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.812750e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.068870e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.085300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.347900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.233190e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.707030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.192369e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.505880e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.197218e-01 │ │ │ │ Vprtstp: contraction number = 1.197218e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3244,32 +3244,32 @@ │ │ │ │ Vprtstp: contraction number = 1.080232e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.668171e-06 │ │ │ │ Vprtstp: contraction number = 1.086670e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.821545e-07 │ │ │ │ Vprtstp: contraction number = 1.091941e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.745491e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.930910e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.174620e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.422410e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: upper corner = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: actual minima = (-30.249, -30.2305, -27.5085) │ │ │ │ Vpmg_setPart: actual maxima = (65.751, 65.7695, 68.4915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.413483938867E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.410000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.80966 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.374 x 6.581 x 6.611 │ │ │ │ Vpbe_ctor2: solute charge = 2.77556e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -3315,30 +3315,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0422608 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.007777 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005320 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.155790e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.190670e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.964900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.371100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.263410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.699770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.408367e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.770791e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.511608e-01 │ │ │ │ Vprtstp: contraction number = 1.511608e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3355,32 +3355,32 @@ │ │ │ │ Vprtstp: contraction number = 1.062405e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.836009e-06 │ │ │ │ Vprtstp: contraction number = 1.072929e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.984242e-07 │ │ │ │ Vprtstp: contraction number = 1.080737e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.720534e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.910678e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.173293e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.417890e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.884571864356E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.210000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.060000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -3401,32 +3401,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.689842 │ │ │ │ +Vacc_SASA: Time elapsed: 2.736621 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.470215e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.600644e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.099100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.666500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.227680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.727300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.247093e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.674547e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.257199e-02 │ │ │ │ Vprtstp: contraction number = 3.257199e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3443,30 +3443,30 @@ │ │ │ │ Vprtstp: contraction number = 1.541269e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.608808e-06 │ │ │ │ Vprtstp: contraction number = 1.652212e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.820839e-07 │ │ │ │ Vprtstp: contraction number = 1.753372e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.700284e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.888035e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.234562e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.489078e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.592645225811E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.030000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.050000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ @@ -3514,30 +3514,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 7853.32 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 3800.2 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.666091 │ │ │ │ +Vacc_SASA: Time elapsed: 2.717627 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.102187e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.168542e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.977500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.521300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.236460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.814610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.746883e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.241387e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051303e-01 │ │ │ │ Vprtstp: contraction number = 1.051303e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3554,30 +3554,30 @@ │ │ │ │ Vprtstp: contraction number = 1.566068e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 4.652962e-06 │ │ │ │ Vprtstp: contraction number = 1.751224e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.683754e-07 │ │ │ │ Vprtstp: contraction number = 1.866285e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.744944e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.931215e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.254623e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.510421e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.382181498242E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.060000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.880000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ @@ -3600,32 +3600,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.659370 │ │ │ │ +Vacc_SASA: Time elapsed: 2.740238 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.465243e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.593386e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.128800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.758700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.223040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.838100e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.587602e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.153694e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.219671e-02 │ │ │ │ Vprtstp: contraction number = 2.219671e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3639,32 +3639,32 @@ │ │ │ │ Vprtstp: contraction number = 9.588702e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.611478e-06 │ │ │ │ Vprtstp: contraction number = 9.903019e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.632204e-07 │ │ │ │ Vprtstp: contraction number = 1.012861e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.528638e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.716582e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.894870e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.158746e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: upper corner = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: actual minima = (-22.1255, -29.651, -28.888) │ │ │ │ Vpmg_setPart: actual maxima = (73.8745, 66.349, 67.112) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.119297547416E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.420000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.000000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.5287 │ │ │ │ Vpbe_ctor2: solute dimensions = 50.733 x 37.661 x 37.832 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -3710,30 +3710,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 10305.9 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4984.29 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.669089 │ │ │ │ +Vacc_SASA: Time elapsed: 2.722573 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.091414e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.161605e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.973700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.920500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.236520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.863940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.069337e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.687077e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.325279e-01 │ │ │ │ Vprtstp: contraction number = 1.325279e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3750,44 +3750,44 @@ │ │ │ │ Vprtstp: contraction number = 1.009444e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.272261e-06 │ │ │ │ Vprtstp: contraction number = 1.024006e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.317723e-07 │ │ │ │ Vprtstp: contraction number = 1.035733e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.731738e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.919708e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.220155e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.487499e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: upper corner = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: actual minima = (10.551, 10.5695, 13.2915) │ │ │ │ Vpmg_setPart: actual maxima = (24.951, 24.9695, 27.6915) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.638817315582E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.240000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.010000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.246467e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.914158e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:33:04 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:09:05 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr │ │ │ │ @@ -4420,32 +4420,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.728044 │ │ │ │ +Vacc_SASA: Time elapsed: 2.779000 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.427932e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.519072e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.846000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.846700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.216400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.795760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.760040e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.916971e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.573903e-02 │ │ │ │ Vprtstp: contraction number = 6.573903e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4516,32 +4516,32 @@ │ │ │ │ Vprtstp: contraction number = 6.827181e-01 │ │ │ │ Vprtstp: iteration = 24 │ │ │ │ Vprtstp: relative residual = 1.259903e-06 │ │ │ │ Vprtstp: contraction number = 6.840214e-01 │ │ │ │ Vprtstp: iteration = 25 │ │ │ │ Vprtstp: relative residual = 8.633870e-07 │ │ │ │ Vprtstp: contraction number = 6.852808e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.308168e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.505422e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.071583e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.333864e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.345051831139E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.720000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.450000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -4587,30 +4587,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 6529.57 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2987.06 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.695939 │ │ │ │ +Vacc_SASA: Time elapsed: 2.736597 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.018187e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.067410e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.876500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.150400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.238780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.856270e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.629619e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.833648e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.216933e-01 │ │ │ │ Vprtstp: contraction number = 1.216933e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4639,32 +4639,32 @@ │ │ │ │ Vprtstp: contraction number = 3.953520e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.724728e-06 │ │ │ │ Vprtstp: contraction number = 4.218661e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.702114e-07 │ │ │ │ Vprtstp: contraction number = 4.465699e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.849886e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.050199e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.261388e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.531222e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.171725099545E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.770000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.470000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -4685,32 +4685,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.675732 │ │ │ │ +Vacc_SASA: Time elapsed: 2.698348 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.415183e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.402950e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.861100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.084800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.223390e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.855110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.576367e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.828074e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.208737e-02 │ │ │ │ Vprtstp: contraction number = 2.208737e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4724,30 +4724,30 @@ │ │ │ │ Vprtstp: contraction number = 9.525881e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.554352e-06 │ │ │ │ Vprtstp: contraction number = 9.854831e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.569345e-07 │ │ │ │ Vprtstp: contraction number = 1.009646e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.491060e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.684442e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.752580e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.023122e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.014263549371E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.010000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.750000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ @@ -4795,30 +4795,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 9211.28 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4239.53 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.681651 │ │ │ │ +Vacc_SASA: Time elapsed: 2.679806 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.983575e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.991475e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.248800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.802600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.238180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.824840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.044714e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.329843e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.291558e-01 │ │ │ │ Vprtstp: contraction number = 1.291558e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4835,32 +4835,32 @@ │ │ │ │ Vprtstp: contraction number = 1.003267e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.195888e-06 │ │ │ │ Vprtstp: contraction number = 1.018284e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.232544e-07 │ │ │ │ Vprtstp: contraction number = 1.030651e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.748058e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.947613e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.155368e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.419341e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.449231705544E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.740000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.260000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -4881,32 +4881,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.009641 │ │ │ │ +Vacc_SASA: Time elapsed: 0.009604 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.695200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.080790e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.819000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.881000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.230680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.805360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.249578e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.583765e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.937868e-02 │ │ │ │ Vprtstp: contraction number = 9.937868e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4923,30 +4923,30 @@ │ │ │ │ Vprtstp: contraction number = 1.252714e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.602930e-06 │ │ │ │ Vprtstp: contraction number = 1.287705e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.415857e-07 │ │ │ │ Vprtstp: contraction number = 1.312312e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.823285e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.017849e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.201354e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.466584e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.561986028141E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.400000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ @@ -4994,30 +4994,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00497505 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.011026 │ │ │ │ +Vacc_SASA: Time elapsed: 0.008030 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.440100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.274700e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.131700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.021400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.217980e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.843740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.460895e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.841012e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.636290e-01 │ │ │ │ Vprtstp: contraction number = 2.636290e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5049,30 +5049,30 @@ │ │ │ │ Vprtstp: contraction number = 3.506954e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.726432e-06 │ │ │ │ Vprtstp: contraction number = 3.673674e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 6.664171e-07 │ │ │ │ Vprtstp: contraction number = 3.860084e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.919694e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.116351e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.919410e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.188465e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.344916094234E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.190000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.290000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ @@ -5095,32 +5095,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.009765 │ │ │ │ +Vacc_SASA: Time elapsed: 0.008608 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.414600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.278200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.903600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.065600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.238270e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.793460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.780570e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.267718e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.352196e-02 │ │ │ │ Vprtstp: contraction number = 6.352196e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5134,30 +5134,30 @@ │ │ │ │ Vprtstp: contraction number = 1.012293e-01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.271886e-06 │ │ │ │ Vprtstp: contraction number = 1.033361e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 6.595226e-07 │ │ │ │ Vprtstp: contraction number = 1.051554e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.553223e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.747349e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.940567e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.206645e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 9.389840581990E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ @@ -5205,30 +5205,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0518244 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.010839 │ │ │ │ +Vacc_SASA: Time elapsed: 0.008073 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.223900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.492500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.104700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.113200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.224240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.851060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.965842e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.499462e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.573900e-01 │ │ │ │ Vprtstp: contraction number = 1.573900e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5245,30 +5245,30 @@ │ │ │ │ Vprtstp: contraction number = 1.046499e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.765958e-06 │ │ │ │ Vprtstp: contraction number = 1.060018e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.889858e-07 │ │ │ │ Vprtstp: contraction number = 1.070160e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.713363e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.911873e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.273758e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.545827e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.361370594878E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.120000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.540000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ @@ -5291,32 +5291,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.679525 │ │ │ │ +Vacc_SASA: Time elapsed: 2.681127 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.320106e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.394069e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.821700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.022200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.209130e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.894590e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.789550e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.394776e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.573435e-02 │ │ │ │ Vprtstp: contraction number = 6.573435e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5387,32 +5387,32 @@ │ │ │ │ Vprtstp: contraction number = 6.841463e-01 │ │ │ │ Vprtstp: iteration = 24 │ │ │ │ Vprtstp: relative residual = 1.230794e-06 │ │ │ │ Vprtstp: contraction number = 6.854643e-01 │ │ │ │ Vprtstp: iteration = 25 │ │ │ │ Vprtstp: relative residual = 8.453252e-07 │ │ │ │ Vprtstp: contraction number = 6.868128e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.910865e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.105732e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.675376e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.951272e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.248457904492E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.960000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.530000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -5458,30 +5458,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 6529.31 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2986.91 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.644216 │ │ │ │ +Vacc_SASA: Time elapsed: 2.640770 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.953962e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.945698e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.102400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.891100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.269930e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.786530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.697002e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.483943e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.206113e-01 │ │ │ │ Vprtstp: contraction number = 1.206113e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5510,32 +5510,32 @@ │ │ │ │ Vprtstp: contraction number = 3.809962e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.385263e-06 │ │ │ │ Vprtstp: contraction number = 4.084139e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.028523e-07 │ │ │ │ Vprtstp: contraction number = 4.351898e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.706430e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.906855e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.491559e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.751948e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.037057682028E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.830000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.950000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -5556,32 +5556,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.629581 │ │ │ │ +Vacc_SASA: Time elapsed: 2.698990 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.314592e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.346557e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.776900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.931700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.221010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.810230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.620116e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.495412e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.233304e-02 │ │ │ │ Vprtstp: contraction number = 2.233304e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5595,32 +5595,32 @@ │ │ │ │ Vprtstp: contraction number = 9.522390e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.574058e-06 │ │ │ │ Vprtstp: contraction number = 9.845638e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.587415e-07 │ │ │ │ Vprtstp: contraction number = 1.008486e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.428914e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.629913e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.870252e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.137227e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.004264667397E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.690000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.080000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -5666,30 +5666,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 9208.92 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4238.63 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.651003 │ │ │ │ +Vacc_SASA: Time elapsed: 2.674471 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.940287e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.982494e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.183500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.239400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.225860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.931620e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.077895e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.009468e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.281343e-01 │ │ │ │ Vprtstp: contraction number = 1.281343e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5706,44 +5706,44 @@ │ │ │ │ Vprtstp: contraction number = 1.003059e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.185212e-06 │ │ │ │ Vprtstp: contraction number = 1.017952e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.220913e-07 │ │ │ │ Vprtstp: contraction number = 1.030122e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.699465e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.898818e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.070251e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.347905e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.314075450214E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.390000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.720000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.252718e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.221791e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:33:47 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:10:39 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr │ │ │ │ @@ -6376,32 +6376,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.752116 │ │ │ │ +Vacc_SASA: Time elapsed: 2.668306 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.592389e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.441607e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.195500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.693100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.241930e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.693480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.919756e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.832886e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.298567e-02 │ │ │ │ Vprtstp: contraction number = 3.298567e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6418,32 +6418,32 @@ │ │ │ │ Vprtstp: contraction number = 1.536726e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.666279e-06 │ │ │ │ Vprtstp: contraction number = 1.683668e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.055929e-07 │ │ │ │ Vprtstp: contraction number = 1.833984e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.736909e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.928666e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.925022e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.172328e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.725356066403E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.610000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.170000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -6489,30 +6489,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 6899.51 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 3158.85 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.674912 │ │ │ │ +Vacc_SASA: Time elapsed: 2.588322 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.126082e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.001545e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.332400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.530000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.257880e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.676020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198956e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201127e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.032281e-01 │ │ │ │ Vprtstp: contraction number = 1.032281e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6529,32 +6529,32 @@ │ │ │ │ Vprtstp: contraction number = 1.485117e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 3.842446e-06 │ │ │ │ Vprtstp: contraction number = 1.674805e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.939533e-07 │ │ │ │ Vprtstp: contraction number = 1.806019e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.766549e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.963967e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.977642e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.218833e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.209791610861E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.930000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.020000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -6575,32 +6575,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.694590 │ │ │ │ +Vacc_SASA: Time elapsed: 2.588762 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.553342e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.330465e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.072500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.543200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.269180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.701790e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.051385e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.057201e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.208737e-02 │ │ │ │ Vprtstp: contraction number = 2.208737e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6614,30 +6614,30 @@ │ │ │ │ Vprtstp: contraction number = 9.525881e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.554352e-06 │ │ │ │ Vprtstp: contraction number = 9.854831e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.569345e-07 │ │ │ │ Vprtstp: contraction number = 1.009646e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.614433e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.809702e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.689162e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.934123e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.014263549371E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.900000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.890000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ @@ -6685,30 +6685,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 9211.28 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4239.53 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.686150 │ │ │ │ +Vacc_SASA: Time elapsed: 2.627443 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.144038e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.048649e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.351500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.706300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.315810e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.731150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.548276e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.557041e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.291558e-01 │ │ │ │ Vprtstp: contraction number = 1.291558e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6725,32 +6725,32 @@ │ │ │ │ Vprtstp: contraction number = 1.003267e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.195888e-06 │ │ │ │ Vprtstp: contraction number = 1.018284e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.232544e-07 │ │ │ │ Vprtstp: contraction number = 1.030651e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.752819e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.953811e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.930637e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.180216e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.449231705544E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.070000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.950000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -6771,32 +6771,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.009516 │ │ │ │ +Vacc_SASA: Time elapsed: 0.007553 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.182420e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.188100e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.413100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.010600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.364720e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.815140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.766689e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.799383e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.464737e-02 │ │ │ │ Vprtstp: contraction number = 8.464737e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6813,32 +6813,32 @@ │ │ │ │ Vprtstp: contraction number = 1.071698e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.052787e-06 │ │ │ │ Vprtstp: contraction number = 1.084632e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.152581e-07 │ │ │ │ Vprtstp: contraction number = 1.094790e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.808038e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.011996e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.996493e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.260907e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 6.368169150406E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.000000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -6884,30 +6884,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00594757 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.010986 │ │ │ │ +Vacc_SASA: Time elapsed: 0.009536 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.091300e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.010720e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.921700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.704900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.289950e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.714090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.988229e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.044749e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.027171e-01 │ │ │ │ Vprtstp: contraction number = 2.027171e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6927,32 +6927,32 @@ │ │ │ │ Vprtstp: contraction number = 1.717621e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.164324e-06 │ │ │ │ Vprtstp: contraction number = 1.754898e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.631488e-07 │ │ │ │ Vprtstp: contraction number = 1.779681e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.080138e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.269858e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.207752e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.454934e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.345277247759E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.120000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.050000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -6973,32 +6973,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.009818 │ │ │ │ +Vacc_SASA: Time elapsed: 0.007679 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.028330e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.910160e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.164900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.668100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.343760e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.712090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.237248e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.310241e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.352196e-02 │ │ │ │ Vprtstp: contraction number = 6.352196e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7012,30 +7012,30 @@ │ │ │ │ Vprtstp: contraction number = 1.012293e-01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.271886e-06 │ │ │ │ Vprtstp: contraction number = 1.033361e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 6.595226e-07 │ │ │ │ Vprtstp: contraction number = 1.051554e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.550291e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.748488e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.697072e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.943701e+00 │ │ │ │ Vpmg_setPart: lower corner = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: upper corner = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: actual minima = (-30.6595, -28.789, -27.497) │ │ │ │ Vpmg_setPart: actual maxima = (65.3405, 67.211, 68.503) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 9.389840581990E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.060000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 5.02661 │ │ │ │ Vpbe_ctor2: solute dimensions = 5.303 x 9.299 x 6.49 │ │ │ │ Vpbe_ctor2: solute charge = -8.32667e-17 │ │ │ │ @@ -7083,30 +7083,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0518244 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.011133 │ │ │ │ +Vacc_SASA: Time elapsed: 0.008049 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.307310e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.102940e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.959000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.676900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.241010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.680860e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.434994e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.526251e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.573900e-01 │ │ │ │ Vprtstp: contraction number = 1.573900e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7123,32 +7123,32 @@ │ │ │ │ Vprtstp: contraction number = 1.046499e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.765958e-06 │ │ │ │ Vprtstp: contraction number = 1.060018e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.889858e-07 │ │ │ │ Vprtstp: contraction number = 1.070160e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.782782e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.970147e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.912793e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.156995e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.361370594878E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.120000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.410000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -7169,32 +7169,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.719639 │ │ │ │ +Vacc_SASA: Time elapsed: 2.618517 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.490404e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.400207e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.298800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.031100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.316220e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.675130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.283608e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.383252e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.328224e-02 │ │ │ │ Vprtstp: contraction number = 3.328224e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7211,32 +7211,32 @@ │ │ │ │ Vprtstp: contraction number = 1.553323e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.764269e-06 │ │ │ │ Vprtstp: contraction number = 1.696908e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.244306e-07 │ │ │ │ Vprtstp: contraction number = 1.838895e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.720247e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.924308e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.925115e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.172658e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.622871644072E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.430000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.300000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.0328757 │ │ │ │ @@ -7282,30 +7282,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 6899.11 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 3158.68 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.646098 │ │ │ │ +Vacc_SASA: Time elapsed: 2.608687 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.084268e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.038841e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.024100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.503400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.251650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.750750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.784198e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.905561e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.025309e-01 │ │ │ │ Vprtstp: contraction number = 1.025309e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7322,32 +7322,32 @@ │ │ │ │ Vprtstp: contraction number = 1.507031e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 3.981847e-06 │ │ │ │ Vprtstp: contraction number = 1.699776e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.281025e-07 │ │ │ │ Vprtstp: contraction number = 1.828555e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.725864e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.917929e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.968661e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.218501e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.075005771448E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.640000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.600000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -7368,32 +7368,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.663457 │ │ │ │ +Vacc_SASA: Time elapsed: 2.645051 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.465727e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.415549e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.120500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.001300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.234060e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.927030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.623383e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.772135e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.233304e-02 │ │ │ │ Vprtstp: contraction number = 2.233304e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7407,32 +7407,32 @@ │ │ │ │ Vprtstp: contraction number = 9.522390e-02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.574058e-06 │ │ │ │ Vprtstp: contraction number = 9.845638e-02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.587415e-07 │ │ │ │ Vprtstp: contraction number = 1.008486e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.488065e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.679246e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.631225e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.903519e+00 │ │ │ │ Vpmg_setPart: lower corner = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: upper corner = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: actual minima = (-22.7365, -29.0115, -28.878) │ │ │ │ Vpmg_setPart: actual maxima = (73.2635, 66.9885, 67.122) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.004264667397E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.530000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.430000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 26.3256 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.571 x 38.32 x 37.678 │ │ │ │ Vpbe_ctor2: solute charge = 0.991 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.01 │ │ │ │ Vpbe_ctor2: xkappa = 0.205309 │ │ │ │ @@ -7478,30 +7478,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 9208.92 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 4238.63 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 2.649363 │ │ │ │ +Vacc_SASA: Time elapsed: 2.575068 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.072090e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.971352e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.081700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.682200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.261690e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.762670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.099409e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.258577e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.281343e-01 │ │ │ │ Vprtstp: contraction number = 1.281343e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7518,34 +7518,34 @@ │ │ │ │ Vprtstp: contraction number = 1.003059e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.185212e-06 │ │ │ │ Vprtstp: contraction number = 1.017952e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.220913e-07 │ │ │ │ Vprtstp: contraction number = 1.030122e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.763052e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.953685e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.022273e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.275025e+00 │ │ │ │ Vpmg_setPart: lower corner = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: upper corner = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: actual minima = (10.1405, 12.011, 13.303) │ │ │ │ Vpmg_setPart: actual maxima = (24.5405, 26.411, 27.703) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.314075450214E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.790000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.660000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.280895e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.465921e+01 │ │ │ ├── ./usr/share/apbs/examples/actin-dimer/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:31:58 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:34:54 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -262,217 +262,217 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.359902 │ │ │ │ +Vacc_SASA: Time elapsed: 7.366003 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.935742e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.875521e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.909910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.470670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.760189e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 3.093672e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.357596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.376956e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7775242.648804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.777567e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.819566e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.252805e+05 │ │ │ │ Vprtstp: contraction number = 5.252805e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.062556 │ │ │ │ Vnewton: Attempting damping, relres = 0.525334 │ │ │ │ Vnewton: Damping accepted, relres = 0.062556 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.255619e-02 │ │ │ │ Vprtstp: contraction number = 6.255619e-02 │ │ │ │ Vnewton: Using errtol_s: 486389.547875 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.776460e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.768827e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.109788e+05 │ │ │ │ Vprtstp: contraction number = 1.109788e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.292368e-02 │ │ │ │ Vprtstp: contraction number = 2.065932e-01 │ │ │ │ Vnewton: Using errtol_s: 100484.762247 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.580447e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.546396e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.281526e+04 │ │ │ │ Vprtstp: contraction number = 3.281526e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.798952e-03 │ │ │ │ Vprtstp: contraction number = 2.939527e-01 │ │ │ │ Vnewton: Using errtol_s: 29537.770540 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.393495e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.340487e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.139405e+04 │ │ │ │ Vprtstp: contraction number = 1.139405e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.318894e-03 │ │ │ │ Vprtstp: contraction number = 3.471731e-01 │ │ │ │ Vnewton: Using errtol_s: 10254.719067 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.208506e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.135077e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.292845e+03 │ │ │ │ Vprtstp: contraction number = 4.292845e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.969084e-04 │ │ │ │ Vprtstp: contraction number = 3.767615e-01 │ │ │ │ Vnewton: Using errtol_s: 3863.583447 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.020158e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.936796e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.746643e+03 │ │ │ │ Vprtstp: contraction number = 1.746643e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.021786e-04 │ │ │ │ Vprtstp: contraction number = 4.068730e-01 │ │ │ │ Vnewton: Using errtol_s: 1571.987642 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.844522e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.745562e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.833563e+02 │ │ │ │ Vprtstp: contraction number = 7.833563e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 9.067555e-05 │ │ │ │ Vprtstp: contraction number = 4.484923e-01 │ │ │ │ Vnewton: Using errtol_s: 705.024393 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.646641e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.540617e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.880760e+02 │ │ │ │ Vprtstp: contraction number = 3.880760e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.492075e-05 │ │ │ │ Vprtstp: contraction number = 4.954009e-01 │ │ │ │ Vnewton: Using errtol_s: 349.269694 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.461419e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.343655e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.071891e+02 │ │ │ │ Vprtstp: contraction number = 2.071891e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.398262e-05 │ │ │ │ Vprtstp: contraction number = 5.338875e-01 │ │ │ │ Vnewton: Using errtol_s: 186.470725 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.256713e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.131136e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.168433e+02 │ │ │ │ Vprtstp: contraction number = 1.168433e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.352487e-05 │ │ │ │ Vprtstp: contraction number = 5.639446e-01 │ │ │ │ Vnewton: Using errtol_s: 105.159166 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004430e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.911572e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.826136e+01 │ │ │ │ Vprtstp: contraction number = 6.826136e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.901399e-06 │ │ │ │ Vprtstp: contraction number = 5.842124e-01 │ │ │ │ Vnewton: Using errtol_s: 61.435293 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086082e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068815e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.091749e+01 │ │ │ │ Vprtstp: contraction number = 4.091749e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.736285e-06 │ │ │ │ Vprtstp: contraction number = 5.994236e-01 │ │ │ │ Vnewton: Using errtol_s: 36.825768 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.165894e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.148407e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.493482e+01 │ │ │ │ Vprtstp: contraction number = 2.493482e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 2.886257e-06 │ │ │ │ Vprtstp: contraction number = 6.093926e-01 │ │ │ │ Vnewton: Using errtol_s: 22.441349 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.248307e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228479e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.538748e+01 │ │ │ │ Vprtstp: contraction number = 1.538748e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 1.781132e-06 │ │ │ │ Vprtstp: contraction number = 6.171079e-01 │ │ │ │ Vnewton: Using errtol_s: 13.848733 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330490e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.309872e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.579209e+00 │ │ │ │ Vprtstp: contraction number = 9.579209e+00 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 1.108813e-06 │ │ │ │ Vprtstp: contraction number = 6.225327e-01 │ │ │ │ Vnewton: Using errtol_s: 8.621289 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.411427e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390902e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.005674e+00 │ │ │ │ Vprtstp: contraction number = 6.005674e+00 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 6.951690e-07 │ │ │ │ Vprtstp: contraction number = 6.269489e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.339246e+02 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.378046e+02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.316373e+02 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.358054e+02 │ │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -481,17 +481,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.412172567798E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.232438411967E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.161638379331E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.293270e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.425140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -537,193 +537,193 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.294338 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.632572 │ │ │ │ +Vacc_SASA: Time elapsed: 7.433307 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.114409e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.115646e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.743860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 9.575490e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.744983e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.905783e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.632323e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.615425e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 9262588.477712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.673524e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.657624e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.740096e+05 │ │ │ │ Vprtstp: contraction number = 9.740096e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.096135 │ │ │ │ Vnewton: Attempting damping, relres = 0.545161 │ │ │ │ Vnewton: Damping accepted, relres = 0.096135 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.613536e-02 │ │ │ │ Vprtstp: contraction number = 9.613536e-02 │ │ │ │ Vnewton: Using errtol_s: 890462.283513 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.769919e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.753670e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.907605e+05 │ │ │ │ Vprtstp: contraction number = 1.907605e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.859794e-02 │ │ │ │ Vprtstp: contraction number = 1.934558e-01 │ │ │ │ Vnewton: Using errtol_s: 172265.062018 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.850057e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.833836e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.138633e+04 │ │ │ │ Vprtstp: contraction number = 5.138633e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.994948e-03 │ │ │ │ Vprtstp: contraction number = 2.685753e-01 │ │ │ │ Vnewton: Using errtol_s: 46266.149079 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.929854e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.914380e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.656736e+04 │ │ │ │ Vprtstp: contraction number = 1.656736e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.610090e-03 │ │ │ │ Vprtstp: contraction number = 3.223437e-01 │ │ │ │ Vnewton: Using errtol_s: 14913.601487 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.010256e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.995176e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.837272e+03 │ │ │ │ Vprtstp: contraction number = 5.837272e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.672493e-04 │ │ │ │ Vprtstp: contraction number = 3.523090e-01 │ │ │ │ Vnewton: Using errtol_s: 5254.196377 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.090130e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.075904e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.147141e+03 │ │ │ │ Vprtstp: contraction number = 2.147141e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.086390e-04 │ │ │ │ Vprtstp: contraction number = 3.678083e-01 │ │ │ │ Vnewton: Using errtol_s: 1932.536910 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.170214e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.156939e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.193498e+02 │ │ │ │ Vprtstp: contraction number = 8.193498e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.961379e-05 │ │ │ │ Vprtstp: contraction number = 3.815864e-01 │ │ │ │ Vnewton: Using errtol_s: 737.429804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.250589e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.237483e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352547e+02 │ │ │ │ Vprtstp: contraction number = 3.352547e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.257526e-05 │ │ │ │ Vprtstp: contraction number = 4.091660e-01 │ │ │ │ Vnewton: Using errtol_s: 301.731240 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.331474e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.318107e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.500666e+02 │ │ │ │ Vprtstp: contraction number = 1.500666e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.458127e-05 │ │ │ │ Vprtstp: contraction number = 4.476179e-01 │ │ │ │ Vnewton: Using errtol_s: 135.060298 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.411830e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.398363e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.280398e+01 │ │ │ │ Vprtstp: contraction number = 7.280398e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.074013e-06 │ │ │ │ Vprtstp: contraction number = 4.851438e-01 │ │ │ │ Vnewton: Using errtol_s: 65.523671 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.492214e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.478909e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.740960e+01 │ │ │ │ Vprtstp: contraction number = 3.740960e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.634908e-06 │ │ │ │ Vprtstp: contraction number = 5.138397e-01 │ │ │ │ Vnewton: Using errtol_s: 33.668661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.573340e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.555324e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.000118e+01 │ │ │ │ Vprtstp: contraction number = 2.000118e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.943416e-06 │ │ │ │ Vprtstp: contraction number = 5.346535e-01 │ │ │ │ Vnewton: Using errtol_s: 18.001066 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.654297e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.631482e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.094514e+01 │ │ │ │ Vprtstp: contraction number = 1.094514e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.063486e-06 │ │ │ │ Vprtstp: contraction number = 5.472249e-01 │ │ │ │ Vnewton: Using errtol_s: 9.850631 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.735179e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.705335e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.085292e+00 │ │ │ │ Vprtstp: contraction number = 6.085292e+00 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 5.912779e-07 │ │ │ │ Vprtstp: contraction number = 5.559810e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.166745e+02 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.204148e+02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.147571e+02 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.188654e+02 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -732,17 +732,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.418972427545E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.355397093328E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.177642501639E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.074200e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.150680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -763,217 +763,217 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.337287 │ │ │ │ +Vacc_SASA: Time elapsed: 7.452741 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.952561e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.201956e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.810520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.038550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.733289e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.705264e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.934184e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.900677e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7837779.438687 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.975621e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.941935e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.264175e+05 │ │ │ │ Vprtstp: contraction number = 5.264175e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.062206 │ │ │ │ Vnewton: Attempting damping, relres = 0.525499 │ │ │ │ Vnewton: Damping accepted, relres = 0.062206 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.220619e-02 │ │ │ │ Vprtstp: contraction number = 6.220619e-02 │ │ │ │ Vnewton: Using errtol_s: 487558.369599 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.073037e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.036914e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.104882e+05 │ │ │ │ Vprtstp: contraction number = 1.104882e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.277305e-02 │ │ │ │ Vprtstp: contraction number = 2.053340e-01 │ │ │ │ Vnewton: Using errtol_s: 100112.332342 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.153950e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.114738e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.234516e+04 │ │ │ │ Vprtstp: contraction number = 3.234516e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.716136e-03 │ │ │ │ Vprtstp: contraction number = 2.909357e-01 │ │ │ │ Vnewton: Using errtol_s: 29126.250452 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.235018e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.194934e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.113222e+04 │ │ │ │ Vprtstp: contraction number = 1.113222e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.278517e-03 │ │ │ │ Vprtstp: contraction number = 3.440448e-01 │ │ │ │ Vnewton: Using errtol_s: 10020.735856 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.315144e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.274066e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.146765e+03 │ │ │ │ Vprtstp: contraction number = 4.146765e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.761620e-04 │ │ │ │ Vprtstp: contraction number = 3.724330e-01 │ │ │ │ Vnewton: Using errtol_s: 3732.052866 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.395248e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.351755e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.647764e+03 │ │ │ │ Vprtstp: contraction number = 1.647764e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.891857e-04 │ │ │ │ Vprtstp: contraction number = 3.973138e-01 │ │ │ │ Vnewton: Using errtol_s: 1482.795933 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.475346e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.429313e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.190477e+02 │ │ │ │ Vprtstp: contraction number = 7.190477e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.256252e-05 │ │ │ │ Vprtstp: contraction number = 4.364099e-01 │ │ │ │ Vnewton: Using errtol_s: 647.106851 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.555918e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.506822e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.514586e+02 │ │ │ │ Vprtstp: contraction number = 3.514586e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.035656e-05 │ │ │ │ Vprtstp: contraction number = 4.888000e-01 │ │ │ │ Vnewton: Using errtol_s: 316.305821 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.636133e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.584342e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.878144e+02 │ │ │ │ Vprtstp: contraction number = 1.878144e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.156625e-05 │ │ │ │ Vprtstp: contraction number = 5.343927e-01 │ │ │ │ Vnewton: Using errtol_s: 169.031531 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.716731e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.662949e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.065907e+02 │ │ │ │ Vprtstp: contraction number = 1.065907e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.223961e-05 │ │ │ │ Vprtstp: contraction number = 5.675353e-01 │ │ │ │ Vnewton: Using errtol_s: 95.931363 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.796847e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.741413e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.270317e+01 │ │ │ │ Vprtstp: contraction number = 6.270317e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.200099e-06 │ │ │ │ Vprtstp: contraction number = 5.882621e-01 │ │ │ │ Vnewton: Using errtol_s: 56.432788 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.877072e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.820545e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.774740e+01 │ │ │ │ Vprtstp: contraction number = 3.774740e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.334473e-06 │ │ │ │ Vprtstp: contraction number = 6.020019e-01 │ │ │ │ Vnewton: Using errtol_s: 33.972645 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.957583e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.902452e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.304758e+01 │ │ │ │ Vprtstp: contraction number = 2.304758e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 2.646517e-06 │ │ │ │ Vprtstp: contraction number = 6.105742e-01 │ │ │ │ Vnewton: Using errtol_s: 20.742819 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.036794e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.981195e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.421587e+01 │ │ │ │ Vprtstp: contraction number = 1.421587e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 1.632386e-06 │ │ │ │ Vprtstp: contraction number = 6.168053e-01 │ │ │ │ Vnewton: Using errtol_s: 12.794282 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.117278e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.059093e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.829808e+00 │ │ │ │ Vprtstp: contraction number = 8.829808e+00 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 1.013913e-06 │ │ │ │ Vprtstp: contraction number = 6.211233e-01 │ │ │ │ Vnewton: Using errtol_s: 7.946827 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.197208e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.135825e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.514712e+00 │ │ │ │ Vprtstp: contraction number = 5.514712e+00 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 6.332457e-07 │ │ │ │ Vprtstp: contraction number = 6.245562e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.324893e+02 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.362232e+02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.294481e+02 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.331638e+02 │ │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -982,17 +982,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.438982867308E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.232481159173E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.161845360142E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.243770e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.116010e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -1038,182 +1038,182 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.338388 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.394876 │ │ │ │ +Vacc_SASA: Time elapsed: 7.099294 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.086094e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.067999e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.830740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.625770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.768567e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.532710e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.413841e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.345277e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 9316156.472817 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.455062e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.384515e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.759901e+05 │ │ │ │ Vprtstp: contraction number = 9.759901e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.095792 │ │ │ │ Vnewton: Attempting damping, relres = 0.545068 │ │ │ │ Vnewton: Damping accepted, relres = 0.095792 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.579182e-02 │ │ │ │ Vprtstp: contraction number = 9.579182e-02 │ │ │ │ Vnewton: Using errtol_s: 892411.563062 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.551765e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.473751e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.903231e+05 │ │ │ │ Vprtstp: contraction number = 1.903231e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.845161e-02 │ │ │ │ Vprtstp: contraction number = 1.926220e-01 │ │ │ │ Vnewton: Using errtol_s: 171898.088650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.632369e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.547134e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.121980e+04 │ │ │ │ Vprtstp: contraction number = 5.121980e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.949951e-03 │ │ │ │ Vprtstp: contraction number = 2.682666e-01 │ │ │ │ Vnewton: Using errtol_s: 46114.513884 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.712251e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.620534e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.657747e+04 │ │ │ │ Vprtstp: contraction number = 1.657747e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.601844e-03 │ │ │ │ Vprtstp: contraction number = 3.236081e-01 │ │ │ │ Vnewton: Using errtol_s: 14923.031227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.792063e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.693172e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.880103e+03 │ │ │ │ Vprtstp: contraction number = 5.880103e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.681354e-04 │ │ │ │ Vprtstp: contraction number = 3.546758e-01 │ │ │ │ Vnewton: Using errtol_s: 5292.838197 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.871985e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.765747e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.176489e+03 │ │ │ │ Vprtstp: contraction number = 2.176489e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.102777e-04 │ │ │ │ Vprtstp: contraction number = 3.701190e-01 │ │ │ │ Vnewton: Using errtol_s: 1958.979878 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.951945e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.837993e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.247695e+02 │ │ │ │ Vprtstp: contraction number = 8.247695e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.968018e-05 │ │ │ │ Vprtstp: contraction number = 3.789284e-01 │ │ │ │ Vnewton: Using errtol_s: 742.313034 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.031711e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.912640e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.261401e+02 │ │ │ │ Vprtstp: contraction number = 3.261401e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.150750e-05 │ │ │ │ Vprtstp: contraction number = 3.954245e-01 │ │ │ │ Vnewton: Using errtol_s: 293.528762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.111607e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.986441e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.384546e+02 │ │ │ │ Vprtstp: contraction number = 1.384546e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.337564e-05 │ │ │ │ Vprtstp: contraction number = 4.245224e-01 │ │ │ │ Vnewton: Using errtol_s: 124.609538 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.192877e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.060314e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.300596e+01 │ │ │ │ Vprtstp: contraction number = 6.300596e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.086783e-06 │ │ │ │ Vprtstp: contraction number = 4.550649e-01 │ │ │ │ Vnewton: Using errtol_s: 56.705427 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.273745e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.133890e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.026431e+01 │ │ │ │ Vprtstp: contraction number = 3.026431e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.923726e-06 │ │ │ │ Vprtstp: contraction number = 4.803401e-01 │ │ │ │ Vnewton: Using errtol_s: 27.237888 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.354541e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.208015e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.506906e+01 │ │ │ │ Vprtstp: contraction number = 1.506906e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.455768e-06 │ │ │ │ Vprtstp: contraction number = 4.979152e-01 │ │ │ │ Vnewton: Using errtol_s: 13.562159 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.435067e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.282999e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.684345e+00 │ │ │ │ Vprtstp: contraction number = 7.684345e+00 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 7.423567e-07 │ │ │ │ Vprtstp: contraction number = 5.099418e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.083680e+02 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.121420e+02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 9.947601e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.029781e+02 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1222,17 +1222,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.434662074417E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.352136568668E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.176012292477E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.112230e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.892170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -1253,217 +1253,217 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.342971 │ │ │ │ +Vacc_SASA: Time elapsed: 15.900055 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.904011e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.870230e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.868860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.686080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.716322e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.478505e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.733466e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.569756e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 15819726.247791 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.774528e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.608684e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.061014e+06 │ │ │ │ Vprtstp: contraction number = 1.061014e+06 │ │ │ │ Vnewton: Attempting damping, relres = 0.062452 │ │ │ │ Vnewton: Attempting damping, relres = 0.525397 │ │ │ │ Vnewton: Damping accepted, relres = 0.062452 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.245176e-02 │ │ │ │ Vprtstp: contraction number = 6.245176e-02 │ │ │ │ Vnewton: Using errtol_s: 987969.694273 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.871024e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.696831e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.221439e+05 │ │ │ │ Vprtstp: contraction number = 2.221439e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.274712e-02 │ │ │ │ Vprtstp: contraction number = 2.041114e-01 │ │ │ │ Vnewton: Using errtol_s: 201655.898404 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.951950e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.770271e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.509302e+04 │ │ │ │ Vprtstp: contraction number = 6.509302e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.704570e-03 │ │ │ │ Vprtstp: contraction number = 2.906202e-01 │ │ │ │ Vnewton: Using errtol_s: 58605.278995 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.033083e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.843417e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.250351e+04 │ │ │ │ Vprtstp: contraction number = 2.250351e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.280353e-03 │ │ │ │ Vprtstp: contraction number = 3.456144e-01 │ │ │ │ Vnewton: Using errtol_s: 20254.828172 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.113173e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.917431e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.447408e+03 │ │ │ │ Vprtstp: contraction number = 8.447408e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.805791e-04 │ │ │ │ Vprtstp: contraction number = 3.753490e-01 │ │ │ │ Vnewton: Using errtol_s: 7602.629655 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.193590e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.991100e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.399185e+03 │ │ │ │ Vprtstp: contraction number = 3.399185e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.933739e-04 │ │ │ │ Vprtstp: contraction number = 4.023769e-01 │ │ │ │ Vnewton: Using errtol_s: 3059.122762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.273782e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.064131e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.505025e+03 │ │ │ │ Vprtstp: contraction number = 1.505025e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.562081e-05 │ │ │ │ Vprtstp: contraction number = 4.427733e-01 │ │ │ │ Vnewton: Using errtol_s: 1354.497766 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.354384e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.136752e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.407337e+02 │ │ │ │ Vprtstp: contraction number = 7.407337e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.214082e-05 │ │ │ │ Vprtstp: contraction number = 4.921797e-01 │ │ │ │ Vnewton: Using errtol_s: 666.656280 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.435394e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.210696e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955938e+02 │ │ │ │ Vprtstp: contraction number = 3.955938e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.250569e-05 │ │ │ │ Vprtstp: contraction number = 5.340591e-01 │ │ │ │ Vnewton: Using errtol_s: 356.033867 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.516592e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.284661e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.238069e+02 │ │ │ │ Vprtstp: contraction number = 2.238069e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.273259e-05 │ │ │ │ Vprtstp: contraction number = 5.657500e-01 │ │ │ │ Vnewton: Using errtol_s: 201.426156 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.597852e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.357056e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.312226e+02 │ │ │ │ Vprtstp: contraction number = 1.312226e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.465385e-06 │ │ │ │ Vprtstp: contraction number = 5.863208e-01 │ │ │ │ Vnewton: Using errtol_s: 118.100345 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.677997e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.429816e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.886374e+01 │ │ │ │ Vprtstp: contraction number = 7.886374e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.486638e-06 │ │ │ │ Vprtstp: contraction number = 6.009922e-01 │ │ │ │ Vnewton: Using errtol_s: 70.977384 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.758172e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.502536e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.812776e+01 │ │ │ │ Vprtstp: contraction number = 4.812776e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 2.738037e-06 │ │ │ │ Vprtstp: contraction number = 6.102647e-01 │ │ │ │ Vnewton: Using errtol_s: 43.314994 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.839378e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.575581e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.971066e+01 │ │ │ │ Vprtstp: contraction number = 2.971066e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 1.690269e-06 │ │ │ │ Vprtstp: contraction number = 6.173289e-01 │ │ │ │ Vnewton: Using errtol_s: 26.739596 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.920472e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648988e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.848360e+01 │ │ │ │ Vprtstp: contraction number = 1.848360e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 1.051550e-06 │ │ │ │ Vprtstp: contraction number = 6.221201e-01 │ │ │ │ Vnewton: Using errtol_s: 16.635240 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.001349e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.722586e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.157246e+01 │ │ │ │ Vprtstp: contraction number = 1.157246e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 6.583687e-07 │ │ │ │ Vprtstp: contraction number = 6.260933e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.330547e+02 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.367813e+02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.209021e+02 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.243441e+02 │ │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1472,15 +1472,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.734614944651E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.465748372430E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.232753607231E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.231900e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.988940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ @@ -1528,182 +1528,182 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.649873 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.346393 │ │ │ │ +Vacc_SASA: Time elapsed: 15.999467 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.174186e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.146990e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.070370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.428870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.663599e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.528044e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.326798e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.036196e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 18647566.992070 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.366053e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.074990e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.941752e+06 │ │ │ │ Vprtstp: contraction number = 1.941752e+06 │ │ │ │ Vnewton: Attempting damping, relres = 0.095497 │ │ │ │ Vnewton: Attempting damping, relres = 0.544786 │ │ │ │ Vnewton: Damping accepted, relres = 0.095497 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.549656e-02 │ │ │ │ Vprtstp: contraction number = 9.549656e-02 │ │ │ │ Vnewton: Using errtol_s: 1780778.449755 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.457436e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.162736e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.788571e+05 │ │ │ │ Vprtstp: contraction number = 3.788571e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.837082e-02 │ │ │ │ Vprtstp: contraction number = 1.923715e-01 │ │ │ │ Vnewton: Using errtol_s: 342571.038812 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.536329e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.235387e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.019639e+05 │ │ │ │ Vprtstp: contraction number = 1.019639e+05 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.923062e-03 │ │ │ │ Vprtstp: contraction number = 2.679828e-01 │ │ │ │ Vnewton: Using errtol_s: 91803.137006 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.615940e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.307360e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.295911e+04 │ │ │ │ Vprtstp: contraction number = 3.295911e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.591047e-03 │ │ │ │ Vprtstp: contraction number = 3.231823e-01 │ │ │ │ Vnewton: Using errtol_s: 29669.150960 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.696890e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.378649e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.167703e+04 │ │ │ │ Vprtstp: contraction number = 1.167703e+04 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.636468e-04 │ │ │ │ Vprtstp: contraction number = 3.542616e-01 │ │ │ │ Vnewton: Using errtol_s: 10510.641014 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.776743e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.450176e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.318326e+03 │ │ │ │ Vprtstp: contraction number = 4.318326e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.084308e-04 │ │ │ │ Vprtstp: contraction number = 3.697898e-01 │ │ │ │ Vnewton: Using errtol_s: 3886.727604 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.856420e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.521988e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.645707e+03 │ │ │ │ Vprtstp: contraction number = 1.645707e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.942966e-05 │ │ │ │ Vprtstp: contraction number = 3.810841e-01 │ │ │ │ Vnewton: Using errtol_s: 1481.169947 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.937005e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.594463e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.631576e+02 │ │ │ │ Vprtstp: contraction number = 6.631576e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.200666e-05 │ │ │ │ Vprtstp: contraction number = 4.029560e-01 │ │ │ │ Vnewton: Using errtol_s: 596.846318 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.017409e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.666239e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.897130e+02 │ │ │ │ Vprtstp: contraction number = 2.897130e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.398265e-05 │ │ │ │ Vprtstp: contraction number = 4.368670e-01 │ │ │ │ Vnewton: Using errtol_s: 260.742452 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.097408e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.737968e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.365123e+02 │ │ │ │ Vprtstp: contraction number = 1.365123e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.588595e-06 │ │ │ │ Vprtstp: contraction number = 4.711978e-01 │ │ │ │ Vnewton: Using errtol_s: 122.861265 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.177819e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.810510e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.809649e+01 │ │ │ │ Vprtstp: contraction number = 6.809649e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.286589e-06 │ │ │ │ Vprtstp: contraction number = 4.988300e-01 │ │ │ │ Vnewton: Using errtol_s: 61.286879 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.257727e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.883752e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.533208e+01 │ │ │ │ Vprtstp: contraction number = 3.533208e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705256e-06 │ │ │ │ Vprtstp: contraction number = 5.188530e-01 │ │ │ │ Vnewton: Using errtol_s: 31.798881 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.337869e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.957051e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.878604e+01 │ │ │ │ Vprtstp: contraction number = 1.878604e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.066833e-07 │ │ │ │ Vprtstp: contraction number = 5.316991e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.074028e+02 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.110996e+02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 9.771770e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.011742e+02 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1712,23 +1712,23 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.745937546040E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 4.708379041028E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 2.354068218640E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.879440e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.708720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.409618e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.023698e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:41:24 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:55:45 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -1986,140 +1986,140 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.286174 │ │ │ │ +Vacc_SASA: Time elapsed: 7.032943 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.090275e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.085703e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.745150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.341690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.703762e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.510888e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521442e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.488823e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7775242.648804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.931822e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.879986e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.519208e+05 │ │ │ │ Vprtstp: contraction number = 4.519208e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.054343 │ │ │ │ Vnewton: Attempting damping, relres = 0.522411 │ │ │ │ Vnewton: Damping accepted, relres = 0.054343 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.434337e-02 │ │ │ │ Vprtstp: contraction number = 5.434337e-02 │ │ │ │ Vnewton: Using errtol_s: 422532.874830 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.904064e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.760410e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.825836e+04 │ │ │ │ Vprtstp: contraction number = 6.825836e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 8.031654e-03 │ │ │ │ Vprtstp: contraction number = 1.477946e-01 │ │ │ │ Vnewton: Using errtol_s: 62448.057923 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.709434e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.484613e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.274799e+04 │ │ │ │ Vprtstp: contraction number = 1.274799e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.476725e-03 │ │ │ │ Vprtstp: contraction number = 1.838631e-01 │ │ │ │ Vnewton: Using errtol_s: 11481.894443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.525123e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.207012e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.642149e+03 │ │ │ │ Vprtstp: contraction number = 2.642149e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.058466e-04 │ │ │ │ Vprtstp: contraction number = 2.071114e-01 │ │ │ │ Vnewton: Using errtol_s: 2378.031723 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.334879e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.918966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.907005e+02 │ │ │ │ Vprtstp: contraction number = 5.907005e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.837606e-05 │ │ │ │ Vprtstp: contraction number = 2.235632e-01 │ │ │ │ Vnewton: Using errtol_s: 531.640431 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.144641e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.637555e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.434663e+02 │ │ │ │ Vprtstp: contraction number = 1.434663e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.660675e-05 │ │ │ │ Vprtstp: contraction number = 2.428738e-01 │ │ │ │ Vnewton: Using errtol_s: 129.121507 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.956964e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.347577e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.897369e+01 │ │ │ │ Vprtstp: contraction number = 3.897369e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.511300e-06 │ │ │ │ Vprtstp: contraction number = 2.716546e-01 │ │ │ │ Vnewton: Using errtol_s: 35.076449 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.762077e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.068815e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.167165e+01 │ │ │ │ Vprtstp: contraction number = 1.167165e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.351022e-06 │ │ │ │ Vprtstp: contraction number = 2.994751e-01 │ │ │ │ Vnewton: Using errtol_s: 10.504522 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.559424e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.791557e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.750775e+00 │ │ │ │ Vprtstp: contraction number = 3.750775e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.341599e-07 │ │ │ │ Vprtstp: contraction number = 3.213567e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.652581e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.015749e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.857677e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.195336e+01 │ │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2128,17 +2128,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.649154177944E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.233253101346E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.165668863925E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.266680e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.034270e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -2184,138 +2184,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.297837 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.349643 │ │ │ │ +Vacc_SASA: Time elapsed: 6.913618 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.299271e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.282204e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 8.014740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.220030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.774998e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.443249e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.093147e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004200e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 9261641.900268 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.134198e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042890e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.279613e+05 │ │ │ │ Vprtstp: contraction number = 8.279613e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.082099 │ │ │ │ Vnewton: Attempting damping, relres = 0.538543 │ │ │ │ Vnewton: Damping accepted, relres = 0.082099 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.209891e-02 │ │ │ │ Vprtstp: contraction number = 8.209891e-02 │ │ │ │ Vnewton: Using errtol_s: 760370.715975 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.231072e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.130754e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.156529e+05 │ │ │ │ Vprtstp: contraction number = 1.156529e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.133997e-02 │ │ │ │ Vprtstp: contraction number = 1.381257e-01 │ │ │ │ Vnewton: Using errtol_s: 105026.724448 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.311594e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.202503e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.966463e+04 │ │ │ │ Vprtstp: contraction number = 1.966463e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.911861e-03 │ │ │ │ Vprtstp: contraction number = 1.685949e-01 │ │ │ │ Vnewton: Using errtol_s: 17706.967510 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.393288e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.274693e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.721579e+03 │ │ │ │ Vprtstp: contraction number = 3.721579e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.617487e-04 │ │ │ │ Vprtstp: contraction number = 1.892129e-01 │ │ │ │ Vnewton: Using errtol_s: 3350.387034 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.474850e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.346722e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.320600e+02 │ │ │ │ Vprtstp: contraction number = 7.320600e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.114465e-05 │ │ │ │ Vprtstp: contraction number = 1.966687e-01 │ │ │ │ Vnewton: Using errtol_s: 658.916270 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.555966e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.420794e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.450384e+02 │ │ │ │ Vprtstp: contraction number = 1.450384e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.409447e-05 │ │ │ │ Vprtstp: contraction number = 1.981101e-01 │ │ │ │ Vnewton: Using errtol_s: 130.537961 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.636320e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.493129e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.437556e+01 │ │ │ │ Vprtstp: contraction number = 3.437556e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.340452e-06 │ │ │ │ Vprtstp: contraction number = 2.370044e-01 │ │ │ │ Vnewton: Using errtol_s: 30.938074 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.716707e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.565071e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.059415e+01 │ │ │ │ Vprtstp: contraction number = 1.059415e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.029507e-06 │ │ │ │ Vprtstp: contraction number = 3.081938e-01 │ │ │ │ Vnewton: Using errtol_s: 9.534923 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.797429e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.637101e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.916133e+00 │ │ │ │ Vprtstp: contraction number = 3.916133e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.805503e-07 │ │ │ │ Vprtstp: contraction number = 3.696433e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.667453e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.041155e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.893858e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.223848e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2324,17 +2324,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.591945419500E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.356288022123E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.178084778246E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.081600e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.880430e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -2355,140 +2355,140 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.319876 │ │ │ │ +Vacc_SASA: Time elapsed: 7.071115 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.103179e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.116498e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.794550e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.444830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.741489e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.525069e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.015155e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.847476e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7837779.438687 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.056239e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.886937e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.514612e+05 │ │ │ │ Vprtstp: contraction number = 4.514612e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.053797 │ │ │ │ Vnewton: Attempting damping, relres = 0.522401 │ │ │ │ Vnewton: Damping accepted, relres = 0.053797 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.379672e-02 │ │ │ │ Vprtstp: contraction number = 5.379672e-02 │ │ │ │ Vnewton: Using errtol_s: 421646.851825 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.152979e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.975283e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.805281e+04 │ │ │ │ Vprtstp: contraction number = 6.805281e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 7.947357e-03 │ │ │ │ Vprtstp: contraction number = 1.477294e-01 │ │ │ │ Vnewton: Using errtol_s: 62289.628218 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.233882e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048172e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.276985e+04 │ │ │ │ Vprtstp: contraction number = 1.276985e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.467975e-03 │ │ │ │ Vprtstp: contraction number = 1.847124e-01 │ │ │ │ Vnewton: Using errtol_s: 11505.665992 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.314612e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.120727e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.685314e+03 │ │ │ │ Vprtstp: contraction number = 2.685314e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.083318e-04 │ │ │ │ Vprtstp: contraction number = 2.100388e-01 │ │ │ │ Vnewton: Using errtol_s: 2416.636290 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.395891e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.193886e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.970818e+02 │ │ │ │ Vprtstp: contraction number = 5.970818e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.855221e-05 │ │ │ │ Vprtstp: contraction number = 2.223326e-01 │ │ │ │ Vnewton: Using errtol_s: 537.297133 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.476497e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.267521e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.381270e+02 │ │ │ │ Vprtstp: contraction number = 1.381270e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.586035e-05 │ │ │ │ Vprtstp: contraction number = 2.313616e-01 │ │ │ │ Vnewton: Using errtol_s: 124.309951 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.557123e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.340866e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.581259e+01 │ │ │ │ Vprtstp: contraction number = 3.581259e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.112278e-06 │ │ │ │ Vprtstp: contraction number = 2.592804e-01 │ │ │ │ Vnewton: Using errtol_s: 32.231131 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.638315e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.413262e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.075720e+01 │ │ │ │ Vprtstp: contraction number = 1.075720e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.235235e-06 │ │ │ │ Vprtstp: contraction number = 3.003774e-01 │ │ │ │ Vnewton: Using errtol_s: 9.681503 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.724275e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.486499e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.606387e+00 │ │ │ │ Vprtstp: contraction number = 3.606387e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.141158e-07 │ │ │ │ Vprtstp: contraction number = 3.352525e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.793939e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.160870e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 6.957970e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.298673e+01 │ │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2497,17 +2497,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.659237014157E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.233789041891E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.168342765954E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.303480e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.006740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -2553,138 +2553,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.338577 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.373740 │ │ │ │ +Vacc_SASA: Time elapsed: 7.062003 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.295737e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.302617e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.887980e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.340100e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.742485e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.567325e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.969506e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.716213e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 9315222.001185 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.010708e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.756166e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.310439e+05 │ │ │ │ Vprtstp: contraction number = 8.310439e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.081942 │ │ │ │ Vnewton: Attempting damping, relres = 0.538517 │ │ │ │ Vnewton: Damping accepted, relres = 0.081942 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.194219e-02 │ │ │ │ Vprtstp: contraction number = 8.194219e-02 │ │ │ │ Vnewton: Using errtol_s: 763309.735899 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.107865e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.845854e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.164941e+05 │ │ │ │ Vprtstp: contraction number = 1.164941e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.135719e-02 │ │ │ │ Vprtstp: contraction number = 1.386000e-01 │ │ │ │ Vnewton: Using errtol_s: 105794.756542 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.188955e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.919253e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.004035e+04 │ │ │ │ Vprtstp: contraction number = 2.004035e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.937352e-03 │ │ │ │ Vprtstp: contraction number = 1.705837e-01 │ │ │ │ Vnewton: Using errtol_s: 18046.864412 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.268826e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.993572e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.874509e+03 │ │ │ │ Vprtstp: contraction number = 3.874509e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.744478e-04 │ │ │ │ Vprtstp: contraction number = 1.932781e-01 │ │ │ │ Vnewton: Using errtol_s: 3488.064314 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.348604e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.067568e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.934449e+02 │ │ │ │ Vprtstp: contraction number = 7.934449e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.666874e-05 │ │ │ │ Vprtstp: contraction number = 2.047515e-01 │ │ │ │ Vnewton: Using errtol_s: 714.186341 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.428245e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.141767e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.631165e+02 │ │ │ │ Vprtstp: contraction number = 1.631165e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.576011e-05 │ │ │ │ Vprtstp: contraction number = 2.055611e-01 │ │ │ │ Vnewton: Using errtol_s: 146.808940 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.507644e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.216063e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.992341e+01 │ │ │ │ Vprtstp: contraction number = 3.992341e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.857249e-06 │ │ │ │ Vprtstp: contraction number = 2.447475e-01 │ │ │ │ Vnewton: Using errtol_s: 35.931127 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.587885e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.289950e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.373524e+01 │ │ │ │ Vprtstp: contraction number = 1.373524e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.327082e-06 │ │ │ │ Vprtstp: contraction number = 3.440488e-01 │ │ │ │ Vnewton: Using errtol_s: 12.362061 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.668123e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.364112e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.506580e+00 │ │ │ │ Vprtstp: contraction number = 5.506580e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.320241e-07 │ │ │ │ Vprtstp: contraction number = 4.008978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.615023e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.984103e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.050707e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.394412e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2693,17 +2693,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.613981699518E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.353039534047E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.176460315654E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.187870e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.884290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -2724,140 +2724,140 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.367535 │ │ │ │ +Vacc_SASA: Time elapsed: 15.674036 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.119439e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.090137e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.831320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.664510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.752034e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.588347e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.988220e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.673333e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 15819726.247791 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.029469e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.713193e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.105286e+05 │ │ │ │ Vprtstp: contraction number = 9.105286e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.054151 │ │ │ │ Vnewton: Attempting damping, relres = 0.522361 │ │ │ │ Vnewton: Damping accepted, relres = 0.054151 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.415081e-02 │ │ │ │ Vprtstp: contraction number = 5.415081e-02 │ │ │ │ Vnewton: Using errtol_s: 856650.988867 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.125891e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.803519e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.365159e+05 │ │ │ │ Vprtstp: contraction number = 1.365159e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 7.938600e-03 │ │ │ │ Vprtstp: contraction number = 1.466017e-01 │ │ │ │ Vnewton: Using errtol_s: 125586.474947 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.206464e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.877835e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.543138e+04 │ │ │ │ Vprtstp: contraction number = 2.543138e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.449191e-03 │ │ │ │ Vprtstp: contraction number = 1.825500e-01 │ │ │ │ Vnewton: Using errtol_s: 22925.804865 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.288092e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.956519e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.291506e+03 │ │ │ │ Vprtstp: contraction number = 5.291506e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.010412e-04 │ │ │ │ Vprtstp: contraction number = 2.077305e-01 │ │ │ │ Vnewton: Using errtol_s: 4762.388621 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.368701e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.031597e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.180651e+03 │ │ │ │ Vprtstp: contraction number = 1.180651e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.716597e-05 │ │ │ │ Vprtstp: contraction number = 2.231123e-01 │ │ │ │ Vnewton: Using errtol_s: 1062.547289 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.449576e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.107889e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.813654e+02 │ │ │ │ Vprtstp: contraction number = 2.813654e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.600723e-05 │ │ │ │ Vprtstp: contraction number = 2.383235e-01 │ │ │ │ Vnewton: Using errtol_s: 253.229951 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.531302e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.185138e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.533652e+01 │ │ │ │ Vprtstp: contraction number = 7.533652e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.285970e-06 │ │ │ │ Vprtstp: contraction number = 2.677522e-01 │ │ │ │ Vnewton: Using errtol_s: 67.802871 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.612793e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.262099e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.308540e+01 │ │ │ │ Vprtstp: contraction number = 2.308540e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.313362e-06 │ │ │ │ Vprtstp: contraction number = 3.064328e-01 │ │ │ │ Vnewton: Using errtol_s: 20.777024 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.693821e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.340269e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.670717e+00 │ │ │ │ Vprtstp: contraction number = 7.670717e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.363948e-07 │ │ │ │ Vprtstp: contraction number = 3.322731e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.689695e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.058460e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.263784e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.612617e+01 │ │ │ │ Vpmg_setPart: lower corner = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: upper corner = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2866,17 +2866,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.013375850535E+01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.468101698845E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.233922430579E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.207920e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.183670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0735516 │ │ │ │ @@ -2922,138 +2922,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.652629 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.201984 │ │ │ │ +Vacc_SASA: Time elapsed: 15.974582 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.368071e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.415843e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (161, 161, 161) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.771330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 7.715880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (081, 081, 081) │ │ │ │ Vbuildops: Galer: (041, 041, 041) │ │ │ │ Vbuildops: Galer: (021, 021, 021) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.733889e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 2.607706e+00 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.039012e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.684918e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 18644287.879827 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.079919e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.724924e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.651555e+06 │ │ │ │ Vprtstp: contraction number = 1.651555e+06 │ │ │ │ Vnewton: Attempting damping, relres = 0.081643 │ │ │ │ Vnewton: Attempting damping, relres = 0.538237 │ │ │ │ Vnewton: Damping accepted, relres = 0.081643 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164291e-02 │ │ │ │ Vprtstp: contraction number = 8.164291e-02 │ │ │ │ Vnewton: Using errtol_s: 1522173.863324 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.175522e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.818259e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.305601e+05 │ │ │ │ Vprtstp: contraction number = 2.305601e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.125644e-02 │ │ │ │ Vprtstp: contraction number = 1.378740e-01 │ │ │ │ Vnewton: Using errtol_s: 209868.227405 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.255052e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.896853e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.940032e+04 │ │ │ │ Vprtstp: contraction number = 3.940032e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.903339e-03 │ │ │ │ Vprtstp: contraction number = 1.690890e-01 │ │ │ │ Vnewton: Using errtol_s: 35486.402387 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.334365e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.975140e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.544305e+03 │ │ │ │ Vprtstp: contraction number = 7.544305e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.642891e-04 │ │ │ │ Vprtstp: contraction number = 1.913948e-01 │ │ │ │ Vnewton: Using errtol_s: 6791.911566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.414700e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.054624e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.522155e+03 │ │ │ │ Vprtstp: contraction number = 1.522155e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.348563e-05 │ │ │ │ Vprtstp: contraction number = 2.017234e-01 │ │ │ │ Vnewton: Using errtol_s: 1370.087193 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.494977e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.133965e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.106660e+02 │ │ │ │ Vprtstp: contraction number = 3.106660e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.499708e-05 │ │ │ │ Vprtstp: contraction number = 2.040818e-01 │ │ │ │ Vnewton: Using errtol_s: 279.609899 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.575039e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.214895e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.690225e+01 │ │ │ │ Vprtstp: contraction number = 7.690225e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.712245e-06 │ │ │ │ Vprtstp: contraction number = 2.475312e-01 │ │ │ │ Vnewton: Using errtol_s: 69.212171 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.656039e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.294642e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.600764e+01 │ │ │ │ Vprtstp: contraction number = 2.600764e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.255497e-06 │ │ │ │ Vprtstp: contraction number = 3.382042e-01 │ │ │ │ Vnewton: Using errtol_s: 23.407850 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.737166e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.375133e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011646e+01 │ │ │ │ Vprtstp: contraction number = 1.011646e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.883437e-07 │ │ │ │ Vprtstp: contraction number = 3.889644e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.612484e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.978903e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 7.526797e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.879505e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -3062,23 +3062,23 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.005009553015E+01 kT │ │ │ │ Vpmg_energy: qfEnergy = 4.710211065569E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 2.354978106920E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.913370e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.111090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.809166e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.448586e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:48:15 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:07:48 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -3431,250 +3431,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.424679 │ │ │ │ +Vacc_SASA: Time elapsed: 7.343377 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.273795e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.158240e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.698260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.715140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.792060e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.879270e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.814753e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.647835e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.075964e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061023e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.301736e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.297212e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.494130e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.492052e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.681898e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.688303e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.874901e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.883937e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.066065e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.083054e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.253831e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.275427e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442430e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.466979e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.632681e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.657525e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.822454e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.848951e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.010108e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.032194e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.197596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.225676e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.385780e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.416789e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.573733e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.600767e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.761245e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.796240e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.951705e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.988761e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.141487e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.181111e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.330202e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.371686e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.518971e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.562166e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.687586e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.768298e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.746184e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.825406e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -3683,17 +3683,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.479770161201E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.169401599673E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.300507194512E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.430100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.592900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -3739,171 +3739,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00578902 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.407130 │ │ │ │ +Vacc_SASA: Time elapsed: 6.993799 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.806315e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.334847e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.725720e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.528420e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.399490e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.642370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.639818e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.633535e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3431662.159805 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.731465e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.725047e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.373293e+05 │ │ │ │ Vprtstp: contraction number = 3.373293e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.089626 │ │ │ │ Vnewton: Attempting damping, relres = 0.541581 │ │ │ │ Vnewton: Damping accepted, relres = 0.089626 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.962597e-02 │ │ │ │ Vprtstp: contraction number = 8.962597e-02 │ │ │ │ Vnewton: Using errtol_s: 307566.035257 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.971890e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.963245e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.223173e+04 │ │ │ │ Vprtstp: contraction number = 6.223173e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.639798e-02 │ │ │ │ Vprtstp: contraction number = 1.829601e-01 │ │ │ │ Vnewton: Using errtol_s: 56272.319668 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.175611e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.163966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.604081e+04 │ │ │ │ Vprtstp: contraction number = 1.604081e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.208259e-03 │ │ │ │ Vprtstp: contraction number = 2.566328e-01 │ │ │ │ Vnewton: Using errtol_s: 14441.323490 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.381406e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.365956e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.994316e+03 │ │ │ │ Vprtstp: contraction number = 4.994316e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.309837e-03 │ │ │ │ Vprtstp: contraction number = 3.112539e-01 │ │ │ │ Vnewton: Using errtol_s: 4494.917566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.588637e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.566718e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.695194e+03 │ │ │ │ Vprtstp: contraction number = 1.695194e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.445882e-04 │ │ │ │ Vprtstp: contraction number = 3.394226e-01 │ │ │ │ Vnewton: Using errtol_s: 1525.676669 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.787261e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.766622e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.988429e+02 │ │ │ │ Vprtstp: contraction number = 5.988429e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.570548e-04 │ │ │ │ Vprtstp: contraction number = 3.532589e-01 │ │ │ │ Vnewton: Using errtol_s: 538.958849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.987825e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.968453e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.157694e+02 │ │ │ │ Vprtstp: contraction number = 2.157694e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.658847e-05 │ │ │ │ Vprtstp: contraction number = 3.603104e-01 │ │ │ │ Vnewton: Using errtol_s: 194.192499 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.185783e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.148736e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.859364e+01 │ │ │ │ Vprtstp: contraction number = 7.859364e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.061225e-05 │ │ │ │ Vprtstp: contraction number = 3.642483e-01 │ │ │ │ Vnewton: Using errtol_s: 70.734280 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.375320e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.354171e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.887021e+01 │ │ │ │ Vprtstp: contraction number = 2.887021e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.571604e-06 │ │ │ │ Vprtstp: contraction number = 3.673351e-01 │ │ │ │ Vnewton: Using errtol_s: 25.983185 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.568917e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.559815e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.070116e+01 │ │ │ │ Vprtstp: contraction number = 1.070116e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.806524e-06 │ │ │ │ Vprtstp: contraction number = 3.706644e-01 │ │ │ │ Vnewton: Using errtol_s: 9.631041 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.759632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.764054e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.050515e+00 │ │ │ │ Vprtstp: contraction number = 4.050515e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.062302e-06 │ │ │ │ Vprtstp: contraction number = 3.785119e-01 │ │ │ │ Vnewton: Using errtol_s: 3.645463 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.962305e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.969009e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.586893e+00 │ │ │ │ Vprtstp: contraction number = 1.586893e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.161843e-07 │ │ │ │ Vprtstp: contraction number = 3.917757e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.484486e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.561804e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.502435e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.578340e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -3912,15 +3912,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.504529533890E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.061382616797E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.339258817013E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.266990e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.386670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -3943,272 +3943,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.640852 │ │ │ │ +Vacc_SASA: Time elapsed: 7.233306 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.630117e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.117807e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 2.150850e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.723280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 8.429370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.881120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.116383e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.046457e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.230986e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.141659e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.517157e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.368084e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.731998e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.555361e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.964384e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.737990e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021375e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.923268e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048104e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010738e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073894e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.029304e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099324e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047260e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.125081e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065504e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.147154e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082922e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.169780e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101472e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.192922e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119693e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.211903e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.138040e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.231261e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156529e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.250864e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174572e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271264e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193055e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.290835e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.210442e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.310153e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228873e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329981e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.247741e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350348e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265712e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.369651e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.284123e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.725957e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.839149e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.945066e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.025731e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4217,15 +4217,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.521116242377E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.321247419853E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.153524159473E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.419500e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.619200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -4273,193 +4273,193 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0721278 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.462942 │ │ │ │ +Vacc_SASA: Time elapsed: 7.278266 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.086497e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.818503e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.799440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.698160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.034610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.535480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.484856e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.396372e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3863048.260999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.494341e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.405594e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.079329e+05 │ │ │ │ Vprtstp: contraction number = 4.079329e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.096763 │ │ │ │ Vnewton: Attempting damping, relres = 0.545251 │ │ │ │ Vnewton: Damping accepted, relres = 0.096763 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.676296e-02 │ │ │ │ Vprtstp: contraction number = 9.676296e-02 │ │ │ │ Vnewton: Using errtol_s: 373799.984181 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.518183e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.429188e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.732785e+04 │ │ │ │ Vprtstp: contraction number = 7.732785e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.807372e-02 │ │ │ │ Vprtstp: contraction number = 1.867834e-01 │ │ │ │ Vnewton: Using errtol_s: 69819.644697 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.538672e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.449174e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.985652e+04 │ │ │ │ Vprtstp: contraction number = 1.985652e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.627077e-03 │ │ │ │ Vprtstp: contraction number = 2.560113e-01 │ │ │ │ Vnewton: Using errtol_s: 17874.621452 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.559050e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.469452e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.114622e+03 │ │ │ │ Vprtstp: contraction number = 6.114622e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.424617e-03 │ │ │ │ Vprtstp: contraction number = 3.078870e-01 │ │ │ │ Vnewton: Using errtol_s: 5503.364448 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.579396e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.489326e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.092890e+03 │ │ │ │ Vprtstp: contraction number = 2.092890e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.875987e-04 │ │ │ │ Vprtstp: contraction number = 3.422665e-01 │ │ │ │ Vnewton: Using errtol_s: 1883.617345 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.599381e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.509064e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.574998e+02 │ │ │ │ Vprtstp: contraction number = 7.574998e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.764801e-04 │ │ │ │ Vprtstp: contraction number = 3.619372e-01 │ │ │ │ Vnewton: Using errtol_s: 681.751152 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.619725e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.529732e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.922283e+02 │ │ │ │ Vprtstp: contraction number = 2.922283e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.808241e-05 │ │ │ │ Vprtstp: contraction number = 3.857795e-01 │ │ │ │ Vnewton: Using errtol_s: 263.005621 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.639053e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.548269e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.230857e+02 │ │ │ │ Vprtstp: contraction number = 1.230857e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.867611e-05 │ │ │ │ Vprtstp: contraction number = 4.211970e-01 │ │ │ │ Vnewton: Using errtol_s: 110.777182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.659637e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568537e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.644162e+01 │ │ │ │ Vprtstp: contraction number = 5.644162e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.314958e-05 │ │ │ │ Vprtstp: contraction number = 4.585554e-01 │ │ │ │ Vnewton: Using errtol_s: 50.797474 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.680148e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.588604e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.814912e+01 │ │ │ │ Vprtstp: contraction number = 2.814912e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.558089e-06 │ │ │ │ Vprtstp: contraction number = 4.987298e-01 │ │ │ │ Vnewton: Using errtol_s: 25.334216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.699938e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.609156e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.477957e+01 │ │ │ │ Vprtstp: contraction number = 1.477957e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.443295e-06 │ │ │ │ Vprtstp: contraction number = 5.250454e-01 │ │ │ │ Vnewton: Using errtol_s: 13.301614 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.719925e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.629408e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.444333e+00 │ │ │ │ Vprtstp: contraction number = 8.444333e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.967333e-06 │ │ │ │ Vprtstp: contraction number = 5.713519e-01 │ │ │ │ Vnewton: Using errtol_s: 7.599902 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.738469e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.649128e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.056221e+00 │ │ │ │ Vprtstp: contraction number = 5.056221e+00 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.177982e-06 │ │ │ │ Vprtstp: contraction number = 5.987712e-01 │ │ │ │ Vnewton: Using errtol_s: 4.550602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.757980e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.669219e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.242153e+00 │ │ │ │ Vprtstp: contraction number = 3.242153e+00 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.553462e-07 │ │ │ │ Vprtstp: contraction number = 6.412203e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.881879e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.965468e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.889049e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.966402e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4468,17 +4468,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.360671447276E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.843358669820E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.205607078702E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.291650e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.286750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -4499,261 +4499,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.510550 │ │ │ │ +Vacc_SASA: Time elapsed: 16.108169 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.797588e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.757834e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.721500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.627130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.721740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.486300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.962383e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.870304e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.971911e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.879406e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.995419e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.901226e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.014301e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.919529e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.033955e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.937934e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.052616e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.956416e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.071974e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.975103e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.091242e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.993754e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.110571e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.012616e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.129856e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.031426e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149124e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.050193e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.165668e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.068814e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.184898e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.087270e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.204344e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.106028e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.224336e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.124622e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.244669e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.143432e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.264292e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.162221e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.284305e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.181200e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.303955e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.199848e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.323627e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.218850e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.343145e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.237731e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.958042e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.037595e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.823315e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.899499e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4762,17 +4762,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.970329890600E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.499206035649E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.787861710155E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.391300e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.824900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -4818,182 +4818,182 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.081031 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.939831 │ │ │ │ +Vacc_SASA: Time elapsed: 15.963884 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.937067e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.831265e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.843810e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.553230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.494330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.463500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.562088e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.444410e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7257742.969900 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.571374e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.453277e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.332655e+05 │ │ │ │ Vprtstp: contraction number = 7.332655e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.092954 │ │ │ │ Vnewton: Attempting damping, relres = 0.543087 │ │ │ │ Vnewton: Damping accepted, relres = 0.092954 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.295377e-02 │ │ │ │ Vprtstp: contraction number = 9.295377e-02 │ │ │ │ Vnewton: Using errtol_s: 674634.557796 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.596116e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.473596e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.375383e+05 │ │ │ │ Vprtstp: contraction number = 1.375383e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.716852e-02 │ │ │ │ Vprtstp: contraction number = 1.846995e-01 │ │ │ │ Vnewton: Using errtol_s: 124604.673279 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.616989e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.493635e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.550512e+04 │ │ │ │ Vprtstp: contraction number = 3.550512e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.404594e-03 │ │ │ │ Vprtstp: contraction number = 2.565507e-01 │ │ │ │ Vnewton: Using errtol_s: 31967.413641 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.637881e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.513353e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.099641e+04 │ │ │ │ Vprtstp: contraction number = 1.099641e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.363650e-03 │ │ │ │ Vprtstp: contraction number = 3.095972e-01 │ │ │ │ Vnewton: Using errtol_s: 9897.022727 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.658689e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.533029e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.730401e+03 │ │ │ │ Vprtstp: contraction number = 3.730401e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.625937e-04 │ │ │ │ Vprtstp: contraction number = 3.392320e-01 │ │ │ │ Vnewton: Using errtol_s: 3357.386399 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.679500e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.552252e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.301607e+03 │ │ │ │ Vprtstp: contraction number = 1.301607e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.614068e-04 │ │ │ │ Vprtstp: contraction number = 3.489169e-01 │ │ │ │ Vnewton: Using errtol_s: 1171.448936 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.700265e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.571330e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.645153e+02 │ │ │ │ Vprtstp: contraction number = 4.645153e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.760250e-05 │ │ │ │ Vprtstp: contraction number = 3.568778e-01 │ │ │ │ Vnewton: Using errtol_s: 418.064161 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.721786e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.590294e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.772219e+02 │ │ │ │ Vprtstp: contraction number = 1.772219e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.197650e-05 │ │ │ │ Vprtstp: contraction number = 3.815199e-01 │ │ │ │ Vnewton: Using errtol_s: 159.499808 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.742744e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609672e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.471028e+01 │ │ │ │ Vprtstp: contraction number = 7.471028e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 9.264488e-06 │ │ │ │ Vprtstp: contraction number = 4.215634e-01 │ │ │ │ Vnewton: Using errtol_s: 67.239276 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.763346e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.628893e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.443502e+01 │ │ │ │ Vprtstp: contraction number = 3.443502e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 4.270137e-06 │ │ │ │ Vprtstp: contraction number = 4.609145e-01 │ │ │ │ Vnewton: Using errtol_s: 30.991559 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.783878e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.647747e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.720700e+01 │ │ │ │ Vprtstp: contraction number = 1.720700e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.133763e-06 │ │ │ │ Vprtstp: contraction number = 4.996942e-01 │ │ │ │ Vnewton: Using errtol_s: 15.486302 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.804218e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.665897e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.259710e+00 │ │ │ │ Vprtstp: contraction number = 9.259710e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.148258e-06 │ │ │ │ Vprtstp: contraction number = 5.381377e-01 │ │ │ │ Vnewton: Using errtol_s: 8.333763 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.826285e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.685488e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.358358e+00 │ │ │ │ Vprtstp: contraction number = 5.358358e+00 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 6.644658e-07 │ │ │ │ Vprtstp: contraction number = 5.786728e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.807065e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.895980e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.567636e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.640950e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -5002,27 +5002,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.140717793128E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.905500135129E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.454863407382E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.245350e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.242180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.852575e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.710830e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:52:36 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:12:48 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -5375,250 +5375,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.481043 │ │ │ │ +Vacc_SASA: Time elapsed: 7.119830 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.326999e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.898934e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.704940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.563650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.639830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.277680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.832327e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.262249e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.077222e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018237e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305214e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.242057e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.502963e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427324e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.695037e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.613915e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.879903e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.803009e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.070932e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.990000e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273286e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.170758e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.462733e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.343584e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.655923e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.525998e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.843697e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.704379e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.037504e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.881982e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.230066e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.069517e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.416137e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.256342e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.612386e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.443107e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.810144e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.626849e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.005300e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.808859e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.196081e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.990249e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.390119e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.171504e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.586169e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.353119e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.753514e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.833268e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.568393e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.639605e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -5627,17 +5627,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.939690296929E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.376673747482E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.692177592704E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.584300e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.780700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -5683,171 +5683,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0309075 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.471460 │ │ │ │ +Vacc_SASA: Time elapsed: 7.106212 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.308300e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.892680e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.746350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.587780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.850360e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.455300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.762088e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.472113e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6495765.822087 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.854625e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.561176e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.362765e+05 │ │ │ │ Vprtstp: contraction number = 6.362765e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.088746 │ │ │ │ Vnewton: Attempting damping, relres = 0.541895 │ │ │ │ Vnewton: Damping accepted, relres = 0.088746 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.874646e-02 │ │ │ │ Vprtstp: contraction number = 8.874646e-02 │ │ │ │ Vnewton: Using errtol_s: 576476.204773 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.089575e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.787469e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.170231e+05 │ │ │ │ Vprtstp: contraction number = 1.170231e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.623146e-02 │ │ │ │ Vprtstp: contraction number = 1.828970e-01 │ │ │ │ Vnewton: Using errtol_s: 105435.741217 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.297040e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.981333e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.955662e+04 │ │ │ │ Vprtstp: contraction number = 2.955662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.095304e-03 │ │ │ │ Vprtstp: contraction number = 2.523066e-01 │ │ │ │ Vnewton: Using errtol_s: 26602.134295 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.491619e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.173494e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.995691e+03 │ │ │ │ Vprtstp: contraction number = 8.995691e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.246378e-03 │ │ │ │ Vprtstp: contraction number = 3.043434e-01 │ │ │ │ Vnewton: Using errtol_s: 8096.182717 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.696040e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.364261e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.013650e+03 │ │ │ │ Vprtstp: contraction number = 3.013650e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.175484e-04 │ │ │ │ Vprtstp: contraction number = 3.350093e-01 │ │ │ │ Vnewton: Using errtol_s: 2712.296685 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.904081e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.555092e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.048604e+03 │ │ │ │ Vprtstp: contraction number = 1.048604e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.452864e-04 │ │ │ │ Vprtstp: contraction number = 3.479510e-01 │ │ │ │ Vnewton: Using errtol_s: 943.746446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.107689e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.744840e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.603662e+02 │ │ │ │ Vprtstp: contraction number = 3.603662e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.992953e-05 │ │ │ │ Vprtstp: contraction number = 3.436628e-01 │ │ │ │ Vnewton: Using errtol_s: 324.330531 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.319339e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.933466e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.297355e+02 │ │ │ │ Vprtstp: contraction number = 1.297355e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.797512e-05 │ │ │ │ Vprtstp: contraction number = 3.600099e-01 │ │ │ │ Vnewton: Using errtol_s: 116.762190 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.530700e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.123112e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.314764e+01 │ │ │ │ Vprtstp: contraction number = 5.314764e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.363712e-06 │ │ │ │ Vprtstp: contraction number = 4.096613e-01 │ │ │ │ Vnewton: Using errtol_s: 47.832946 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.736005e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.295083e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.432172e+01 │ │ │ │ Vprtstp: contraction number = 2.432172e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.369821e-06 │ │ │ │ Vprtstp: contraction number = 4.576253e-01 │ │ │ │ Vnewton: Using errtol_s: 21.889567 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.944633e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.487749e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.198142e+01 │ │ │ │ Vprtstp: contraction number = 1.198142e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.660048e-06 │ │ │ │ Vprtstp: contraction number = 4.926220e-01 │ │ │ │ Vnewton: Using errtol_s: 10.783282 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.152933e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.682593e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.178209e+00 │ │ │ │ Vprtstp: contraction number = 6.178209e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 8.560021e-07 │ │ │ │ Vprtstp: contraction number = 5.156491e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.557682e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.639257e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.368858e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.443804e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -5856,15 +5856,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.088785414018E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.513083652575E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.773034744692E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.230900e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.233180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -5887,272 +5887,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.491264 │ │ │ │ +Vacc_SASA: Time elapsed: 7.229353 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.422321e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.090581e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.696420e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.557680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.725370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.467120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.257099e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.740123e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.356588e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.830919e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.604606e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.049548e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.780227e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.231261e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.983815e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.412608e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018514e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.591317e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038988e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.772033e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059260e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.953477e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078216e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013420e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097491e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031470e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116906e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049468e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.135631e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067338e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155483e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085408e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174598e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103749e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193629e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121981e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.213601e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140355e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233448e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158341e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.253521e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.175928e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.273554e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193717e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.294621e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.211170e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.315453e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.227536e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.335937e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.245738e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.252852e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.332493e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.859278e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.933755e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -6161,15 +6161,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.529259077785E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.922111986755E-02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.727400e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.505500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -6217,149 +6217,149 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00111335 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.547252 │ │ │ │ +Vacc_SASA: Time elapsed: 7.192889 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.509189e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.119698e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.685940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.575570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.116080e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.446560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.445759e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.349859e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 659220.576503 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.455465e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.358997e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.405229e+04 │ │ │ │ Vprtstp: contraction number = 7.405229e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.101194 │ │ │ │ Vnewton: Attempting damping, relres = 0.547249 │ │ │ │ Vnewton: Damping accepted, relres = 0.101194 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011936e-01 │ │ │ │ Vprtstp: contraction number = 1.011936e-01 │ │ │ │ Vnewton: Using errtol_s: 66708.882844 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478335e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.380097e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.227539e+04 │ │ │ │ Vprtstp: contraction number = 1.227539e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.676045e-02 │ │ │ │ Vprtstp: contraction number = 1.656277e-01 │ │ │ │ Vnewton: Using errtol_s: 11048.836228 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.497006e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.397366e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.508807e+03 │ │ │ │ Vprtstp: contraction number = 2.508807e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.425225e-03 │ │ │ │ Vprtstp: contraction number = 2.043635e-01 │ │ │ │ Vnewton: Using errtol_s: 2257.978588 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.516467e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.413549e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.967621e+02 │ │ │ │ Vprtstp: contraction number = 5.967621e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 8.147347e-04 │ │ │ │ Vprtstp: contraction number = 2.378632e-01 │ │ │ │ Vnewton: Using errtol_s: 537.089910 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.535593e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.430788e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.589401e+02 │ │ │ │ Vprtstp: contraction number = 1.589401e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 2.169933e-04 │ │ │ │ Vprtstp: contraction number = 2.663361e-01 │ │ │ │ Vnewton: Using errtol_s: 143.046443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.555609e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.448496e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.567685e+01 │ │ │ │ Vprtstp: contraction number = 4.567685e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 6.236027e-05 │ │ │ │ Vprtstp: contraction number = 2.873834e-01 │ │ │ │ Vnewton: Using errtol_s: 41.109175 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.574262e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.466009e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.380678e+01 │ │ │ │ Vprtstp: contraction number = 1.380678e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.884969e-05 │ │ │ │ Vprtstp: contraction number = 3.022708e-01 │ │ │ │ Vnewton: Using errtol_s: 12.426102 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.593535e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.483446e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.334509e+00 │ │ │ │ Vprtstp: contraction number = 4.334509e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.917683e-06 │ │ │ │ Vprtstp: contraction number = 3.139406e-01 │ │ │ │ Vnewton: Using errtol_s: 3.901058 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612296e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.500820e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.401869e+00 │ │ │ │ Vprtstp: contraction number = 1.401869e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.913900e-06 │ │ │ │ Vprtstp: contraction number = 3.234205e-01 │ │ │ │ Vnewton: Using errtol_s: 1.261682 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.631443e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.518262e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.640279e-01 │ │ │ │ Vprtstp: contraction number = 4.640279e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.335135e-07 │ │ │ │ Vprtstp: contraction number = 3.310066e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.004720e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.088317e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.817097e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.891591e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -6368,15 +6368,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.628092645566E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.231942662448E-02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.316080e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.282240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ @@ -6399,261 +6399,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.708914 │ │ │ │ +Vacc_SASA: Time elapsed: 15.693403 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.819853e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.713252e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.722500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.549080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.604270e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.316020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.837755e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.711847e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.847221e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.720939e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.870929e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.743325e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.891255e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762243e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.911432e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.781144e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.931043e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.798212e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.950367e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.816872e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.970246e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.836015e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.988889e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.855133e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.008343e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.873567e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.025989e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.892575e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.045922e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.911193e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.069029e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.929696e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.090808e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.948397e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.110384e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.967192e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.130191e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.985979e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149706e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.004727e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.169407e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.023426e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.189032e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.042206e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.208672e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.060878e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.228317e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.079713e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.060666e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.139736e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.827668e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.901281e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -6662,17 +6662,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.345658970657E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.376279132276E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.692311982408E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.487900e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.412200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -6718,171 +6718,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0354778 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.544085 │ │ │ │ +Vacc_SASA: Time elapsed: 15.569570 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.882485e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.778765e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.739110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.505980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.540000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.341490e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.441231e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.280920e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7084866.598925 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.450619e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.289840e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.984768e+05 │ │ │ │ Vprtstp: contraction number = 6.984768e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.089369 │ │ │ │ Vnewton: Attempting damping, relres = 0.542089 │ │ │ │ Vnewton: Damping accepted, relres = 0.089369 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.936880e-02 │ │ │ │ Vprtstp: contraction number = 8.936880e-02 │ │ │ │ Vnewton: Using errtol_s: 633166.041219 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.473752e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.312679e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.273163e+05 │ │ │ │ Vprtstp: contraction number = 1.273163e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.619364e-02 │ │ │ │ Vprtstp: contraction number = 1.812001e-01 │ │ │ │ Vnewton: Using errtol_s: 114729.758442 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.493676e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.331846e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.151737e+04 │ │ │ │ Vprtstp: contraction number = 3.151737e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.003932e-03 │ │ │ │ Vprtstp: contraction number = 2.472534e-01 │ │ │ │ Vnewton: Using errtol_s: 28367.322157 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.511982e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.350606e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.393741e+03 │ │ │ │ Vprtstp: contraction number = 9.393741e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.193311e-03 │ │ │ │ Vprtstp: contraction number = 2.980349e-01 │ │ │ │ Vnewton: Using errtol_s: 8454.451884 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.532130e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.370107e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.092776e+03 │ │ │ │ Vprtstp: contraction number = 3.092776e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.928814e-04 │ │ │ │ Vprtstp: contraction number = 3.292363e-01 │ │ │ │ Vnewton: Using errtol_s: 2783.512220 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.552655e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.389293e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.061371e+03 │ │ │ │ Vprtstp: contraction number = 1.061371e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.348278e-04 │ │ │ │ Vprtstp: contraction number = 3.431770e-01 │ │ │ │ Vnewton: Using errtol_s: 955.237298 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.573451e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.408711e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.607964e+02 │ │ │ │ Vprtstp: contraction number = 3.607964e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.583260e-05 │ │ │ │ Vprtstp: contraction number = 3.399342e-01 │ │ │ │ Vnewton: Using errtol_s: 324.717847 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.593852e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.428256e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.293597e+02 │ │ │ │ Vprtstp: contraction number = 1.293597e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.643277e-05 │ │ │ │ Vprtstp: contraction number = 3.585389e-01 │ │ │ │ Vnewton: Using errtol_s: 116.423976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.614137e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.447694e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.299042e+01 │ │ │ │ Vprtstp: contraction number = 5.299042e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 6.731454e-06 │ │ │ │ Vprtstp: contraction number = 4.096360e-01 │ │ │ │ Vnewton: Using errtol_s: 47.691450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.634480e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.467095e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.428459e+01 │ │ │ │ Vprtstp: contraction number = 2.428459e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.084907e-06 │ │ │ │ Vprtstp: contraction number = 4.582824e-01 │ │ │ │ Vnewton: Using errtol_s: 21.856153 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.654867e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.486465e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.197548e+01 │ │ │ │ Vprtstp: contraction number = 1.197548e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.521262e-06 │ │ │ │ Vprtstp: contraction number = 4.931307e-01 │ │ │ │ Vnewton: Using errtol_s: 10.777941 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.675094e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.505632e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.181341e+00 │ │ │ │ Vprtstp: contraction number = 6.181341e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.852242e-07 │ │ │ │ Vprtstp: contraction number = 5.161662e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.502837e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.581624e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.397916e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.469532e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -6891,27 +6891,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.684722914233E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.513063949705E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.773049125938E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.244800e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.229990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.702071e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.530483e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:56:47 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:17:21 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -7264,250 +7264,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.447755 │ │ │ │ +Vacc_SASA: Time elapsed: 7.027318 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.292706e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.803407e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.719200e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.381530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.579630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.043780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.805768e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.148008e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073775e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004839e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.303157e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219075e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.494767e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.399212e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.683561e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.577154e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.867589e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740307e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.054101e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.914489e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.241851e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.095003e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.427579e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.275946e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.618209e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.457799e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.808055e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.636204e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.997677e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.815964e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.189832e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.993162e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.380278e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.172069e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.569168e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.350882e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.755850e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.525640e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.947133e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.707453e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.138017e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.889045e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.327349e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.073688e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.502459e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.255513e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.671161e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.750410e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.483702e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.551031e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -7516,17 +7516,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.966602122039E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.975619983960E+01 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.589187237063E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.967200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.250700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -7572,160 +7572,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00234933 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.407393 │ │ │ │ +Vacc_SASA: Time elapsed: 6.903313 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.620428e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.030944e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.727540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.649260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.978160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.607057e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.280511e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2418328.609890 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.701078e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.372776e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.297991e+05 │ │ │ │ Vprtstp: contraction number = 2.297991e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.085636 │ │ │ │ Vnewton: Attempting damping, relres = 0.540011 │ │ │ │ Vnewton: Damping accepted, relres = 0.085636 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.563556e-02 │ │ │ │ Vprtstp: contraction number = 8.563556e-02 │ │ │ │ Vnewton: Using errtol_s: 207094.936691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.939428e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.601740e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.943259e+04 │ │ │ │ Vprtstp: contraction number = 3.943259e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.467770e-02 │ │ │ │ Vprtstp: contraction number = 1.713972e-01 │ │ │ │ Vnewton: Using errtol_s: 35495.493076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.141339e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.796966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.192651e+03 │ │ │ │ Vprtstp: contraction number = 9.192651e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.421180e-03 │ │ │ │ Vprtstp: contraction number = 2.330870e-01 │ │ │ │ Vnewton: Using errtol_s: 8273.537556 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.342126e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.992008e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.625902e+03 │ │ │ │ Vprtstp: contraction number = 2.625902e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 9.772537e-04 │ │ │ │ Vprtstp: contraction number = 2.856481e-01 │ │ │ │ Vnewton: Using errtol_s: 2363.320499 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.543366e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.185535e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.336695e+02 │ │ │ │ Vprtstp: contraction number = 8.336695e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.102569e-04 │ │ │ │ Vprtstp: contraction number = 3.174784e-01 │ │ │ │ Vnewton: Using errtol_s: 750.303246 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.742901e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.380730e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.790113e+02 │ │ │ │ Vprtstp: contraction number = 2.790113e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.038363e-04 │ │ │ │ Vprtstp: contraction number = 3.346783e-01 │ │ │ │ Vnewton: Using errtol_s: 251.110249 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.944122e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.575749e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.595120e+01 │ │ │ │ Vprtstp: contraction number = 9.595120e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.570900e-05 │ │ │ │ Vprtstp: contraction number = 3.438971e-01 │ │ │ │ Vnewton: Using errtol_s: 86.356086 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.146965e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.766637e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.363636e+01 │ │ │ │ Vprtstp: contraction number = 3.363636e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.251804e-05 │ │ │ │ Vprtstp: contraction number = 3.505570e-01 │ │ │ │ Vnewton: Using errtol_s: 30.272729 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.344147e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.959432e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.212621e+01 │ │ │ │ Vprtstp: contraction number = 1.212621e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.512865e-06 │ │ │ │ Vprtstp: contraction number = 3.605089e-01 │ │ │ │ Vnewton: Using errtol_s: 10.913589 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.524851e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.153703e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.547757e+00 │ │ │ │ Vprtstp: contraction number = 4.547757e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.692484e-06 │ │ │ │ Vprtstp: contraction number = 3.750353e-01 │ │ │ │ Vnewton: Using errtol_s: 4.092981 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.726628e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.352127e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.787566e+00 │ │ │ │ Vprtstp: contraction number = 1.787566e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.652567e-07 │ │ │ │ Vprtstp: contraction number = 3.930654e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.279358e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.359224e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.228650e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.295110e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -7734,17 +7734,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.201138998655E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 4.154611536454E+02 kT │ │ │ │ Vpmg_energy: dielEnergy = 2.802895931375E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.375200e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.301820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -7765,272 +7765,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.498878 │ │ │ │ +Vacc_SASA: Time elapsed: 7.261761 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.401713e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.096989e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.683090e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.380780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.981770e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.116140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.826427e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.402955e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.919811e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.493829e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.126577e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.714720e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.318915e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.895667e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.512106e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.078921e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.701597e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.260903e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.892771e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.442420e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008517e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.623653e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027541e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.804445e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.046443e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.984162e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065262e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016670e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.084409e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035068e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103638e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053372e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.122608e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.071535e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140621e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089748e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.159648e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107989e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.178373e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126356e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.195986e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.144742e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.214816e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.162761e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233470e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180996e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.252523e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.199047e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271366e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.217276e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.032442e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.115429e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.913175e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.980976e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8039,17 +8039,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.651047489982E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.716292902858E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.798539842617E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.068200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.770500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -8095,160 +8095,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00429089 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.481427 │ │ │ │ +Vacc_SASA: Time elapsed: 7.183393 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.001766e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.605843e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.730880e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.398920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.183640e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.056890e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385718e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.325756e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3456404.072365 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.394908e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.334825e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.424168e+05 │ │ │ │ Vprtstp: contraction number = 3.424168e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.089811 │ │ │ │ Vnewton: Attempting damping, relres = 0.542258 │ │ │ │ Vnewton: Damping accepted, relres = 0.089811 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.981102e-02 │ │ │ │ Vprtstp: contraction number = 8.981102e-02 │ │ │ │ Vnewton: Using errtol_s: 310423.190924 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.419234e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.358235e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.148381e+04 │ │ │ │ Vprtstp: contraction number = 6.148381e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.602901e-02 │ │ │ │ Vprtstp: contraction number = 1.784748e-01 │ │ │ │ Vnewton: Using errtol_s: 55402.729239 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.437747e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.377795e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.483491e+04 │ │ │ │ Vprtstp: contraction number = 1.483491e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.863008e-03 │ │ │ │ Vprtstp: contraction number = 2.410011e-01 │ │ │ │ Vnewton: Using errtol_s: 13352.116026 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.458436e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.397088e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.268024e+03 │ │ │ │ Vprtstp: contraction number = 4.268024e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111340e-03 │ │ │ │ Vprtstp: contraction number = 2.876878e-01 │ │ │ │ Vnewton: Using errtol_s: 3841.240882 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.479654e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.416667e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.355750e+03 │ │ │ │ Vprtstp: contraction number = 1.355750e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.530190e-04 │ │ │ │ Vprtstp: contraction number = 3.176516e-01 │ │ │ │ Vnewton: Using errtol_s: 1220.176206 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.500437e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.435359e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.554936e+02 │ │ │ │ Vprtstp: contraction number = 4.554936e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.186043e-04 │ │ │ │ Vprtstp: contraction number = 3.359715e-01 │ │ │ │ Vnewton: Using errtol_s: 409.944430 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.520780e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.455022e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.577730e+02 │ │ │ │ Vprtstp: contraction number = 1.577730e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.108191e-05 │ │ │ │ Vprtstp: contraction number = 3.463779e-01 │ │ │ │ Vnewton: Using errtol_s: 141.995679 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.541400e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.474986e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.547816e+01 │ │ │ │ Vprtstp: contraction number = 5.547816e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.444575e-05 │ │ │ │ Vprtstp: contraction number = 3.516328e-01 │ │ │ │ Vnewton: Using errtol_s: 49.930345 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.561658e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.494525e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.964653e+01 │ │ │ │ Vprtstp: contraction number = 1.964653e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.115686e-06 │ │ │ │ Vprtstp: contraction number = 3.541309e-01 │ │ │ │ Vnewton: Using errtol_s: 17.681880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581861e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.513897e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.015901e+00 │ │ │ │ Vprtstp: contraction number = 7.015901e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.826844e-06 │ │ │ │ Vprtstp: contraction number = 3.571063e-01 │ │ │ │ Vnewton: Using errtol_s: 6.314311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.602193e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.532873e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.553268e+00 │ │ │ │ Vprtstp: contraction number = 2.553268e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.648357e-07 │ │ │ │ Vprtstp: contraction number = 3.639258e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.326894e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.411610e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.228950e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.296797e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8257,17 +8257,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.579314308709E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.986093532858E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.486705407480E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.364790e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.256060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -8288,261 +8288,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.661951 │ │ │ │ +Vacc_SASA: Time elapsed: 16.113604 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.817819e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.755163e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.771300e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.453650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.580210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.331160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.809826e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.732810e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.819227e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.742128e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.842747e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.765540e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.862320e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.785247e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.882079e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804924e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.901521e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824245e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.920991e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.843823e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.940304e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.863275e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.957897e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.882962e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.977802e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.901868e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.997604e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.921570e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.016908e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.941132e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.036530e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.960551e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.056087e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.980067e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.075544e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.999717e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.095180e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.019195e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.114765e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.038614e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.134157e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.058086e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.153531e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.077429e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.172512e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.096921e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.191296e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.115658e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.969594e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.048636e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.983127e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.053914e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8551,17 +8551,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.659936219773E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.771591154168E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.850889250612E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.708000e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.698700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -8607,160 +8607,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0122306 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.172346 │ │ │ │ +Vacc_SASA: Time elapsed: 16.359293 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.833790e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.846536e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.675490e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.457970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.571410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.284970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.399176e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.324122e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 5774426.010351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.408356e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.333286e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.536200e+05 │ │ │ │ Vprtstp: contraction number = 5.536200e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.086816 │ │ │ │ Vnewton: Attempting damping, relres = 0.540697 │ │ │ │ Vnewton: Damping accepted, relres = 0.086816 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.681646e-02 │ │ │ │ Vprtstp: contraction number = 8.681646e-02 │ │ │ │ Vnewton: Using errtol_s: 501315.229123 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.431767e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.356290e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.813919e+04 │ │ │ │ Vprtstp: contraction number = 9.813919e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.530865e-02 │ │ │ │ Vprtstp: contraction number = 1.763335e-01 │ │ │ │ Vnewton: Using errtol_s: 88398.668796 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.451206e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.375507e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.359807e+04 │ │ │ │ Vprtstp: contraction number = 2.359807e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.678183e-03 │ │ │ │ Vprtstp: contraction number = 2.402683e-01 │ │ │ │ Vnewton: Using errtol_s: 21239.395305 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.470940e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.394703e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.835940e+03 │ │ │ │ Vprtstp: contraction number = 6.835940e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.065460e-03 │ │ │ │ Vprtstp: contraction number = 2.896703e-01 │ │ │ │ Vnewton: Using errtol_s: 6152.421286 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.490974e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.413995e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.186690e+03 │ │ │ │ Vprtstp: contraction number = 2.186690e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.408183e-04 │ │ │ │ Vprtstp: contraction number = 3.198790e-01 │ │ │ │ Vnewton: Using errtol_s: 1968.030266 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.510166e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.433250e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.369221e+02 │ │ │ │ Vprtstp: contraction number = 7.369221e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.148566e-04 │ │ │ │ Vprtstp: contraction number = 3.370025e-01 │ │ │ │ Vnewton: Using errtol_s: 663.231119 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.529886e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.452467e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.557331e+02 │ │ │ │ Vprtstp: contraction number = 2.557331e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.985850e-05 │ │ │ │ Vprtstp: contraction number = 3.470283e-01 │ │ │ │ Vnewton: Using errtol_s: 230.159953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.549772e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.471757e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.020719e+01 │ │ │ │ Vprtstp: contraction number = 9.020719e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.405966e-05 │ │ │ │ Vprtstp: contraction number = 3.527394e-01 │ │ │ │ Vnewton: Using errtol_s: 81.186485 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.568177e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.490956e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.225420e+01 │ │ │ │ Vprtstp: contraction number = 3.225420e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.027128e-06 │ │ │ │ Vprtstp: contraction number = 3.575568e-01 │ │ │ │ Vnewton: Using errtol_s: 29.028780 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.588214e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.510139e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.171930e+01 │ │ │ │ Vprtstp: contraction number = 1.171930e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.826566e-06 │ │ │ │ Vprtstp: contraction number = 3.633419e-01 │ │ │ │ Vnewton: Using errtol_s: 10.547373 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.608050e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.529425e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.353564e+00 │ │ │ │ Vprtstp: contraction number = 4.353564e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.785449e-07 │ │ │ │ Vprtstp: contraction number = 3.714865e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.246188e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.323225e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.205829e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.276147e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8769,27 +8769,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.126180200466E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.029835397910E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.515709858498E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.273810e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.245580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.633877e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.554420e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:02:10 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:21:17 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -9142,250 +9142,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.472007 │ │ │ │ +Vacc_SASA: Time elapsed: 7.237636 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.329028e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.031475e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.764400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.451460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.558610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.029760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.831502e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.417756e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079328e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033060e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292236e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.254942e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.483193e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.439769e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.671182e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.625486e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.861451e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.805262e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.056033e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.986005e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.249701e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.167178e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.450169e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.342022e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.643669e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.523231e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.833759e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.704144e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.026603e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.885100e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.219061e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.065194e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.406521e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.245517e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.594554e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.427156e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.789285e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.607507e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.981809e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.786240e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.173808e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.967086e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.368025e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.147631e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.560565e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.327422e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.729330e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.809038e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.525019e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.593512e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -9394,17 +9394,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.475399192616E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.444578731292E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 7.168962891577E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.022500e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.664300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -9450,171 +9450,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.244357 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.394220 │ │ │ │ +Vacc_SASA: Time elapsed: 7.262033 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.393853e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.146294e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.695580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.434470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.627410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.382780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.743866e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.465582e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7151537.194828 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.837145e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.559262e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.220296e+05 │ │ │ │ Vprtstp: contraction number = 7.220296e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.092215 │ │ │ │ Vnewton: Attempting damping, relres = 0.543248 │ │ │ │ Vnewton: Damping accepted, relres = 0.092215 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.221458e-02 │ │ │ │ Vprtstp: contraction number = 9.221458e-02 │ │ │ │ Vnewton: Using errtol_s: 659475.973035 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.073330e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.801276e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.360213e+05 │ │ │ │ Vprtstp: contraction number = 1.360213e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.716437e-02 │ │ │ │ Vprtstp: contraction number = 1.861351e-01 │ │ │ │ Vnewton: Using errtol_s: 122751.620274 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.275708e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.001564e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.560242e+04 │ │ │ │ Vprtstp: contraction number = 3.560242e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.482910e-03 │ │ │ │ Vprtstp: contraction number = 2.611753e-01 │ │ │ │ Vnewton: Using errtol_s: 32059.695083 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.477090e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.206649e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.131656e+04 │ │ │ │ Vprtstp: contraction number = 1.131656e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.424570e-03 │ │ │ │ Vprtstp: contraction number = 3.177779e-01 │ │ │ │ Vnewton: Using errtol_s: 10187.862459 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.681562e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.408583e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.913208e+03 │ │ │ │ Vprtstp: contraction number = 3.913208e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.925362e-04 │ │ │ │ Vprtstp: contraction number = 3.457439e-01 │ │ │ │ Vnewton: Using errtol_s: 3522.390814 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.883347e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.611666e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.383064e+03 │ │ │ │ Vprtstp: contraction number = 1.383064e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.740621e-04 │ │ │ │ Vprtstp: contraction number = 3.533996e-01 │ │ │ │ Vnewton: Using errtol_s: 1244.811552 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.062504e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.812143e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.895564e+02 │ │ │ │ Vprtstp: contraction number = 4.895564e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.160970e-05 │ │ │ │ Vprtstp: contraction number = 3.539524e-01 │ │ │ │ Vnewton: Using errtol_s: 440.604077 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.263938e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.012435e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.817812e+02 │ │ │ │ Vprtstp: contraction number = 1.817812e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.287666e-05 │ │ │ │ Vprtstp: contraction number = 3.713159e-01 │ │ │ │ Vnewton: Using errtol_s: 163.603290 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.470791e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.212866e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.297744e+01 │ │ │ │ Vprtstp: contraction number = 7.297744e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 9.184003e-06 │ │ │ │ Vprtstp: contraction number = 4.014573e-01 │ │ │ │ Vnewton: Using errtol_s: 65.679739 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.674666e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.419443e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.147662e+01 │ │ │ │ Vprtstp: contraction number = 3.147662e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.961242e-06 │ │ │ │ Vprtstp: contraction number = 4.313197e-01 │ │ │ │ Vnewton: Using errtol_s: 28.328967 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.877666e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.623311e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.429069e+01 │ │ │ │ Vprtstp: contraction number = 1.429069e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.798442e-06 │ │ │ │ Vprtstp: contraction number = 4.540096e-01 │ │ │ │ Vnewton: Using errtol_s: 12.861624 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.082154e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.825523e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.773546e+00 │ │ │ │ Vprtstp: contraction number = 6.773546e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 8.524311e-07 │ │ │ │ Vprtstp: contraction number = 4.739831e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.507761e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.586411e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.522208e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.593437e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -9623,17 +9623,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.623170000406E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.125246141954E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.603584772163E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.267890e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.268750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -9654,272 +9654,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.619138 │ │ │ │ +Vacc_SASA: Time elapsed: 7.518320 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.538190e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.377579e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.741300e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.530630e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.241040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.508070e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.206683e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.915217e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.301274e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.009768e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.532271e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.248135e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.721209e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.444799e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.913602e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.640955e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010539e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.837450e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028817e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003411e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047777e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023031e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066150e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042491e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085348e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062225e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104583e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081657e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123639e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101371e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141911e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120888e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.160556e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140663e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.179580e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.160441e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198737e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180034e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.218008e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.199610e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.237258e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219490e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.256426e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.239260e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.275284e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.258956e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.294166e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.278698e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.312958e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.298419e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.064546e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.149929e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.217438e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.291021e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -9928,17 +9928,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.730884767842E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 2.814808503921E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.606300e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.925000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -9984,160 +9984,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.000691975 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.396120 │ │ │ │ +Vacc_SASA: Time elapsed: 7.470826 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.440059e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.480180e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.712090e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.541550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.633310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.442150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.420768e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.406777e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 951047.684475 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.430213e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.416170e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.162547e+05 │ │ │ │ Vprtstp: contraction number = 1.162547e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.112161 │ │ │ │ Vnewton: Attempting damping, relres = 0.552182 │ │ │ │ Vnewton: Damping accepted, relres = 0.112161 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.121606e-01 │ │ │ │ Vprtstp: contraction number = 1.121606e-01 │ │ │ │ Vnewton: Using errtol_s: 106670.078940 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452595e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.439424e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.126153e+04 │ │ │ │ Vprtstp: contraction number = 2.126153e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.016407e-02 │ │ │ │ Vprtstp: contraction number = 1.797785e-01 │ │ │ │ Vnewton: Using errtol_s: 19176.991465 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.471432e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.458497e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.910429e+03 │ │ │ │ Vprtstp: contraction number = 4.910429e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.647657e-03 │ │ │ │ Vprtstp: contraction number = 2.304920e-01 │ │ │ │ Vnewton: Using errtol_s: 4420.143642 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.490066e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478200e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.327403e+03 │ │ │ │ Vprtstp: contraction number = 1.327403e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.256188e-03 │ │ │ │ Vprtstp: contraction number = 2.702841e-01 │ │ │ │ Vnewton: Using errtol_s: 1194.694354 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.508616e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.497495e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.951603e+02 │ │ │ │ Vprtstp: contraction number = 3.951603e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.739525e-04 │ │ │ │ Vprtstp: contraction number = 2.976884e-01 │ │ │ │ Vnewton: Using errtol_s: 355.646671 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.527280e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.517613e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.251397e+02 │ │ │ │ Vprtstp: contraction number = 1.251397e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.184231e-04 │ │ │ │ Vprtstp: contraction number = 3.166794e-01 │ │ │ │ Vnewton: Using errtol_s: 112.625980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.545249e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.537740e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.114263e+01 │ │ │ │ Vprtstp: contraction number = 4.114263e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.893431e-05 │ │ │ │ Vprtstp: contraction number = 3.287731e-01 │ │ │ │ Vnewton: Using errtol_s: 37.028389 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.563214e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.557652e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.383573e+01 │ │ │ │ Vprtstp: contraction number = 1.383573e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.309310e-05 │ │ │ │ Vprtstp: contraction number = 3.362869e-01 │ │ │ │ Vnewton: Using errtol_s: 12.452161 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581220e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.577938e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725230e+00 │ │ │ │ Vprtstp: contraction number = 4.725230e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.471602e-06 │ │ │ │ Vprtstp: contraction number = 3.415236e-01 │ │ │ │ Vnewton: Using errtol_s: 4.252707 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.599420e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.597177e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.633794e+00 │ │ │ │ Vprtstp: contraction number = 1.633794e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.546100e-06 │ │ │ │ Vprtstp: contraction number = 3.457598e-01 │ │ │ │ Vnewton: Using errtol_s: 1.470415 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.618071e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.616486e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.703633e-01 │ │ │ │ Vprtstp: contraction number = 5.703633e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.397489e-07 │ │ │ │ Vprtstp: contraction number = 3.491035e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.117445e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.196963e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.246299e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.319780e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -10146,17 +10146,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.677193160789E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 2.890717240309E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.315340e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.324330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -10177,261 +10177,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.188332 │ │ │ │ +Vacc_SASA: Time elapsed: 16.544036 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.765909e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.799637e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.686960e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.468130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.481110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.484360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.818414e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.820269e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.827635e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.829660e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.850729e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.853191e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.869107e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.872797e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.887964e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.892410e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.906581e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.912004e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.925186e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.931694e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.943966e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.950607e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.962551e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.970346e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.981122e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.990058e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.000038e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.009568e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.019163e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.029102e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.038442e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048487e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.056979e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.067910e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.076053e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.087515e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.094729e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.107034e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.113452e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.126437e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131922e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.145751e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.150708e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.165095e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.169537e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.184464e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.188330e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.203801e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.848484e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.925306e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.986729e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.059277e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -10440,15 +10440,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.633470349209E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.444874244202E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 7.168739971796E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.504200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.657700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ @@ -10496,171 +10496,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.23862 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.590073 │ │ │ │ +Vacc_SASA: Time elapsed: 16.376898 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.905214e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.879500e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.761910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.441970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.505610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.371060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.402927e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.415384e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8022421.271471 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.412063e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.424542e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.182694e+05 │ │ │ │ Vprtstp: contraction number = 8.182694e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.093297 │ │ │ │ Vnewton: Attempting damping, relres = 0.543649 │ │ │ │ Vnewton: Damping accepted, relres = 0.093297 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.329693e-02 │ │ │ │ Vprtstp: contraction number = 9.329693e-02 │ │ │ │ Vnewton: Using errtol_s: 748467.258105 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.435594e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.448419e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.535104e+05 │ │ │ │ Vprtstp: contraction number = 1.535104e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.727080e-02 │ │ │ │ Vprtstp: contraction number = 1.851165e-01 │ │ │ │ Vnewton: Using errtol_s: 138553.663149 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.454977e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.468605e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.960039e+04 │ │ │ │ Vprtstp: contraction number = 3.960039e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.444863e-03 │ │ │ │ Vprtstp: contraction number = 2.573628e-01 │ │ │ │ Vnewton: Using errtol_s: 35658.564568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.474878e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.488841e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.238461e+04 │ │ │ │ Vprtstp: contraction number = 1.238461e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.389740e-03 │ │ │ │ Vprtstp: contraction number = 3.126620e-01 │ │ │ │ Vnewton: Using errtol_s: 11149.079578 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.494322e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.509154e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.220923e+03 │ │ │ │ Vprtstp: contraction number = 4.220923e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.735885e-04 │ │ │ │ Vprtstp: contraction number = 3.407749e-01 │ │ │ │ Vnewton: Using errtol_s: 3799.326730 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.513818e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.529489e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.473378e+03 │ │ │ │ Vprtstp: contraction number = 1.473378e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.652984e-04 │ │ │ │ Vprtstp: contraction number = 3.490339e-01 │ │ │ │ Vnewton: Using errtol_s: 1326.093695 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.532942e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.549804e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.152403e+02 │ │ │ │ Vprtstp: contraction number = 5.152403e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.780294e-05 │ │ │ │ Vprtstp: contraction number = 3.496884e-01 │ │ │ │ Vnewton: Using errtol_s: 463.719535 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.552278e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.569844e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.890344e+02 │ │ │ │ Vprtstp: contraction number = 1.890344e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.120696e-05 │ │ │ │ Vprtstp: contraction number = 3.668838e-01 │ │ │ │ Vnewton: Using errtol_s: 170.131203 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.570926e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.590277e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.514797e+01 │ │ │ │ Vprtstp: contraction number = 7.514797e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.430525e-06 │ │ │ │ Vprtstp: contraction number = 3.975357e-01 │ │ │ │ Vnewton: Using errtol_s: 67.633227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.590587e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.610760e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.220080e+01 │ │ │ │ Vprtstp: contraction number = 3.220080e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.612467e-06 │ │ │ │ Vprtstp: contraction number = 4.284985e-01 │ │ │ │ Vnewton: Using errtol_s: 28.980733 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609160e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.631049e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.453992e+01 │ │ │ │ Vprtstp: contraction number = 1.453992e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.631169e-06 │ │ │ │ Vprtstp: contraction number = 4.515389e-01 │ │ │ │ Vnewton: Using errtol_s: 13.085928 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.627869e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.651223e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.875948e+00 │ │ │ │ Vprtstp: contraction number = 6.875948e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.713824e-07 │ │ │ │ Vprtstp: contraction number = 4.729015e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.395016e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.473608e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.518918e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.590765e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -10669,27 +10669,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.853787896122E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.125276033199E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.603543842121E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.188670e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.218680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.652737e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.677504e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:06:16 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:25:13 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -11042,250 +11042,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.462553 │ │ │ │ +Vacc_SASA: Time elapsed: 7.385619 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.307704e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.187452e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.642600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.500460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.482340e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.322900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.812832e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.609059e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074069e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.054843e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.296150e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.288664e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.485541e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.484425e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.671034e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.675476e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.857864e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.866693e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048132e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.059131e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.236442e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.252429e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.430020e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.446484e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.618755e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.641418e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.807983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.854001e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.993014e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.048042e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.184111e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.244647e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.374268e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.439153e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.564207e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.635348e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.805665e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.830914e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.041043e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.024132e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.265256e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.217295e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.451254e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.410558e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.642082e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.601351e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.812701e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.889920e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.791684e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.863162e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11294,17 +11294,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.108926489514E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.835800313442E+02 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.215330905259E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.252800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.340600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -11350,160 +11350,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.001948 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.366071 │ │ │ │ +Vacc_SASA: Time elapsed: 7.335583 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.511017e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.419639e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.800940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.453880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.479770e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.421450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.736726e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.679485e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1613641.621006 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.831447e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.771966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.672701e+05 │ │ │ │ Vprtstp: contraction number = 1.672701e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.093643 │ │ │ │ Vnewton: Attempting damping, relres = 0.544180 │ │ │ │ Vnewton: Damping accepted, relres = 0.093643 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.364296e-02 │ │ │ │ Vprtstp: contraction number = 9.364296e-02 │ │ │ │ Vnewton: Using errtol_s: 151106.180064 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.068348e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.017341e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.923422e+04 │ │ │ │ Vprtstp: contraction number = 2.923422e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.630658e-02 │ │ │ │ Vprtstp: contraction number = 1.741357e-01 │ │ │ │ Vnewton: Using errtol_s: 26312.974291 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.266142e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.223939e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.609437e+03 │ │ │ │ Vprtstp: contraction number = 6.609437e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.686501e-03 │ │ │ │ Vprtstp: contraction number = 2.260744e-01 │ │ │ │ Vnewton: Using errtol_s: 5948.690797 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.471101e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.427413e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.798444e+03 │ │ │ │ Vprtstp: contraction number = 1.798444e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.003087e-03 │ │ │ │ Vprtstp: contraction number = 2.720974e-01 │ │ │ │ Vnewton: Using errtol_s: 1618.623129 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.665468e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.628708e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.516770e+02 │ │ │ │ Vprtstp: contraction number = 5.516770e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.076965e-04 │ │ │ │ Vprtstp: contraction number = 3.067495e-01 │ │ │ │ Vnewton: Using errtol_s: 496.511822 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.860969e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.832682e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.808462e+02 │ │ │ │ Vprtstp: contraction number = 1.808462e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.008662e-04 │ │ │ │ Vprtstp: contraction number = 3.278106e-01 │ │ │ │ Vnewton: Using errtol_s: 162.761828 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.058351e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.035275e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.118139e+01 │ │ │ │ Vprtstp: contraction number = 6.118139e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.412361e-05 │ │ │ │ Vprtstp: contraction number = 3.383059e-01 │ │ │ │ Vnewton: Using errtol_s: 55.063279 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.256963e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.240403e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.100954e+01 │ │ │ │ Vprtstp: contraction number = 2.100954e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.171796e-05 │ │ │ │ Vprtstp: contraction number = 3.433974e-01 │ │ │ │ Vnewton: Using errtol_s: 18.908586 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.449134e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.445142e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.287024e+00 │ │ │ │ Vprtstp: contraction number = 7.287024e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.064299e-06 │ │ │ │ Vprtstp: contraction number = 3.468436e-01 │ │ │ │ Vnewton: Using errtol_s: 6.558322 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.643218e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.648835e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.550680e+00 │ │ │ │ Vprtstp: contraction number = 2.550680e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.422628e-06 │ │ │ │ Vprtstp: contraction number = 3.500304e-01 │ │ │ │ Vnewton: Using errtol_s: 2.295612 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.838356e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.854170e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.008406e-01 │ │ │ │ Vprtstp: contraction number = 9.008406e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.024390e-07 │ │ │ │ Vprtstp: contraction number = 3.531767e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.253494e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.332219e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.337652e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.409416e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11512,17 +11512,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.604850020008E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.451766100693E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.154345982163E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.321730e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.320830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -11543,272 +11543,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.559082 │ │ │ │ +Vacc_SASA: Time elapsed: 7.434528 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.449368e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.278507e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.772690e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.455300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.600180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.312330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.931342e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.932280e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.025047e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.025071e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.248588e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.254327e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.433419e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.448403e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.622016e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.640435e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.809744e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.833353e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.999407e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002440e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018271e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021674e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.037194e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040891e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.055496e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060105e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074099e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079281e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.092481e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098540e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111206e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.117546e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.129767e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.136409e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.148477e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155633e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.167294e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174768e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.185889e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193775e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.204115e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212801e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222371e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232002e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.240958e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.250972e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.259526e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.269835e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.278082e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289172e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.994953e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.074505e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.111946e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.182641e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11817,17 +11817,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.931678298316E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.306896751937E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.531231404824E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.407400e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.039300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 1.300000e-05 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -11873,193 +11873,193 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.211097 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.416127 │ │ │ │ +Vacc_SASA: Time elapsed: 7.412562 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.314354e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.282284e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.664270e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.452280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.415120e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.318150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.394658e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.405705e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6738070.309592 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.403682e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.414897e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.878637e+05 │ │ │ │ Vprtstp: contraction number = 6.878637e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.093216 │ │ │ │ Vnewton: Attempting damping, relres = 0.543864 │ │ │ │ Vnewton: Damping accepted, relres = 0.093216 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.321581e-02 │ │ │ │ Vprtstp: contraction number = 9.321581e-02 │ │ │ │ Vnewton: Using errtol_s: 628094.651911 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.426409e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.438631e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.296036e+05 │ │ │ │ Vprtstp: contraction number = 1.296036e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.735879e-02 │ │ │ │ Vprtstp: contraction number = 1.862215e-01 │ │ │ │ Vnewton: Using errtol_s: 116964.740632 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.445366e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.458612e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.402622e+04 │ │ │ │ Vprtstp: contraction number = 3.402622e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.547490e-03 │ │ │ │ Vprtstp: contraction number = 2.619705e-01 │ │ │ │ Vnewton: Using errtol_s: 30641.306038 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.465969e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478249e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.090470e+04 │ │ │ │ Vprtstp: contraction number = 1.090470e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.456938e-03 │ │ │ │ Vprtstp: contraction number = 3.203829e-01 │ │ │ │ Vnewton: Using errtol_s: 9816.950613 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.485542e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.498410e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.894978e+03 │ │ │ │ Vprtstp: contraction number = 3.894978e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.203198e-04 │ │ │ │ Vprtstp: contraction number = 3.571324e-01 │ │ │ │ Vnewton: Using errtol_s: 3505.951173 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.504883e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.518396e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.485775e+03 │ │ │ │ Vprtstp: contraction number = 1.485775e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.984627e-04 │ │ │ │ Vprtstp: contraction number = 3.814246e-01 │ │ │ │ Vnewton: Using errtol_s: 1337.255961 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.523643e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.538525e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.014858e+02 │ │ │ │ Vprtstp: contraction number = 6.014858e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.034105e-05 │ │ │ │ Vprtstp: contraction number = 4.048168e-01 │ │ │ │ Vnewton: Using errtol_s: 541.343626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.542739e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.559184e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.638957e+02 │ │ │ │ Vprtstp: contraction number = 2.638957e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.524853e-05 │ │ │ │ Vprtstp: contraction number = 4.387363e-01 │ │ │ │ Vnewton: Using errtol_s: 237.507104 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.562178e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.579970e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.262556e+02 │ │ │ │ Vprtstp: contraction number = 1.262556e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.686391e-05 │ │ │ │ Vprtstp: contraction number = 4.784287e-01 │ │ │ │ Vnewton: Using errtol_s: 113.630225 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581426e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.600369e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.580661e+01 │ │ │ │ Vprtstp: contraction number = 6.580661e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.789758e-06 │ │ │ │ Vprtstp: contraction number = 5.212170e-01 │ │ │ │ Vnewton: Using errtol_s: 59.226009 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.600980e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.620662e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.615710e+01 │ │ │ │ Vprtstp: contraction number = 3.615710e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.829486e-06 │ │ │ │ Vprtstp: contraction number = 5.494446e-01 │ │ │ │ Vnewton: Using errtol_s: 32.541413 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.621362e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.640952e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.063008e+01 │ │ │ │ Vprtstp: contraction number = 2.063008e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 2.755549e-06 │ │ │ │ Vprtstp: contraction number = 5.705677e-01 │ │ │ │ Vnewton: Using errtol_s: 18.567080 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.640857e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.661093e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.211023e+01 │ │ │ │ Vprtstp: contraction number = 1.211023e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.617557e-06 │ │ │ │ Vprtstp: contraction number = 5.870182e-01 │ │ │ │ Vnewton: Using errtol_s: 10.899214 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.659652e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.681413e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.261707e+00 │ │ │ │ Vprtstp: contraction number = 7.261707e+00 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 9.699420e-07 │ │ │ │ Vprtstp: contraction number = 5.996338e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.804406e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.880243e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.917863e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.988655e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12068,17 +12068,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.021244083579E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.026826573171E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.129339951363E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.180140e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.187090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -12099,261 +12099,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.333417 │ │ │ │ +Vacc_SASA: Time elapsed: 16.695280 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.783833e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.811478e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.679820e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.370830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.327200e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.770420e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.862530e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.886568e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.871949e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.895361e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.895594e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.917281e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.915356e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.934893e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.935200e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.952566e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.954939e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.970155e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.974235e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.987727e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.994152e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.005383e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.012621e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.023184e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.032330e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.040982e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.052050e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.058722e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.071929e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.076324e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.091344e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.090805e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.110403e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105397e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.129627e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.120010e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149044e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.134469e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.168633e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.149046e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.188090e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.163975e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.207348e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.181750e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.226951e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.199497e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.246426e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.216873e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.996016e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.071431e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.413741e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.477837e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12362,17 +12362,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.165566732606E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.340422491969E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.679021613149E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.348200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.911100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 8.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -12418,193 +12418,193 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.211587 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.937464 │ │ │ │ +Vacc_SASA: Time elapsed: 15.828428 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.947332e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.824977e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.626560e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.383700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.266370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.632060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.465602e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.417955e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8285587.408912 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.474707e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.427141e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.439767e+05 │ │ │ │ Vprtstp: contraction number = 8.439767e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.093056 │ │ │ │ Vnewton: Attempting damping, relres = 0.543707 │ │ │ │ Vnewton: Damping accepted, relres = 0.093056 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.305605e-02 │ │ │ │ Vprtstp: contraction number = 9.305605e-02 │ │ │ │ Vnewton: Using errtol_s: 771024.060477 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.498313e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.451196e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.575262e+05 │ │ │ │ Vprtstp: contraction number = 1.575262e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.715846e-02 │ │ │ │ Vprtstp: contraction number = 1.843885e-01 │ │ │ │ Vnewton: Using errtol_s: 142167.953902 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.518294e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.471915e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.047316e+04 │ │ │ │ Vprtstp: contraction number = 4.047316e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.398299e-03 │ │ │ │ Vprtstp: contraction number = 2.563341e-01 │ │ │ │ Vnewton: Using errtol_s: 36442.493025 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.538355e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.492628e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.265955e+04 │ │ │ │ Vprtstp: contraction number = 1.265955e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.375423e-03 │ │ │ │ Vprtstp: contraction number = 3.127169e-01 │ │ │ │ Vnewton: Using errtol_s: 11396.183497 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.558411e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.513528e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.418878e+03 │ │ │ │ Vprtstp: contraction number = 4.418878e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.800426e-04 │ │ │ │ Vprtstp: contraction number = 3.490147e-01 │ │ │ │ Vnewton: Using errtol_s: 3977.435333 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.578463e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.533584e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.644482e+03 │ │ │ │ Vprtstp: contraction number = 1.644482e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.786343e-04 │ │ │ │ Vprtstp: contraction number = 3.721217e-01 │ │ │ │ Vnewton: Using errtol_s: 1480.089823 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.598542e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.554072e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.478261e+02 │ │ │ │ Vprtstp: contraction number = 6.478261e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.036914e-05 │ │ │ │ Vprtstp: contraction number = 3.939286e-01 │ │ │ │ Vnewton: Using errtol_s: 583.049663 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.618527e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.574481e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.772344e+02 │ │ │ │ Vprtstp: contraction number = 2.772344e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.011396e-05 │ │ │ │ Vprtstp: contraction number = 4.279428e-01 │ │ │ │ Vnewton: Using errtol_s: 249.511882 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.638749e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.595120e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.301479e+02 │ │ │ │ Vprtstp: contraction number = 1.301479e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.413700e-05 │ │ │ │ Vprtstp: contraction number = 4.694500e-01 │ │ │ │ Vnewton: Using errtol_s: 117.133345 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.658928e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.615425e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.695205e+01 │ │ │ │ Vprtstp: contraction number = 6.695205e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.272497e-06 │ │ │ │ Vprtstp: contraction number = 5.144300e-01 │ │ │ │ Vnewton: Using errtol_s: 60.256908 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.678931e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.636136e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.650946e+01 │ │ │ │ Vprtstp: contraction number = 3.650946e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.965746e-06 │ │ │ │ Vprtstp: contraction number = 5.453073e-01 │ │ │ │ Vnewton: Using errtol_s: 32.858531 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.698892e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.656575e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.073747e+01 │ │ │ │ Vprtstp: contraction number = 2.073747e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 2.252553e-06 │ │ │ │ Vprtstp: contraction number = 5.680025e-01 │ │ │ │ Vnewton: Using errtol_s: 18.663727 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.718834e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.677236e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.213300e+01 │ │ │ │ Vprtstp: contraction number = 1.213300e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.317915e-06 │ │ │ │ Vprtstp: contraction number = 5.850760e-01 │ │ │ │ Vnewton: Using errtol_s: 10.919699 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.738978e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.697715e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.261261e+00 │ │ │ │ Vprtstp: contraction number = 7.261261e+00 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.887354e-07 │ │ │ │ Vprtstp: contraction number = 5.984722e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.899123e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.973144e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.960291e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.022933e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12613,27 +12613,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.328637769519E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.051514241768E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.245601958271E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.177820e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.238990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.765162e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.724320e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:09:31 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:28:59 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -12986,250 +12986,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.357141 │ │ │ │ +Vacc_SASA: Time elapsed: 7.478261 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.200432e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.287046e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.625780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.542290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.512800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.367740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.672973e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.715953e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060563e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.063412e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.287545e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.293247e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472474e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.482482e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.632986e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.672770e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.795353e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.863966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.959763e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.054025e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.119110e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.246028e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.280468e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.436127e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442196e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.627116e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.607564e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.817103e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.778196e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.008090e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.942593e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.195991e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.108152e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.390018e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.270431e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.583442e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.431166e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.775709e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.595047e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.969505e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.761444e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.159613e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.926430e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.352593e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.092578e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.543862e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.251496e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.328872e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.721135e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.793170e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -13238,17 +13238,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.135373636445E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.691003222948E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 8.436188542984E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.625600e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.542000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -13294,160 +13294,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00329728 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.243678 │ │ │ │ +Vacc_SASA: Time elapsed: 7.333777 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.704388e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.711054e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.609730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.538470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.245210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.537270e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.176132e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.651104e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2672785.067134 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.263769e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.743945e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.848718e+05 │ │ │ │ Vprtstp: contraction number = 2.848718e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.096187 │ │ │ │ Vnewton: Attempting damping, relres = 0.545650 │ │ │ │ Vnewton: Damping accepted, relres = 0.096187 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.618699e-02 │ │ │ │ Vprtstp: contraction number = 9.618699e-02 │ │ │ │ Vnewton: Using errtol_s: 257087.160547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.461799e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.986501e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.201088e+04 │ │ │ │ Vprtstp: contraction number = 5.201088e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.751490e-02 │ │ │ │ Vprtstp: contraction number = 1.820922e-01 │ │ │ │ Vnewton: Using errtol_s: 46813.558642 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.622274e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.182567e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.230808e+04 │ │ │ │ Vprtstp: contraction number = 1.230808e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.144590e-03 │ │ │ │ Vprtstp: contraction number = 2.366322e-01 │ │ │ │ Vnewton: Using errtol_s: 11077.597147 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.782777e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.387823e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.460119e+03 │ │ │ │ Vprtstp: contraction number = 3.460119e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.165151e-03 │ │ │ │ Vprtstp: contraction number = 2.811258e-01 │ │ │ │ Vnewton: Using errtol_s: 3114.198540 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.942208e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.590434e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.085640e+03 │ │ │ │ Vprtstp: contraction number = 1.085640e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.655733e-04 │ │ │ │ Vprtstp: contraction number = 3.137561e-01 │ │ │ │ Vnewton: Using errtol_s: 977.098856 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.103323e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.796598e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.609545e+02 │ │ │ │ Vprtstp: contraction number = 3.609545e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.215452e-04 │ │ │ │ Vprtstp: contraction number = 3.324784e-01 │ │ │ │ Vnewton: Using errtol_s: 324.864231 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.265241e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.001024e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.235133e+02 │ │ │ │ Vprtstp: contraction number = 1.235133e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.159074e-05 │ │ │ │ Vprtstp: contraction number = 3.421833e-01 │ │ │ │ Vnewton: Using errtol_s: 111.163117 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.427208e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.203526e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.301270e+01 │ │ │ │ Vprtstp: contraction number = 4.301270e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.448364e-05 │ │ │ │ Vprtstp: contraction number = 3.482419e-01 │ │ │ │ Vnewton: Using errtol_s: 38.711660 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.590156e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.403905e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.517421e+01 │ │ │ │ Vprtstp: contraction number = 1.517421e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.109589e-06 │ │ │ │ Vprtstp: contraction number = 3.527835e-01 │ │ │ │ Vnewton: Using errtol_s: 13.656834 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.754202e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.611207e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.423218e+00 │ │ │ │ Vprtstp: contraction number = 5.423218e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.826149e-06 │ │ │ │ Vprtstp: contraction number = 3.573964e-01 │ │ │ │ Vnewton: Using errtol_s: 4.880904 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.919930e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.818022e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.968727e+00 │ │ │ │ Vprtstp: contraction number = 1.968727e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.629250e-07 │ │ │ │ Vprtstp: contraction number = 3.630180e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.868205e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.941857e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.332467e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.406365e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -13456,17 +13456,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.950394306049E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.339241623976E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.685521460249E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.256130e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.306290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -13487,272 +13487,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.339579 │ │ │ │ +Vacc_SASA: Time elapsed: 7.524920 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.264983e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.366810e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.641700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.487300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.220320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.565120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.960675e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.910347e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.048677e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.004712e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.244836e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.240126e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.409275e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.433741e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.571365e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.628526e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.731975e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.822226e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.891850e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001541e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.049768e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020755e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.215522e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040415e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.379608e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060848e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.540124e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081651e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.699980e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102026e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.863031e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121299e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002686e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140493e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019046e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.159823e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035286e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.178875e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051458e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198040e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067685e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.217197e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.083964e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.236410e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100178e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255639e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.116085e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.274965e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.132042e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.294120e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.481119e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.555148e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.182313e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.256015e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -13761,17 +13761,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.295996694910E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.633599871123E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.058700e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.583600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -13817,149 +13817,149 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00296493 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 6.903720 │ │ │ │ +Vacc_SASA: Time elapsed: 7.446773 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.909471e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.466748e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.619570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.482300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.119210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.457560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.231801e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.402549e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1184087.054280 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.240764e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.411964e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.354114e+05 │ │ │ │ Vprtstp: contraction number = 1.354114e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.103158 │ │ │ │ Vnewton: Attempting damping, relres = 0.548288 │ │ │ │ Vnewton: Damping accepted, relres = 0.103158 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.031582e-01 │ │ │ │ Vprtstp: contraction number = 1.031582e-01 │ │ │ │ Vnewton: Using errtol_s: 122148.348169 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.260643e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.434918e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.326538e+04 │ │ │ │ Vprtstp: contraction number = 2.326538e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.769124e-02 │ │ │ │ Vprtstp: contraction number = 1.714961e-01 │ │ │ │ Vnewton: Using errtol_s: 20947.970777 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.276715e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.453981e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.939304e+03 │ │ │ │ Vprtstp: contraction number = 4.939304e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.754561e-03 │ │ │ │ Vprtstp: contraction number = 2.122271e-01 │ │ │ │ Vnewton: Using errtol_s: 4445.727289 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292733e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.473301e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.225369e+03 │ │ │ │ Vprtstp: contraction number = 1.225369e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 9.313919e-04 │ │ │ │ Vprtstp: contraction number = 2.480695e-01 │ │ │ │ Vnewton: Using errtol_s: 1102.849143 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.309065e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.492338e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.425596e+02 │ │ │ │ Vprtstp: contraction number = 3.425596e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 2.603732e-04 │ │ │ │ Vprtstp: contraction number = 2.795528e-01 │ │ │ │ Vnewton: Using errtol_s: 308.304585 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.324996e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.511450e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.033702e+02 │ │ │ │ Vprtstp: contraction number = 1.033702e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 7.856958e-05 │ │ │ │ Vprtstp: contraction number = 3.017575e-01 │ │ │ │ Vnewton: Using errtol_s: 93.033224 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.341080e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.530699e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.261191e+01 │ │ │ │ Vprtstp: contraction number = 3.261191e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.478764e-05 │ │ │ │ Vprtstp: contraction number = 3.154865e-01 │ │ │ │ Vnewton: Using errtol_s: 29.350728 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.357097e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.549520e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.060426e+01 │ │ │ │ Vprtstp: contraction number = 1.060426e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.060077e-06 │ │ │ │ Vprtstp: contraction number = 3.251651e-01 │ │ │ │ Vnewton: Using errtol_s: 9.543833 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.373192e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.568586e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.527652e+00 │ │ │ │ Vprtstp: contraction number = 3.527652e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.681295e-06 │ │ │ │ Vprtstp: contraction number = 3.326637e-01 │ │ │ │ Vnewton: Using errtol_s: 3.174887 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.389063e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.588112e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.192253e+00 │ │ │ │ Vprtstp: contraction number = 1.192253e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.062069e-07 │ │ │ │ Vprtstp: contraction number = 3.379736e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.693407e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.766048e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.005310e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.078003e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -13968,17 +13968,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.599961867885E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.358968211460E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.264650e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.334540e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -13999,261 +13999,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 15.387174 │ │ │ │ +Vacc_SASA: Time elapsed: 16.800268 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.682619e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.825202e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.621730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.535410e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.225630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.427930e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.578354e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.794621e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.587859e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804284e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.607649e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.828620e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.623706e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.849078e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.639598e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.869208e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.655696e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.888999e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.673363e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.908861e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.689403e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.929067e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.705248e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.949305e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.721146e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.969429e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.736959e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.988161e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.752925e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.007538e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.769021e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.027287e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.785065e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.047702e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.801084e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.067741e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.817167e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.088044e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.833176e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.107667e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.849083e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.126621e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.865100e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.146297e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.881222e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.166038e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.897354e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.185967e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.312776e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.386400e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.067607e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.140912e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -14262,17 +14262,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.987808702613E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.699917781088E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 8.464002723965E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.518700e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.888900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -14318,160 +14318,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0125918 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 15.402039 │ │ │ │ +Vacc_SASA: Time elapsed: 16.758005 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.738600e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.872075e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.633370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.465760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.342320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.663550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.092304e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.397410e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3745818.555400 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.101282e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.406834e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.036148e+05 │ │ │ │ Vprtstp: contraction number = 4.036148e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.097470 │ │ │ │ Vnewton: Attempting damping, relres = 0.545903 │ │ │ │ Vnewton: Damping accepted, relres = 0.097470 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.746961e-02 │ │ │ │ Vprtstp: contraction number = 9.746961e-02 │ │ │ │ Vnewton: Using errtol_s: 365103.476411 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.121198e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.430962e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.291408e+04 │ │ │ │ Vprtstp: contraction number = 7.291408e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.752435e-02 │ │ │ │ Vprtstp: contraction number = 1.797929e-01 │ │ │ │ Vnewton: Using errtol_s: 65643.018240 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.137579e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.451327e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.675888e+04 │ │ │ │ Vprtstp: contraction number = 1.675888e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.026892e-03 │ │ │ │ Vprtstp: contraction number = 2.297884e-01 │ │ │ │ Vnewton: Using errtol_s: 15084.007144 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.153943e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.471670e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.533188e+03 │ │ │ │ Vprtstp: contraction number = 4.533188e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.089215e-03 │ │ │ │ Vprtstp: contraction number = 2.704853e-01 │ │ │ │ Vnewton: Using errtol_s: 4080.002297 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.170273e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.491894e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.369611e+03 │ │ │ │ Vprtstp: contraction number = 1.369611e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.290808e-04 │ │ │ │ Vprtstp: contraction number = 3.021265e-01 │ │ │ │ Vnewton: Using errtol_s: 1232.676861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.186771e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.512606e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.398009e+02 │ │ │ │ Vprtstp: contraction number = 4.398009e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.056716e-04 │ │ │ │ Vprtstp: contraction number = 3.211115e-01 │ │ │ │ Vnewton: Using errtol_s: 395.826722 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.203052e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.533158e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.460593e+02 │ │ │ │ Vprtstp: contraction number = 1.460593e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.509370e-05 │ │ │ │ Vprtstp: contraction number = 3.321014e-01 │ │ │ │ Vnewton: Using errtol_s: 131.454614 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219277e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.554028e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.960244e+01 │ │ │ │ Vprtstp: contraction number = 4.960244e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.191794e-05 │ │ │ │ Vprtstp: contraction number = 3.396035e-01 │ │ │ │ Vnewton: Using errtol_s: 44.642449 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.235454e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.575170e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.713194e+01 │ │ │ │ Vprtstp: contraction number = 1.713194e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.116267e-06 │ │ │ │ Vprtstp: contraction number = 3.453841e-01 │ │ │ │ Vnewton: Using errtol_s: 15.418791 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.251660e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.595430e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.017264e+00 │ │ │ │ Vprtstp: contraction number = 6.017264e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.445758e-06 │ │ │ │ Vprtstp: contraction number = 3.512303e-01 │ │ │ │ Vnewton: Using errtol_s: 5.415546 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.267837e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.616062e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.154066e+00 │ │ │ │ Vprtstp: contraction number = 2.154066e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.175534e-07 │ │ │ │ Vprtstp: contraction number = 3.579807e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.880437e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.955378e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.351773e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.426184e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -14480,27 +14480,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.620792182088E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.339466431031E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.686807644409E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.242300e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.264380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.289910e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.641579e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:11:43 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:32:53 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -14853,250 +14853,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.297186 │ │ │ │ +Vacc_SASA: Time elapsed: 7.221080 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.186252e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.027772e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.585350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.545680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.143490e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.475500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.611117e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.417209e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048763e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034767e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.246794e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.268958e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.409512e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.460774e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.570672e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.653297e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.733795e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.846772e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.897599e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.037738e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.060767e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.228651e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.222967e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.419165e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.385577e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.609301e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.546498e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.800959e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.710215e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.995127e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.872215e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.186131e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.037666e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.375323e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.199539e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.567242e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.363529e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.760226e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.526423e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.950941e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.690736e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.143275e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.854178e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.332903e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.017402e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.525617e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.181297e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.253839e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.725852e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.799474e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15105,17 +15105,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.410514495807E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.129100557647E+00 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.350100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.597700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -15161,160 +15161,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.000190853 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.235623 │ │ │ │ +Vacc_SASA: Time elapsed: 7.419290 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.300099e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.423633e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.610680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.441980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.146320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.391710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.058129e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.595223e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1032634.725607 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.146901e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.689617e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.090058e+05 │ │ │ │ Vprtstp: contraction number = 1.090058e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.095383 │ │ │ │ Vnewton: Attempting damping, relres = 0.544753 │ │ │ │ Vnewton: Damping accepted, relres = 0.095383 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.538325e-02 │ │ │ │ Vprtstp: contraction number = 9.538325e-02 │ │ │ │ Vnewton: Using errtol_s: 98496.056858 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.346443e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.926648e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.829312e+04 │ │ │ │ Vprtstp: contraction number = 1.829312e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.595089e-02 │ │ │ │ Vprtstp: contraction number = 1.672295e-01 │ │ │ │ Vnewton: Using errtol_s: 16471.442714 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.509364e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.124694e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.867524e+03 │ │ │ │ Vprtstp: contraction number = 3.867524e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.370960e-03 │ │ │ │ Vprtstp: contraction number = 2.113337e-01 │ │ │ │ Vnewton: Using errtol_s: 3480.970171 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.671243e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.326341e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.812010e+02 │ │ │ │ Vprtstp: contraction number = 9.812010e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 8.551815e-04 │ │ │ │ Vprtstp: contraction number = 2.536908e-01 │ │ │ │ Vnewton: Using errtol_s: 883.090100 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.834167e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.527092e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.836594e+02 │ │ │ │ Vprtstp: contraction number = 2.836594e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 2.472259e-04 │ │ │ │ Vprtstp: contraction number = 2.890917e-01 │ │ │ │ Vnewton: Using errtol_s: 255.294034 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.996157e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.725094e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.927772e+01 │ │ │ │ Vprtstp: contraction number = 8.927772e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 7.781068e-05 │ │ │ │ Vprtstp: contraction number = 3.147352e-01 │ │ │ │ Vnewton: Using errtol_s: 80.350015 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.159527e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.924489e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.937189e+01 │ │ │ │ Vprtstp: contraction number = 2.937189e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.559929e-05 │ │ │ │ Vprtstp: contraction number = 3.289945e-01 │ │ │ │ Vnewton: Using errtol_s: 26.434712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.321744e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.116532e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.890447e+00 │ │ │ │ Vprtstp: contraction number = 9.890447e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.620089e-06 │ │ │ │ Vprtstp: contraction number = 3.367316e-01 │ │ │ │ Vnewton: Using errtol_s: 8.901403 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.485300e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.306564e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.377400e+00 │ │ │ │ Vprtstp: contraction number = 3.377400e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.943597e-06 │ │ │ │ Vprtstp: contraction number = 3.414810e-01 │ │ │ │ Vnewton: Using errtol_s: 3.039660 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648881e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.496895e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.164729e+00 │ │ │ │ Vprtstp: contraction number = 1.164729e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.015127e-06 │ │ │ │ Vprtstp: contraction number = 3.448595e-01 │ │ │ │ Vnewton: Using errtol_s: 1.048256 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.811981e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.683137e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.047354e-01 │ │ │ │ Vprtstp: contraction number = 4.047354e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.527500e-07 │ │ │ │ Vprtstp: contraction number = 3.474933e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.881002e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.953729e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.244299e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.315692e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15323,17 +15323,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.262250874476E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 7.842003689004E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.259810e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.311230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -15354,272 +15354,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.287389 │ │ │ │ +Vacc_SASA: Time elapsed: 7.282022 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.144098e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.133142e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.641000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.551530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.153740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.518220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.842717e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.743280e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.931693e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.837284e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.130712e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.063102e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.292395e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.248568e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.455287e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.436291e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.617910e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.625772e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.781983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.814724e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.945396e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.991107e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.108021e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016918e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.269848e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034812e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.431452e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053055e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.594100e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.071813e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.754971e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090894e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.915631e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109996e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007882e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.129102e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024026e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.148192e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040212e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.167496e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056375e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.186929e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.072562e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206639e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088631e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.225742e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104772e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.244640e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121103e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.262758e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.493561e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.566684e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.029643e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.103579e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15628,17 +15628,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.028844380467E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.611210700866E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.863079386675E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.338300e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.275800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -15684,171 +15684,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0377574 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.300933 │ │ │ │ +Vacc_SASA: Time elapsed: 7.440374 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.058720e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.179942e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.602540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.512190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.187000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.875530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232836e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.378103e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6079198.405761 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.241575e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.387409e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.898758e+05 │ │ │ │ Vprtstp: contraction number = 5.898758e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.088148 │ │ │ │ Vnewton: Attempting damping, relres = 0.541560 │ │ │ │ Vnewton: Damping accepted, relres = 0.088148 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.814828e-02 │ │ │ │ Vprtstp: contraction number = 8.814828e-02 │ │ │ │ Vnewton: Using errtol_s: 535870.896065 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.261029e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.411422e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.077049e+05 │ │ │ │ Vprtstp: contraction number = 1.077049e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.598309e-02 │ │ │ │ Vprtstp: contraction number = 1.813205e-01 │ │ │ │ Vnewton: Using errtol_s: 97164.364787 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.276829e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.430995e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.746148e+04 │ │ │ │ Vprtstp: contraction number = 2.746148e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.065921e-03 │ │ │ │ Vprtstp: contraction number = 2.543889e-01 │ │ │ │ Vnewton: Using errtol_s: 24717.539236 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292702e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.449814e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.490060e+03 │ │ │ │ Vprtstp: contraction number = 8.490060e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.256932e-03 │ │ │ │ Vprtstp: contraction number = 3.091382e-01 │ │ │ │ Vnewton: Using errtol_s: 7641.136045 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.308476e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.469945e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.906153e+03 │ │ │ │ Vprtstp: contraction number = 2.906153e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.302464e-04 │ │ │ │ Vprtstp: contraction number = 3.422990e-01 │ │ │ │ Vnewton: Using errtol_s: 2615.553137 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.324277e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.490231e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.038756e+03 │ │ │ │ Vprtstp: contraction number = 1.038756e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.537840e-04 │ │ │ │ Vprtstp: contraction number = 3.574324e-01 │ │ │ │ Vnewton: Using errtol_s: 934.883311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.339986e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.510638e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.756989e+02 │ │ │ │ Vprtstp: contraction number = 3.756989e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.562081e-05 │ │ │ │ Vprtstp: contraction number = 3.616814e-01 │ │ │ │ Vnewton: Using errtol_s: 338.129920 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355760e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.530493e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.372077e+02 │ │ │ │ Vprtstp: contraction number = 1.372077e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.031307e-05 │ │ │ │ Vprtstp: contraction number = 3.652064e-01 │ │ │ │ Vnewton: Using errtol_s: 123.487196 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.371647e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.550784e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.308624e+01 │ │ │ │ Vprtstp: contraction number = 5.308624e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.859206e-06 │ │ │ │ Vprtstp: contraction number = 3.869039e-01 │ │ │ │ Vnewton: Using errtol_s: 47.777672 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.387648e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.571194e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.247149e+01 │ │ │ │ Vprtstp: contraction number = 2.247149e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.326814e-06 │ │ │ │ Vprtstp: contraction number = 4.233015e-01 │ │ │ │ Vnewton: Using errtol_s: 20.224360 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.403443e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.592092e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.031380e+01 │ │ │ │ Vprtstp: contraction number = 1.031380e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.526916e-06 │ │ │ │ Vprtstp: contraction number = 4.589724e-01 │ │ │ │ Vnewton: Using errtol_s: 9.282423 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.419299e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612475e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.018395e+00 │ │ │ │ Vprtstp: contraction number = 5.018395e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.429527e-07 │ │ │ │ Vprtstp: contraction number = 4.865709e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.985683e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.058950e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.508288e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.585379e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15857,17 +15857,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.101910647011E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.806992325165E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.916747531828E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.199020e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.219910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -15888,261 +15888,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.249149 │ │ │ │ +Vacc_SASA: Time elapsed: 16.674597 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.769814e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.813710e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.656560e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.474030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.249100e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.361680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.617351e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.818998e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.626161e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.828212e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.645956e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.851630e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.662030e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.871460e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.677996e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.891277e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.694089e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910662e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.710270e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.930448e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.726491e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.948876e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.742513e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.967796e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.758661e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.986826e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.774864e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.005631e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.791194e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.024949e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.807406e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.044182e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.823568e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.062389e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.839742e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.078497e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.855703e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.098636e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.872146e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.118575e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.888295e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.137598e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.904356e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.158301e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.920405e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.177918e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936303e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.197477e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.311586e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.386008e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.952020e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.023436e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -16151,17 +16151,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.017893422646E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.611562953522E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.865716990042E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.383200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.526800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -16207,171 +16207,171 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0371069 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.279879 │ │ │ │ +Vacc_SASA: Time elapsed: 16.746202 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.856986e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.906724e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.629310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.505410e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.145740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.408650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.142848e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.413516e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6935084.404705 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.151459e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.422789e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.727592e+05 │ │ │ │ Vprtstp: contraction number = 6.727592e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.088102 │ │ │ │ Vnewton: Attempting damping, relres = 0.541455 │ │ │ │ Vnewton: Damping accepted, relres = 0.088102 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.810224e-02 │ │ │ │ Vprtstp: contraction number = 8.810224e-02 │ │ │ │ Vnewton: Using errtol_s: 610996.445538 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.171095e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.447581e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.225330e+05 │ │ │ │ Vprtstp: contraction number = 1.225330e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.593368e-02 │ │ │ │ Vprtstp: contraction number = 1.808544e-01 │ │ │ │ Vnewton: Using errtol_s: 110501.406789 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.187068e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.468277e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.085731e+04 │ │ │ │ Vprtstp: contraction number = 3.085731e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.004954e-03 │ │ │ │ Vprtstp: contraction number = 2.513515e-01 │ │ │ │ Vnewton: Using errtol_s: 27774.696268 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.203216e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.489421e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.402021e+03 │ │ │ │ Vprtstp: contraction number = 9.402021e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.220185e-03 │ │ │ │ Vprtstp: contraction number = 3.046688e-01 │ │ │ │ Vnewton: Using errtol_s: 8462.082872 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219317e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.509961e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.175895e+03 │ │ │ │ Vprtstp: contraction number = 3.175895e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.121575e-04 │ │ │ │ Vprtstp: contraction number = 3.377829e-01 │ │ │ │ Vnewton: Using errtol_s: 2858.347084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.235640e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.529051e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.121720e+03 │ │ │ │ Vprtstp: contraction number = 1.121720e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.455722e-04 │ │ │ │ Vprtstp: contraction number = 3.531955e-01 │ │ │ │ Vnewton: Using errtol_s: 1009.555317 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.252199e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.550229e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.008316e+02 │ │ │ │ Vprtstp: contraction number = 4.008316e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.201806e-05 │ │ │ │ Vprtstp: contraction number = 3.573352e-01 │ │ │ │ Vnewton: Using errtol_s: 360.749636 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.268398e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.571407e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.444166e+02 │ │ │ │ Vprtstp: contraction number = 1.444166e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.874168e-05 │ │ │ │ Vprtstp: contraction number = 3.602918e-01 │ │ │ │ Vnewton: Using errtol_s: 129.975153 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.284625e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.592291e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.512662e+01 │ │ │ │ Vprtstp: contraction number = 5.512662e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.154062e-06 │ │ │ │ Vprtstp: contraction number = 3.817193e-01 │ │ │ │ Vnewton: Using errtol_s: 49.614025 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.300644e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.612333e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.308362e+01 │ │ │ │ Vprtstp: contraction number = 2.308362e+01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.995677e-06 │ │ │ │ Vprtstp: contraction number = 4.187379e-01 │ │ │ │ Vnewton: Using errtol_s: 20.775274 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.316444e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.632628e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051871e+01 │ │ │ │ Vprtstp: contraction number = 1.051871e+01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.365066e-06 │ │ │ │ Vprtstp: contraction number = 4.556784e-01 │ │ │ │ Vnewton: Using errtol_s: 9.466845 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.332348e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.653935e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.098076e+00 │ │ │ │ Vprtstp: contraction number = 5.098076e+00 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 6.616025e-07 │ │ │ │ Vprtstp: contraction number = 4.846672e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.019667e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.093014e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.573444e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.645674e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -16380,27 +16380,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.129100275217E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.806947604587E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.916855498576E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.244900e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.240840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.354437e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.681023e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:13:58 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:36:48 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -16753,250 +16753,250 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.223770 │ │ │ │ +Vacc_SASA: Time elapsed: 7.371522 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.054554e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.180347e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.656380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.587500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.123410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.416410e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.488622e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.627323e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036797e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.058732e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.136321e+05 │ │ │ │ Vprtstp: contraction number = 2.136321e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047663 │ │ │ │ Vnewton: Attempting damping, relres = 0.515490 │ │ │ │ Vnewton: Damping accepted, relres = 0.047663 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.766304e-02 │ │ │ │ Vprtstp: contraction number = 4.766304e-02 │ │ │ │ Vnewton: Using errtol_s: 204994.485638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238662e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292710e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.587025e+04 │ │ │ │ Vprtstp: contraction number = 4.587025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.727679e-03 │ │ │ │ Vprtstp: contraction number = 2.040927e-01 │ │ │ │ Vnewton: Using errtol_s: 41837.880528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.402637e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.483278e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.391016e+04 │ │ │ │ Vprtstp: contraction number = 1.391016e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.912173e-03 │ │ │ │ Vprtstp: contraction number = 2.993697e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.995351 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.564862e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.675490e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.237707e+03 │ │ │ │ Vprtstp: contraction number = 5.237707e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.096054e-03 │ │ │ │ Vprtstp: contraction number = 3.763697e-01 │ │ │ │ Vnewton: Using errtol_s: 4714.028550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.725001e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.867929e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.331453e+03 │ │ │ │ Vprtstp: contraction number = 2.331453e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.878779e-04 │ │ │ │ Vprtstp: contraction number = 4.451223e-01 │ │ │ │ Vnewton: Using errtol_s: 2098.319320 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.886653e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.059058e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189035e+03 │ │ │ │ Vprtstp: contraction number = 1.189035e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.488161e-04 │ │ │ │ Vprtstp: contraction number = 5.099966e-01 │ │ │ │ Vnewton: Using errtol_s: 1070.135650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.048621e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.249512e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.678182e+02 │ │ │ │ Vprtstp: contraction number = 6.678182e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.397467e-04 │ │ │ │ Vprtstp: contraction number = 5.616468e-01 │ │ │ │ Vnewton: Using errtol_s: 601.038216 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.209888e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.440905e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.994733e+02 │ │ │ │ Vprtstp: contraction number = 3.994733e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.359319e-05 │ │ │ │ Vprtstp: contraction number = 5.981764e-01 │ │ │ │ Vnewton: Using errtol_s: 359.526862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.371162e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.634028e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.488647e+02 │ │ │ │ Vprtstp: contraction number = 2.488647e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.207703e-05 │ │ │ │ Vprtstp: contraction number = 6.229817e-01 │ │ │ │ Vnewton: Using errtol_s: 223.978670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.531378e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.823598e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.588671e+02 │ │ │ │ Vprtstp: contraction number = 1.588671e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.324425e-05 │ │ │ │ Vprtstp: contraction number = 6.383669e-01 │ │ │ │ Vnewton: Using errtol_s: 142.980568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.692924e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.017604e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.030284e+02 │ │ │ │ Vprtstp: contraction number = 1.030284e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.155954e-05 │ │ │ │ Vprtstp: contraction number = 6.485194e-01 │ │ │ │ Vnewton: Using errtol_s: 92.725673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.857338e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.205181e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.760657e+01 │ │ │ │ Vprtstp: contraction number = 6.760657e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.414722e-05 │ │ │ │ Vprtstp: contraction number = 6.561932e-01 │ │ │ │ Vnewton: Using errtol_s: 60.845953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.018850e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.398452e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.480217e+01 │ │ │ │ Vprtstp: contraction number = 4.480217e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 9.375216e-06 │ │ │ │ Vprtstp: contraction number = 6.626894e-01 │ │ │ │ Vnewton: Using errtol_s: 40.321969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.181214e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.591206e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990735e+01 │ │ │ │ Vprtstp: contraction number = 2.990735e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 6.258355e-06 │ │ │ │ Vprtstp: contraction number = 6.675424e-01 │ │ │ │ Vnewton: Using errtol_s: 26.916626 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.343670e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.781963e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.008505e+01 │ │ │ │ Vprtstp: contraction number = 2.008505e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 4.202958e-06 │ │ │ │ Vprtstp: contraction number = 6.715755e-01 │ │ │ │ Vnewton: Using errtol_s: 18.076547 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.506785e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.972855e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356100e+01 │ │ │ │ Vprtstp: contraction number = 1.356100e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 2.837748e-06 │ │ │ │ Vprtstp: contraction number = 6.751787e-01 │ │ │ │ Vnewton: Using errtol_s: 12.204901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.680122e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.163024e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.198733e+00 │ │ │ │ Vprtstp: contraction number = 9.198733e+00 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 1.924909e-06 │ │ │ │ Vprtstp: contraction number = 6.783227e-01 │ │ │ │ Vnewton: Using errtol_s: 8.278861 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.842933e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.352494e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.265697e+00 │ │ │ │ Vprtstp: contraction number = 6.265697e+00 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.311147e-06 │ │ │ │ Vprtstp: contraction number = 6.811478e-01 │ │ │ │ Vnewton: Using errtol_s: 5.639128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.005303e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.547887e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.284635e+00 │ │ │ │ Vprtstp: contraction number = 4.284635e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 8.965941e-07 │ │ │ │ Vprtstp: contraction number = 6.838241e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.180976e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.255144e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.739576e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.813061e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -17005,15 +17005,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.751162440734E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.947112425311E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.674060402300E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.385800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.647900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -17061,160 +17061,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0113169 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.314741 │ │ │ │ +Vacc_SASA: Time elapsed: 7.257344 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.778232e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.757782e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.627480e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.506740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.233380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.422230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.094896e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.665534e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2854416.159669 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.182681e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.759748e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.073946e+05 │ │ │ │ Vprtstp: contraction number = 3.073946e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.097301 │ │ │ │ Vnewton: Attempting damping, relres = 0.546102 │ │ │ │ Vnewton: Damping accepted, relres = 0.097301 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.730086e-02 │ │ │ │ Vprtstp: contraction number = 9.730086e-02 │ │ │ │ Vnewton: Using errtol_s: 277737.152012 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.382024e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.999560e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.422127e+04 │ │ │ │ Vprtstp: contraction number = 5.422127e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.709795e-02 │ │ │ │ Vprtstp: contraction number = 1.757225e-01 │ │ │ │ Vnewton: Using errtol_s: 48804.661136 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.542287e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.191454e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.206353e+04 │ │ │ │ Vprtstp: contraction number = 1.206353e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 3.803701e-03 │ │ │ │ Vprtstp: contraction number = 2.224653e-01 │ │ │ │ Vnewton: Using errtol_s: 10857.344468 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.703771e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.373747e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.177380e+03 │ │ │ │ Vprtstp: contraction number = 3.177380e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.001847e-03 │ │ │ │ Vprtstp: contraction number = 2.633874e-01 │ │ │ │ Vnewton: Using errtol_s: 2859.687867 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.866407e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.559913e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.523572e+02 │ │ │ │ Vprtstp: contraction number = 9.523572e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.002837e-04 │ │ │ │ Vprtstp: contraction number = 2.997301e-01 │ │ │ │ Vnewton: Using errtol_s: 857.134538 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.028665e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.756431e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.079890e+02 │ │ │ │ Vprtstp: contraction number = 3.079890e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.711021e-05 │ │ │ │ Vprtstp: contraction number = 3.233949e-01 │ │ │ │ Vnewton: Using errtol_s: 277.192960 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.192394e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.953884e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.041211e+02 │ │ │ │ Vprtstp: contraction number = 1.041211e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.282966e-05 │ │ │ │ Vprtstp: contraction number = 3.380660e-01 │ │ │ │ Vnewton: Using errtol_s: 93.709510 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.359487e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.161077e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.682551e+01 │ │ │ │ Vprtstp: contraction number = 3.682551e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.161114e-05 │ │ │ │ Vprtstp: contraction number = 3.536784e-01 │ │ │ │ Vnewton: Using errtol_s: 33.143025 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.524040e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.370982e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.414772e+01 │ │ │ │ Vprtstp: contraction number = 1.414772e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.460791e-06 │ │ │ │ Vprtstp: contraction number = 3.841820e-01 │ │ │ │ Vnewton: Using errtol_s: 12.732955 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.698176e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.578884e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.014294e+00 │ │ │ │ Vprtstp: contraction number = 6.014294e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.896313e-06 │ │ │ │ Vprtstp: contraction number = 4.251068e-01 │ │ │ │ Vnewton: Using errtol_s: 5.412865 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.863580e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.787438e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.770154e+00 │ │ │ │ Vprtstp: contraction number = 2.770154e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.734323e-07 │ │ │ │ Vprtstp: contraction number = 4.605951e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.894662e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.968878e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.285390e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.358475e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -17223,17 +17223,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.831261294961E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.781344550664E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 8.939288545980E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.268060e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.313990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -17254,272 +17254,272 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.216963 │ │ │ │ +Vacc_SASA: Time elapsed: 7.525952 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.059565e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.385638e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.639240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.517080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.198180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.488180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.885009e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.879523e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.971678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.972531e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.113974e+05 │ │ │ │ Vprtstp: contraction number = 2.113974e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.047573 │ │ │ │ Vnewton: Attempting damping, relres = 0.515375 │ │ │ │ Vnewton: Damping accepted, relres = 0.047573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.757263e-02 │ │ │ │ Vprtstp: contraction number = 4.757263e-02 │ │ │ │ Vnewton: Using errtol_s: 203448.048803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.168109e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.208394e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.589098e+04 │ │ │ │ Vprtstp: contraction number = 4.589098e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.811582e-03 │ │ │ │ Vprtstp: contraction number = 2.062443e-01 │ │ │ │ Vnewton: Using errtol_s: 41959.996661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.327649e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.404801e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404662e+04 │ │ │ │ Vprtstp: contraction number = 1.404662e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.960291e-03 │ │ │ │ Vprtstp: contraction number = 3.017139e-01 │ │ │ │ Vnewton: Using errtol_s: 12659.913691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.486870e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.600233e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.279840e+03 │ │ │ │ Vprtstp: contraction number = 5.279840e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.111524e-03 │ │ │ │ Vprtstp: contraction number = 3.754781e-01 │ │ │ │ Vnewton: Using errtol_s: 4753.520446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.646676e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.799318e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.336921e+03 │ │ │ │ Vprtstp: contraction number = 2.336921e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.918609e-04 │ │ │ │ Vprtstp: contraction number = 4.425102e-01 │ │ │ │ Vnewton: Using errtol_s: 2103.481419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.805204e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000236e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194576e+03 │ │ │ │ Vprtstp: contraction number = 1.194576e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.514070e-04 │ │ │ │ Vprtstp: contraction number = 5.111344e-01 │ │ │ │ Vnewton: Using errtol_s: 1075.161658 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.963208e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020079e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.792983e+02 │ │ │ │ Vprtstp: contraction number = 6.792983e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.429594e-04 │ │ │ │ Vprtstp: contraction number = 5.686374e-01 │ │ │ │ Vnewton: Using errtol_s: 611.377148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.122125e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040144e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.154648e+02 │ │ │ │ Vprtstp: contraction number = 4.154648e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.743449e-05 │ │ │ │ Vprtstp: contraction number = 6.116036e-01 │ │ │ │ Vnewton: Using errtol_s: 373.920435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.281747e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059717e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660684e+02 │ │ │ │ Vprtstp: contraction number = 2.660684e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.599388e-05 │ │ │ │ Vprtstp: contraction number = 6.404095e-01 │ │ │ │ Vnewton: Using errtol_s: 239.462182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.442100e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079816e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755593e+02 │ │ │ │ Vprtstp: contraction number = 1.755593e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.694626e-05 │ │ │ │ Vprtstp: contraction number = 6.598268e-01 │ │ │ │ Vnewton: Using errtol_s: 158.003576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.602391e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099530e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183176e+02 │ │ │ │ Vprtstp: contraction number = 1.183176e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.489979e-05 │ │ │ │ Vprtstp: contraction number = 6.739462e-01 │ │ │ │ Vnewton: Using errtol_s: 106.485913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.761355e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119117e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.102710e+01 │ │ │ │ Vprtstp: contraction number = 8.102710e+01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.705205e-05 │ │ │ │ Vprtstp: contraction number = 6.848271e-01 │ │ │ │ Vnewton: Using errtol_s: 72.924443 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.921004e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137325e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.628393e+01 │ │ │ │ Vprtstp: contraction number = 5.628393e+01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.184488e-05 │ │ │ │ Vprtstp: contraction number = 6.946308e-01 │ │ │ │ Vnewton: Using errtol_s: 50.655566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008027e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156720e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.955755e+01 │ │ │ │ Vprtstp: contraction number = 3.955755e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.324836e-06 │ │ │ │ Vprtstp: contraction number = 7.028213e-01 │ │ │ │ Vnewton: Using errtol_s: 35.601810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024012e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174771e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.808103e+01 │ │ │ │ Vprtstp: contraction number = 2.808103e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.909617e-06 │ │ │ │ Vprtstp: contraction number = 7.098779e-01 │ │ │ │ Vnewton: Using errtol_s: 25.272937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040027e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193778e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.010039e+01 │ │ │ │ Vprtstp: contraction number = 2.010039e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 4.230100e-06 │ │ │ │ Vprtstp: contraction number = 7.157995e-01 │ │ │ │ Vnewton: Using errtol_s: 18.090355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056058e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.211976e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.449222e+01 │ │ │ │ Vprtstp: contraction number = 1.449222e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 3.049867e-06 │ │ │ │ Vprtstp: contraction number = 7.209918e-01 │ │ │ │ Vnewton: Using errtol_s: 13.042997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.072162e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.230442e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.051084e+01 │ │ │ │ Vprtstp: contraction number = 1.051084e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 2.211992e-06 │ │ │ │ Vprtstp: contraction number = 7.252749e-01 │ │ │ │ Vnewton: Using errtol_s: 9.459758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088194e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.249104e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.663626e+00 │ │ │ │ Vprtstp: contraction number = 7.663626e+00 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.612800e-06 │ │ │ │ Vprtstp: contraction number = 7.291164e-01 │ │ │ │ Vnewton: Using errtol_s: 6.897264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104222e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.266618e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.612195e+00 │ │ │ │ Vprtstp: contraction number = 5.612195e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 1.181079e-06 │ │ │ │ Vprtstp: contraction number = 7.323158e-01 │ │ │ │ Vnewton: Using errtol_s: 5.050976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120161e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.284945e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.124624e+00 │ │ │ │ Vprtstp: contraction number = 4.124624e+00 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 8.680215e-07 │ │ │ │ Vprtstp: contraction number = 7.349396e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.440441e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.514009e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 4.090128e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.163442e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -17528,17 +17528,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.114658040660E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.255454137160E+02 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.687649926413E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.391800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.856200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -17584,160 +17584,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00476673 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.315589 │ │ │ │ +Vacc_SASA: Time elapsed: 7.397175 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.440819e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.519188e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.638990e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.538500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.377260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.466260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.225798e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390727e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1723088.414735 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.234754e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.400136e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.042446e+05 │ │ │ │ Vprtstp: contraction number = 2.042446e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.108739 │ │ │ │ Vnewton: Attempting damping, relres = 0.550663 │ │ │ │ Vnewton: Damping accepted, relres = 0.108739 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.087385e-01 │ │ │ │ Vprtstp: contraction number = 1.087385e-01 │ │ │ │ Vnewton: Using errtol_s: 187366.060856 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.257418e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.421623e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.786866e+04 │ │ │ │ Vprtstp: contraction number = 3.786866e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.981324e-02 │ │ │ │ Vprtstp: contraction number = 1.822100e-01 │ │ │ │ Vnewton: Using errtol_s: 34139.969757 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.273464e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.439438e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.828513e+03 │ │ │ │ Vprtstp: contraction number = 8.828513e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.612234e-03 │ │ │ │ Vprtstp: contraction number = 2.327854e-01 │ │ │ │ Vnewton: Using errtol_s: 7947.287090 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289431e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457619e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.384276e+03 │ │ │ │ Vprtstp: contraction number = 2.384276e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.245382e-03 │ │ │ │ Vprtstp: contraction number = 2.700171e-01 │ │ │ │ Vnewton: Using errtol_s: 2145.903122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305615e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.477039e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.047320e+02 │ │ │ │ Vprtstp: contraction number = 7.047320e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.680970e-04 │ │ │ │ Vprtstp: contraction number = 2.955696e-01 │ │ │ │ Vnewton: Using errtol_s: 634.263634 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321839e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.495348e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.207559e+02 │ │ │ │ Vprtstp: contraction number = 2.207559e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.153050e-04 │ │ │ │ Vprtstp: contraction number = 3.132463e-01 │ │ │ │ Vnewton: Using errtol_s: 198.680750 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.337960e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.513691e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.166503e+01 │ │ │ │ Vprtstp: contraction number = 7.166503e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.743196e-05 │ │ │ │ Vprtstp: contraction number = 3.246343e-01 │ │ │ │ Vnewton: Using errtol_s: 64.498581 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.354079e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.531012e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.385676e+01 │ │ │ │ Vprtstp: contraction number = 2.385676e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.246082e-05 │ │ │ │ Vprtstp: contraction number = 3.328924e-01 │ │ │ │ Vnewton: Using errtol_s: 21.471088 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.370046e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.546495e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.086151e+00 │ │ │ │ Vprtstp: contraction number = 8.086151e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.223542e-06 │ │ │ │ Vprtstp: contraction number = 3.389459e-01 │ │ │ │ Vnewton: Using errtol_s: 7.277537 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.386268e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.561194e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.777094e+00 │ │ │ │ Vprtstp: contraction number = 2.777094e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.450526e-06 │ │ │ │ Vprtstp: contraction number = 3.434383e-01 │ │ │ │ Vnewton: Using errtol_s: 2.499385 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.402308e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.575590e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.633001e-01 │ │ │ │ Vprtstp: contraction number = 9.633001e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.031489e-07 │ │ │ │ Vprtstp: contraction number = 3.468734e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.887572e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.963042e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.983026e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.056153e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -17746,17 +17746,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.878540629655E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.319538441543E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.644040185021E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.243510e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.243380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -17777,261 +17777,261 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.231526 │ │ │ │ +Vacc_SASA: Time elapsed: 16.176233 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.767635e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.760782e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.584820e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.361460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.081270e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.089180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.600054e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.773401e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.608937e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.782618e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.298565e+05 │ │ │ │ Vprtstp: contraction number = 4.298565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.048079 │ │ │ │ Vnewton: Attempting damping, relres = 0.515481 │ │ │ │ Vnewton: Damping accepted, relres = 0.048079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.807904e-02 │ │ │ │ Vprtstp: contraction number = 4.807904e-02 │ │ │ │ Vnewton: Using errtol_s: 418259.137179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.628595e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804155e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.275297e+04 │ │ │ │ Vprtstp: contraction number = 9.275297e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.791706e-03 │ │ │ │ Vprtstp: contraction number = 2.036585e-01 │ │ │ │ Vnewton: Using errtol_s: 85182.030508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.644631e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.822111e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.830324e+04 │ │ │ │ Vprtstp: contraction number = 2.830324e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.931540e-03 │ │ │ │ Vprtstp: contraction number = 2.993901e-01 │ │ │ │ Vnewton: Using errtol_s: 25502.653903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.660559e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.839809e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066383e+04 │ │ │ │ Vprtstp: contraction number = 1.066383e+04 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.103407e-03 │ │ │ │ Vprtstp: contraction number = 3.763916e-01 │ │ │ │ Vnewton: Using errtol_s: 9598.985602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.676616e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.857805e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725476e+03 │ │ │ │ Vprtstp: contraction number = 4.725476e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.889004e-04 │ │ │ │ Vprtstp: contraction number = 4.430826e-01 │ │ │ │ Vnewton: Using errtol_s: 4253.143226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.692550e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.873553e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402868e+03 │ │ │ │ Vprtstp: contraction number = 2.402868e+03 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.485940e-04 │ │ │ │ Vprtstp: contraction number = 5.084757e-01 │ │ │ │ Vnewton: Using errtol_s: 2162.620089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.708466e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.888547e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352802e+03 │ │ │ │ Vprtstp: contraction number = 1.352802e+03 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.399556e-04 │ │ │ │ Vprtstp: contraction number = 5.629888e-01 │ │ │ │ Vnewton: Using errtol_s: 1217.530795 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.724241e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.903752e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.164880e+02 │ │ │ │ Vprtstp: contraction number = 8.164880e+02 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.447037e-05 │ │ │ │ Vprtstp: contraction number = 6.035512e-01 │ │ │ │ Vnewton: Using errtol_s: 734.842122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740325e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.918691e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157033e+02 │ │ │ │ Vprtstp: contraction number = 5.157033e+02 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.335238e-05 │ │ │ │ Vprtstp: contraction number = 6.316106e-01 │ │ │ │ Vnewton: Using errtol_s: 464.134076 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.756289e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.935521e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.352095e+02 │ │ │ │ Vprtstp: contraction number = 3.352095e+02 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 3.467926e-05 │ │ │ │ Vprtstp: contraction number = 6.500040e-01 │ │ │ │ Vnewton: Using errtol_s: 301.688999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.772260e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.951862e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.222234e+02 │ │ │ │ Vprtstp: contraction number = 2.222234e+02 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.299022e-05 │ │ │ │ Vprtstp: contraction number = 6.629387e-01 │ │ │ │ Vnewton: Using errtol_s: 200.001301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.788207e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.971006e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.495221e+02 │ │ │ │ Vprtstp: contraction number = 1.495221e+02 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.546887e-05 │ │ │ │ Vprtstp: contraction number = 6.728456e-01 │ │ │ │ Vnewton: Using errtol_s: 134.569993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.804153e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.990017e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018836e+02 │ │ │ │ Vprtstp: contraction number = 1.018836e+02 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.054041e-05 │ │ │ │ Vprtstp: contraction number = 6.813949e-01 │ │ │ │ Vnewton: Using errtol_s: 91.695311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.819994e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.009747e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.012825e+01 │ │ │ │ Vprtstp: contraction number = 7.012825e+01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 7.255144e-06 │ │ │ │ Vprtstp: contraction number = 6.883171e-01 │ │ │ │ Vnewton: Using errtol_s: 63.115450 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.836092e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.034642e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.869976e+01 │ │ │ │ Vprtstp: contraction number = 4.869976e+01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 5.038252e-06 │ │ │ │ Vprtstp: contraction number = 6.944386e-01 │ │ │ │ Vnewton: Using errtol_s: 43.829803 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.852200e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.055212e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.408035e+01 │ │ │ │ Vprtstp: contraction number = 3.408035e+01 │ │ │ │ Vprtstp: iteration = 16 │ │ │ │ Vprtstp: relative residual = 3.525795e-06 │ │ │ │ Vprtstp: contraction number = 6.998052e-01 │ │ │ │ Vnewton: Using errtol_s: 30.672326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.868416e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.074586e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401453e+01 │ │ │ │ Vprtstp: contraction number = 2.401453e+01 │ │ │ │ Vprtstp: iteration = 17 │ │ │ │ Vprtstp: relative residual = 2.484432e-06 │ │ │ │ Vprtstp: contraction number = 7.046444e-01 │ │ │ │ Vnewton: Using errtol_s: 21.613084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.884442e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.094647e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.702723e+01 │ │ │ │ Vprtstp: contraction number = 1.702723e+01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.761558e-06 │ │ │ │ Vprtstp: contraction number = 7.090385e-01 │ │ │ │ Vnewton: Using errtol_s: 15.324508 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.900655e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.114552e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214065e+01 │ │ │ │ Vprtstp: contraction number = 1.214065e+01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 1.256015e-06 │ │ │ │ Vprtstp: contraction number = 7.130137e-01 │ │ │ │ Vnewton: Using errtol_s: 10.926584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.916808e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.134320e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.699962e+00 │ │ │ │ Vprtstp: contraction number = 8.699962e+00 │ │ │ │ Vprtstp: iteration = 20 │ │ │ │ Vprtstp: relative residual = 9.000575e-07 │ │ │ │ Vprtstp: contraction number = 7.165978e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.291771e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.363451e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 3.763653e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.830861e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -18040,15 +18040,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.211144338750E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.301973448783E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.153004707320E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.973700e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.487600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ @@ -18096,160 +18096,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0260263 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.301236 │ │ │ │ +Vacc_SASA: Time elapsed: 16.843751 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.840544e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.893509e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.613690e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.444250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.194300e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.405130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.121890e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.347632e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4514465.797290 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.130689e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.356863e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.961912e+05 │ │ │ │ Vprtstp: contraction number = 4.961912e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.099852 │ │ │ │ Vnewton: Attempting damping, relres = 0.546981 │ │ │ │ Vnewton: Damping accepted, relres = 0.099852 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.985216e-02 │ │ │ │ Vprtstp: contraction number = 9.985216e-02 │ │ │ │ Vnewton: Using errtol_s: 450779.157003 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.150656e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.379518e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.942393e+04 │ │ │ │ Vprtstp: contraction number = 8.942393e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.783565e-02 │ │ │ │ Vprtstp: contraction number = 1.786206e-01 │ │ │ │ Vnewton: Using errtol_s: 80518.432475 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.166954e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.399459e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.031115e+04 │ │ │ │ Vprtstp: contraction number = 2.031115e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.049611e-03 │ │ │ │ Vprtstp: contraction number = 2.270515e-01 │ │ │ │ Vnewton: Using errtol_s: 18281.831872 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.183346e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.420796e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.419185e+03 │ │ │ │ Vprtstp: contraction number = 5.419185e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.080391e-03 │ │ │ │ Vprtstp: contraction number = 2.667887e-01 │ │ │ │ Vnewton: Using errtol_s: 4877.386053 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.199624e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442321e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.625333e+03 │ │ │ │ Vprtstp: contraction number = 1.625333e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.240293e-04 │ │ │ │ Vprtstp: contraction number = 2.999187e-01 │ │ │ │ Vnewton: Using errtol_s: 1462.819304 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.216032e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.463794e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.216368e+02 │ │ │ │ Vprtstp: contraction number = 5.216368e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.039939e-04 │ │ │ │ Vprtstp: contraction number = 3.209397e-01 │ │ │ │ Vnewton: Using errtol_s: 469.476847 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.232495e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.483380e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.735595e+02 │ │ │ │ Vprtstp: contraction number = 1.735595e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.460082e-05 │ │ │ │ Vprtstp: contraction number = 3.327198e-01 │ │ │ │ Vnewton: Using errtol_s: 156.204227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.248874e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.504558e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.923935e+01 │ │ │ │ Vprtstp: contraction number = 5.923935e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.180993e-05 │ │ │ │ Vprtstp: contraction number = 3.413193e-01 │ │ │ │ Vnewton: Using errtol_s: 53.315519 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.265102e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.525616e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.118946e+01 │ │ │ │ Vprtstp: contraction number = 2.118946e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.224316e-06 │ │ │ │ Vprtstp: contraction number = 3.576919e-01 │ │ │ │ Vnewton: Using errtol_s: 19.070529 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.281379e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.546547e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.237698e+00 │ │ │ │ Vprtstp: contraction number = 8.237698e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.642261e-06 │ │ │ │ Vprtstp: contraction number = 3.887637e-01 │ │ │ │ Vnewton: Using errtol_s: 7.413930 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.297708e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.566375e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.509994e+00 │ │ │ │ Vprtstp: contraction number = 3.509994e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.997494e-07 │ │ │ │ Vprtstp: contraction number = 4.260891e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.883661e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.957090e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.360409e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.432265e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -18258,27 +18258,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.259341430721E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.116108930828E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.059930084642E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.233470e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.329150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.319936e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.594063e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:16:11 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:40:35 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -18631,129 +18631,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.311986 │ │ │ │ +Vacc_SASA: Time elapsed: 7.640056 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.580395e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.997328e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.606810e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.475880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.214800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.693440e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000451e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051417e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088908e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.153463e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.288781e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.392468e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.452767e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.573828e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.615418e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.783736e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.780358e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.008259e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.945078e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.233028e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.109550e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.468638e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273716e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.686346e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.398895e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.471085e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.804480e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.880137e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -18762,17 +18762,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.432004946158E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.213065901878E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.590634025531E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.379900e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.156200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -18818,127 +18818,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00609308 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.230342 │ │ │ │ +Vacc_SASA: Time elapsed: 7.304563 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.001568e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.255196e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.608610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.652580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.143700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.989150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.383350e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.879224e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3435589.940646 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.471267e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.982690e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.946642e+05 │ │ │ │ Vprtstp: contraction number = 2.946642e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.078398 │ │ │ │ Vnewton: Attempting damping, relres = 0.536416 │ │ │ │ Vnewton: Damping accepted, relres = 0.078398 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.839769e-02 │ │ │ │ Vprtstp: contraction number = 7.839769e-02 │ │ │ │ Vnewton: Using errtol_s: 269342.316546 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.668578e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.242905e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.926470e+04 │ │ │ │ Vprtstp: contraction number = 3.926470e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.037644e-02 │ │ │ │ Vprtstp: contraction number = 1.323565e-01 │ │ │ │ Vnewton: Using errtol_s: 35649.206105 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.828665e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.429256e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.330351e+03 │ │ │ │ Vprtstp: contraction number = 6.330351e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.659520e-03 │ │ │ │ Vprtstp: contraction number = 1.599315e-01 │ │ │ │ Vnewton: Using errtol_s: 5701.430665 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.991504e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.620219e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.149005e+03 │ │ │ │ Vprtstp: contraction number = 1.149005e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.009992e-04 │ │ │ │ Vprtstp: contraction number = 1.813772e-01 │ │ │ │ Vnewton: Using errtol_s: 1034.109707 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.150416e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.825226e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.271091e+02 │ │ │ │ Vprtstp: contraction number = 2.271091e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.949440e-05 │ │ │ │ Vprtstp: contraction number = 1.976564e-01 │ │ │ │ Vnewton: Using errtol_s: 204.398353 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.312593e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.032944e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.795044e+01 │ │ │ │ Vprtstp: contraction number = 4.795044e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.256128e-05 │ │ │ │ Vprtstp: contraction number = 2.111338e-01 │ │ │ │ Vnewton: Using errtol_s: 43.155404 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.473019e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.230649e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.083630e+01 │ │ │ │ Vprtstp: contraction number = 1.083630e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.838717e-06 │ │ │ │ Vprtstp: contraction number = 2.259895e-01 │ │ │ │ Vnewton: Using errtol_s: 9.752668 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.635326e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.413869e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677103e+00 │ │ │ │ Vprtstp: contraction number = 2.677103e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.013038e-07 │ │ │ │ Vprtstp: contraction number = 2.470496e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.375468e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.446661e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.686930e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.768160e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -18947,17 +18947,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.647117283033E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.061546373318E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.342705487083E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.248860e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.305500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -18978,129 +18978,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.338098 │ │ │ │ +Vacc_SASA: Time elapsed: 7.571473 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.610634e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.927615e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.636670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.458420e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.441140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.231360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.709794e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.545246e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.801330e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.640174e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.004211e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.908912e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.172116e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.162694e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.337171e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.357293e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.509989e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.553584e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.680823e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.750246e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.849954e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.953572e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.020125e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.147909e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.442097e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.516429e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.754846e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.824823e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19109,17 +19109,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.317231145309E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.397951074417E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.196103394551E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.108200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.401200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -19165,149 +19165,149 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0717616 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.352051 │ │ │ │ +Vacc_SASA: Time elapsed: 7.556783 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.284854e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.619270e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.777940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.521610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.312650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.562840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.167592e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.348369e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3849668.809256 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.254988e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.443372e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.552766e+05 │ │ │ │ Vprtstp: contraction number = 3.552766e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.084988 │ │ │ │ Vnewton: Attempting damping, relres = 0.539692 │ │ │ │ Vnewton: Damping accepted, relres = 0.084988 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.498801e-02 │ │ │ │ Vprtstp: contraction number = 8.498801e-02 │ │ │ │ Vnewton: Using errtol_s: 327175.687931 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.456666e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.687952e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.008831e+04 │ │ │ │ Vprtstp: contraction number = 5.008831e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.180515e-02 │ │ │ │ Vprtstp: contraction number = 1.389037e-01 │ │ │ │ Vnewton: Using errtol_s: 45445.906193 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.621143e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.898232e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.515214e+03 │ │ │ │ Vprtstp: contraction number = 8.515214e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.991773e-03 │ │ │ │ Vprtstp: contraction number = 1.687207e-01 │ │ │ │ Vnewton: Using errtol_s: 7667.665331 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.790928e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011444e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.650417e+03 │ │ │ │ Vprtstp: contraction number = 1.650417e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.858749e-04 │ │ │ │ Vprtstp: contraction number = 1.937344e-01 │ │ │ │ Vnewton: Using errtol_s: 1485.490751 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.957732e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032492e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.445276e+02 │ │ │ │ Vprtstp: contraction number = 3.445276e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 8.054589e-05 │ │ │ │ Vprtstp: contraction number = 2.087357e-01 │ │ │ │ Vnewton: Using errtol_s: 310.075011 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.126806e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051357e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.228113e+01 │ │ │ │ Vprtstp: contraction number = 9.228113e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.157878e-05 │ │ │ │ Vprtstp: contraction number = 2.679067e-01 │ │ │ │ Vnewton: Using errtol_s: 83.071163 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.294225e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070321e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.340270e+01 │ │ │ │ Vprtstp: contraction number = 3.340270e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.809088e-06 │ │ │ │ Vprtstp: contraction number = 3.618873e-01 │ │ │ │ Vnewton: Using errtol_s: 30.062402 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.459836e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089386e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.311951e+01 │ │ │ │ Vprtstp: contraction number = 1.311951e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.067793e-06 │ │ │ │ Vprtstp: contraction number = 3.928491e-01 │ │ │ │ Vnewton: Using errtol_s: 11.809988 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.624421e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107669e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.550050e+00 │ │ │ │ Vprtstp: contraction number = 5.550050e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.297525e-06 │ │ │ │ Vprtstp: contraction number = 4.229508e-01 │ │ │ │ Vnewton: Using errtol_s: 4.995043 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.794491e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126942e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.408064e+00 │ │ │ │ Vprtstp: contraction number = 2.408064e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 5.629926e-07 │ │ │ │ Vprtstp: contraction number = 4.338972e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.757140e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.832013e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.047459e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.120902e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19316,17 +19316,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.480336832725E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.844029166481E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.209478882547E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.289690e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.293340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -19347,129 +19347,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.366556 │ │ │ │ +Vacc_SASA: Time elapsed: 16.824288 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.823292e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.883987e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.629550e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.498780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.096620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.520250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183522e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.336917e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.192310e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.346263e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212018e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.370630e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228305e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.390897e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.244425e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.410998e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.260530e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.432228e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.276620e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.449858e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292604e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.467733e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.308587e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.488003e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.373116e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.444318e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.672098e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.745077e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19478,17 +19478,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.111204276616E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.618165500075E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.858858240156E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.605100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.938400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -19534,138 +19534,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0804427 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.252299 │ │ │ │ +Vacc_SASA: Time elapsed: 16.911861 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.905450e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.978814e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.612440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.429710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.259950e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.255350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.519914e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.710314e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7226173.981930 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.528590e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.719301e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.363534e+05 │ │ │ │ Vprtstp: contraction number = 6.363534e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.081351 │ │ │ │ Vnewton: Attempting damping, relres = 0.537664 │ │ │ │ Vnewton: Damping accepted, relres = 0.081351 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.135112e-02 │ │ │ │ Vprtstp: contraction number = 8.135112e-02 │ │ │ │ Vnewton: Using errtol_s: 587857.310633 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.548142e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.741211e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.753275e+04 │ │ │ │ Vprtstp: contraction number = 8.753275e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.104343e-02 │ │ │ │ Vprtstp: contraction number = 1.357502e-01 │ │ │ │ Vnewton: Using errtol_s: 79801.757672 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.564180e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.760376e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.461031e+04 │ │ │ │ Vprtstp: contraction number = 1.461031e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.821090e-03 │ │ │ │ Vprtstp: contraction number = 1.649025e-01 │ │ │ │ Vnewton: Using errtol_s: 13159.512971 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.580172e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.778057e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.736183e+03 │ │ │ │ Vprtstp: contraction number = 2.736183e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.408124e-04 │ │ │ │ Vprtstp: contraction number = 1.871475e-01 │ │ │ │ Vnewton: Using errtol_s: 2462.769628 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.596196e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.798073e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.483227e+02 │ │ │ │ Vprtstp: contraction number = 5.483227e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.829255e-05 │ │ │ │ Vprtstp: contraction number = 2.003817e-01 │ │ │ │ Vnewton: Using errtol_s: 493.493873 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612116e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.818512e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.327802e+02 │ │ │ │ Vprtstp: contraction number = 1.327802e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.654140e-05 │ │ │ │ Vprtstp: contraction number = 2.422139e-01 │ │ │ │ Vnewton: Using errtol_s: 119.531057 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.628166e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.839011e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.724135e+01 │ │ │ │ Vprtstp: contraction number = 4.724135e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.883780e-06 │ │ │ │ Vprtstp: contraction number = 3.557002e-01 │ │ │ │ Vnewton: Using errtol_s: 42.517221 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.644264e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.857926e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.799945e+01 │ │ │ │ Vprtstp: contraction number = 1.799945e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.242401e-06 │ │ │ │ Vprtstp: contraction number = 3.811157e-01 │ │ │ │ Vnewton: Using errtol_s: 16.203980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.660217e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.876193e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.792899e+00 │ │ │ │ Vprtstp: contraction number = 7.792899e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 9.705840e-07 │ │ │ │ Vprtstp: contraction number = 4.328325e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.526693e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.599151e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.823634e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.893032e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19674,27 +19674,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.121256399906E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.906327571511E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.455577366311E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.209970e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.294870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.681908e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.902743e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:18:01 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:43:47 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -20047,129 +20047,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.306738 │ │ │ │ +Vacc_SASA: Time elapsed: 7.535329 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.562076e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.884337e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.643140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.649340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.243960e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.421990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.988257e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036611e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086646e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.129887e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.287116e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.378554e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.449347e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.560163e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.611842e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.755941e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.774399e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.953996e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936784e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.148863e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.099945e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.343090e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.263331e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.539038e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.388699e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.461329e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.635910e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.709706e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -20178,15 +20178,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.829504544268E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.542693128993E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.766198316119E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.311300e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.236200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -20234,127 +20234,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0324776 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.228248 │ │ │ │ +Vacc_SASA: Time elapsed: 7.076124 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.450462e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.488732e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.613170e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.565910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.200200e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.329380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.417216e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.705930e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6495890.956801 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.504777e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.795987e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.477908e+05 │ │ │ │ Vprtstp: contraction number = 5.477908e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.076573 │ │ │ │ Vnewton: Attempting damping, relres = 0.536204 │ │ │ │ Vnewton: Damping accepted, relres = 0.076573 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.657334e-02 │ │ │ │ Vprtstp: contraction number = 7.657334e-02 │ │ │ │ Vnewton: Using errtol_s: 497412.042043 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.706289e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.023738e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.388713e+04 │ │ │ │ Vprtstp: contraction number = 7.388713e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.027070e-02 │ │ │ │ Vprtstp: contraction number = 1.341289e-01 │ │ │ │ Vnewton: Using errtol_s: 66717.354364 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.867090e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.204975e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.213780e+04 │ │ │ │ Vprtstp: contraction number = 1.213780e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.681990e-03 │ │ │ │ Vprtstp: contraction number = 1.637659e-01 │ │ │ │ Vnewton: Using errtol_s: 10926.025346 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.026660e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.402469e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.238925e+03 │ │ │ │ Vprtstp: contraction number = 2.238925e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.102037e-04 │ │ │ │ Vprtstp: contraction number = 1.844265e-01 │ │ │ │ Vnewton: Using errtol_s: 2015.049122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.194989e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.598265e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.343882e+02 │ │ │ │ Vprtstp: contraction number = 4.343882e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.018448e-05 │ │ │ │ Vprtstp: contraction number = 1.940160e-01 │ │ │ │ Vnewton: Using errtol_s: 390.951807 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.358797e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.795024e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.935633e+01 │ │ │ │ Vprtstp: contraction number = 7.935633e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.099479e-05 │ │ │ │ Vprtstp: contraction number = 1.826848e-01 │ │ │ │ Vnewton: Using errtol_s: 71.420957 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.519739e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.984822e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.530287e+01 │ │ │ │ Vprtstp: contraction number = 1.530287e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.120201e-06 │ │ │ │ Vprtstp: contraction number = 1.928369e-01 │ │ │ │ Vnewton: Using errtol_s: 13.772596 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.680041e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.160685e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.453153e+00 │ │ │ │ Vprtstp: contraction number = 3.453153e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.784317e-07 │ │ │ │ Vprtstp: contraction number = 2.256539e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.388188e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.460231e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.605309e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.677034e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -20363,17 +20363,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.483471509223E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.516233054559E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.774236140842E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.203880e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.230490e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -20394,129 +20394,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.320174 │ │ │ │ +Vacc_SASA: Time elapsed: 7.200387 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.605188e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.462889e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.641970e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.448190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.208960e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.029140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.753297e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.240360e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.843192e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.330017e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.049122e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.553956e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.213024e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.743070e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.377853e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.915870e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.544578e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.118360e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.710804e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.314334e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.877275e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.513830e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.041181e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.712051e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.414164e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.486415e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.628872e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.696276e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -20525,17 +20525,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.849546283812E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.146958313419E-02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.539100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.700200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -20581,127 +20581,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00106787 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.291504 │ │ │ │ +Vacc_SASA: Time elapsed: 7.389334 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.646503e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.783860e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.690530e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.477840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.227920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.419110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.117759e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.832939e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 652367.043511 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.205690e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.925323e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.625442e+04 │ │ │ │ Vprtstp: contraction number = 6.625442e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.091545 │ │ │ │ Vnewton: Attempting damping, relres = 0.542935 │ │ │ │ Vnewton: Damping accepted, relres = 0.091545 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.154497e-02 │ │ │ │ Vprtstp: contraction number = 9.154497e-02 │ │ │ │ Vnewton: Using errtol_s: 59720.919943 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.402224e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.144260e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.669735e+03 │ │ │ │ Vprtstp: contraction number = 8.669735e+03 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.196277e-02 │ │ │ │ Vprtstp: contraction number = 1.306764e-01 │ │ │ │ Vnewton: Using errtol_s: 7804.116477 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.563323e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.325934e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.277730e+03 │ │ │ │ Vprtstp: contraction number = 1.277730e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.762772e-03 │ │ │ │ Vprtstp: contraction number = 1.473548e-01 │ │ │ │ Vnewton: Using errtol_s: 1149.974141 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.723217e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.496677e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.050893e+02 │ │ │ │ Vprtstp: contraction number = 2.050893e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.829401e-04 │ │ │ │ Vprtstp: contraction number = 1.605086e-01 │ │ │ │ Vnewton: Using errtol_s: 184.580789 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.884830e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.686053e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.556662e+01 │ │ │ │ Vprtstp: contraction number = 3.556662e+01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.906742e-05 │ │ │ │ Vprtstp: contraction number = 1.734198e-01 │ │ │ │ Vnewton: Using errtol_s: 32.009971 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.046219e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.871442e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.633566e+00 │ │ │ │ Vprtstp: contraction number = 6.633566e+00 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.151612e-06 │ │ │ │ Vprtstp: contraction number = 1.865109e-01 │ │ │ │ Vnewton: Using errtol_s: 5.970210 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.206046e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005491e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.319897e+00 │ │ │ │ Vprtstp: contraction number = 1.319897e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.820919e-06 │ │ │ │ Vprtstp: contraction number = 1.989725e-01 │ │ │ │ Vnewton: Using errtol_s: 1.187907 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.365608e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024180e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.771301e-01 │ │ │ │ Vprtstp: contraction number = 2.771301e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.823263e-07 │ │ │ │ Vprtstp: contraction number = 2.099634e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.371720e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.444545e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.551222e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.623348e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -20710,15 +20710,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.030362261326E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.051459785687E-02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.275920e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.347440e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ @@ -20741,129 +20741,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.250843 │ │ │ │ +Vacc_SASA: Time elapsed: 16.641295 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.812211e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.857560e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.617040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.510650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.140980e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.479920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.138877e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233127e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.147807e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.242253e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.167917e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.264249e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184069e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.283555e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200263e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.303317e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.216502e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322502e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232769e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.340520e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.248842e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.358332e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265134e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.377150e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.389062e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.460257e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.597628e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.670554e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -20872,17 +20872,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.211035436477E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.542244232526E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.766290532541E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.642200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.609600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -20928,127 +20928,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0370217 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.320134 │ │ │ │ +Vacc_SASA: Time elapsed: 16.474358 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.904476e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.920388e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.639770e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.458140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.210580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.419030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.476755e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.593375e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7064626.020092 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.485387e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.602625e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.009458e+05 │ │ │ │ Vprtstp: contraction number = 6.009458e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.077277 │ │ │ │ Vnewton: Attempting damping, relres = 0.536445 │ │ │ │ Vnewton: Damping accepted, relres = 0.077277 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.727667e-02 │ │ │ │ Vprtstp: contraction number = 7.727667e-02 │ │ │ │ Vnewton: Using errtol_s: 545930.796082 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.504940e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.624924e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.090350e+04 │ │ │ │ Vprtstp: contraction number = 8.090350e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.034337e-02 │ │ │ │ Vprtstp: contraction number = 1.338486e-01 │ │ │ │ Vnewton: Using errtol_s: 73072.056615 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521063e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.644772e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.317148e+04 │ │ │ │ Vprtstp: contraction number = 1.317148e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.678394e-03 │ │ │ │ Vprtstp: contraction number = 1.622676e-01 │ │ │ │ Vnewton: Using errtol_s: 11857.226595 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.537166e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.664801e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.401584e+03 │ │ │ │ Vprtstp: contraction number = 2.401584e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.059541e-04 │ │ │ │ Vprtstp: contraction number = 1.822898e-01 │ │ │ │ Vnewton: Using errtol_s: 2161.451428 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.553277e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.683624e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.616256e+02 │ │ │ │ Vprtstp: contraction number = 4.616256e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.880932e-05 │ │ │ │ Vprtstp: contraction number = 1.922161e-01 │ │ │ │ Vnewton: Using errtol_s: 415.465831 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.569453e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.703669e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.389879e+01 │ │ │ │ Vprtstp: contraction number = 8.389879e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.068835e-05 │ │ │ │ Vprtstp: contraction number = 1.817458e-01 │ │ │ │ Vnewton: Using errtol_s: 75.509189 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.585487e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.723334e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.600785e+01 │ │ │ │ Vprtstp: contraction number = 1.600785e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.039328e-06 │ │ │ │ Vprtstp: contraction number = 1.907991e-01 │ │ │ │ Vnewton: Using errtol_s: 14.407086 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.601636e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740986e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.576512e+00 │ │ │ │ Vprtstp: contraction number = 3.576512e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.556310e-07 │ │ │ │ Vprtstp: contraction number = 2.234222e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.376819e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.449066e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.637995e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.709510e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -21057,27 +21057,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.057106214068E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.516201956521E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.774250460752E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.210240e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.222280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.624194e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.767709e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:19:49 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:46:59 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -21430,129 +21430,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.299036 │ │ │ │ +Vacc_SASA: Time elapsed: 7.525015 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.543268e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.792341e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.671040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.482670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.323570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.379290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.973552e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022870e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089157e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.115065e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.293867e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350234e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.467847e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.549082e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.639244e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.741552e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.807933e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.923804e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.977032e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.105220e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.146074e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.302281e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.314757e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.483712e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.447842e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.521866e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.619530e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.690914e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21561,17 +21561,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.136518672902E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 4.355357372613E+01 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.752320511857E+01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.191800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.690700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -21617,127 +21617,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00231815 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 6.900635 │ │ │ │ +Vacc_SASA: Time elapsed: 7.516171 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.538136e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.119406e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.618030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368960e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.118510e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.249230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.383136e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.636014e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2402140.419777 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.473406e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.729054e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.993407e+05 │ │ │ │ Vprtstp: contraction number = 1.993407e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.074788 │ │ │ │ Vnewton: Attempting damping, relres = 0.535005 │ │ │ │ Vnewton: Damping accepted, relres = 0.074788 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.478844e-02 │ │ │ │ Vprtstp: contraction number = 7.478844e-02 │ │ │ │ Vnewton: Using errtol_s: 179652.345700 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.675779e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.963383e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.540846e+04 │ │ │ │ Vprtstp: contraction number = 2.540846e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.520223e-03 │ │ │ │ Vprtstp: contraction number = 1.272954e-01 │ │ │ │ Vnewton: Using errtol_s: 22868.913120 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.847127e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.172236e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.863220e+03 │ │ │ │ Vprtstp: contraction number = 3.863220e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.447432e-03 │ │ │ │ Vprtstp: contraction number = 1.520376e-01 │ │ │ │ Vnewton: Using errtol_s: 3476.934666 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.011190e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.357222e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.609951e+02 │ │ │ │ Vprtstp: contraction number = 6.609951e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.476530e-04 │ │ │ │ Vprtstp: contraction number = 1.710982e-01 │ │ │ │ Vnewton: Using errtol_s: 594.897360 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.174214e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.560832e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.229316e+02 │ │ │ │ Vprtstp: contraction number = 1.229316e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.605831e-05 │ │ │ │ Vprtstp: contraction number = 1.859792e-01 │ │ │ │ Vnewton: Using errtol_s: 110.638524 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.335670e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.765478e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.422381e+01 │ │ │ │ Vprtstp: contraction number = 2.422381e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.075836e-06 │ │ │ │ Vprtstp: contraction number = 1.970510e-01 │ │ │ │ Vnewton: Using errtol_s: 21.801431 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.498883e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.970766e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.026312e+00 │ │ │ │ Vprtstp: contraction number = 5.026312e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.883187e-06 │ │ │ │ Vprtstp: contraction number = 2.074947e-01 │ │ │ │ Vnewton: Using errtol_s: 4.523681 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.659678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.176304e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.096485e+00 │ │ │ │ Vprtstp: contraction number = 1.096485e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.108154e-07 │ │ │ │ Vprtstp: contraction number = 2.181490e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.405031e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.476747e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.705736e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.774331e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21746,15 +21746,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.937401577775E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 4.174168231022E+02 kT │ │ │ │ Vpmg_energy: dielEnergy = 2.811735250011E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.290350e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.328290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -21777,129 +21777,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.311516 │ │ │ │ +Vacc_SASA: Time elapsed: 7.465876 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.593871e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.808897e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.584900e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.505290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.168110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.519220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.734753e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.312407e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.822766e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.406192e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.025774e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.639336e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.188262e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.829609e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.349142e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.022327e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.511433e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.215950e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.673811e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.410954e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.833915e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.608457e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.000126e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.802669e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.391609e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.462814e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.644093e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.717268e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21908,15 +21908,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.911964187079E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.802931672989E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.840794517786E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.195600e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.870100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -21964,127 +21964,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00427913 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.306944 │ │ │ │ +Vacc_SASA: Time elapsed: 7.462527 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.189330e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.441196e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.609830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.561180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.185810e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.658170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.129937e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.988987e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3438753.706105 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.217983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.083625e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.983675e+05 │ │ │ │ Vprtstp: contraction number = 2.983675e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.078821 │ │ │ │ Vnewton: Attempting damping, relres = 0.537150 │ │ │ │ Vnewton: Damping accepted, relres = 0.078821 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.882110e-02 │ │ │ │ Vprtstp: contraction number = 7.882110e-02 │ │ │ │ Vnewton: Using errtol_s: 271046.361497 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.417805e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.330303e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.000218e+04 │ │ │ │ Vprtstp: contraction number = 4.000218e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.049665e-02 │ │ │ │ Vprtstp: contraction number = 1.331706e-01 │ │ │ │ Vnewton: Using errtol_s: 36095.399051 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.579817e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.538426e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.428391e+03 │ │ │ │ Vprtstp: contraction number = 6.428391e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.682686e-03 │ │ │ │ Vprtstp: contraction number = 1.603069e-01 │ │ │ │ Vnewton: Using errtol_s: 5786.342471 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.744633e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.747244e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.149080e+03 │ │ │ │ Vprtstp: contraction number = 1.149080e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.007422e-04 │ │ │ │ Vprtstp: contraction number = 1.787275e-01 │ │ │ │ Vnewton: Using errtol_s: 1034.178484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.908433e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.951879e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.202083e+02 │ │ │ │ Vprtstp: contraction number = 2.202083e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.763359e-05 │ │ │ │ Vprtstp: contraction number = 1.916378e-01 │ │ │ │ Vnewton: Using errtol_s: 198.187725 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.071583e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.015564e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.389925e+01 │ │ │ │ Vprtstp: contraction number = 4.389925e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.148943e-05 │ │ │ │ Vprtstp: contraction number = 1.993531e-01 │ │ │ │ Vnewton: Using errtol_s: 39.509333 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.238150e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036476e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.964795e+00 │ │ │ │ Vprtstp: contraction number = 8.964795e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.346291e-06 │ │ │ │ Vprtstp: contraction number = 2.042129e-01 │ │ │ │ Vnewton: Using errtol_s: 8.068316 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.400407e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057335e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.877921e+00 │ │ │ │ Vprtstp: contraction number = 1.877921e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.914947e-07 │ │ │ │ Vprtstp: contraction number = 2.094773e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.398473e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.470676e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.748735e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.823726e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -22093,17 +22093,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.727005736130E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.988671053842E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.487788509003E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.271260e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.312480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -22124,129 +22124,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.283520 │ │ │ │ +Vacc_SASA: Time elapsed: 16.656119 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.821277e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.862931e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.625070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.571220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.232030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.468260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143813e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.269108e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.152707e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.278420e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.172697e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302812e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.189061e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.322730e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.205375e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.343870e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.221864e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.364726e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238176e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.385428e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.254239e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.406783e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.270424e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427683e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.389586e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.462227e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.748597e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.822611e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -22255,17 +22255,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.095882318015E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.878073055635E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.902406349449E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.614500e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.705700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -22311,127 +22311,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0124605 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.283597 │ │ │ │ +Vacc_SASA: Time elapsed: 16.649700 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.890737e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.928601e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.605490e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.444480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.142110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.341610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.480292e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.645241e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 5736524.194850 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.489130e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.654536e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.767730e+05 │ │ │ │ Vprtstp: contraction number = 4.767730e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.075286 │ │ │ │ Vnewton: Attempting damping, relres = 0.535307 │ │ │ │ Vnewton: Damping accepted, relres = 0.075286 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.528638e-02 │ │ │ │ Vprtstp: contraction number = 7.528638e-02 │ │ │ │ Vnewton: Using errtol_s: 431882.117004 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.508420e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.678379e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.255964e+04 │ │ │ │ Vprtstp: contraction number = 6.255964e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.827684e-03 │ │ │ │ Vprtstp: contraction number = 1.305373e-01 │ │ │ │ Vnewton: Using errtol_s: 56376.745785 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.524506e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.698696e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.936134e+03 │ │ │ │ Vprtstp: contraction number = 9.936134e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.558974e-03 │ │ │ │ Vprtstp: contraction number = 1.586309e-01 │ │ │ │ Vnewton: Using errtol_s: 8943.094496 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.540509e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.718922e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.786775e+03 │ │ │ │ Vprtstp: contraction number = 1.786775e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.803288e-04 │ │ │ │ Vprtstp: contraction number = 1.798162e-01 │ │ │ │ Vnewton: Using errtol_s: 1608.113190 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.556420e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.738606e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.548476e+02 │ │ │ │ Vprtstp: contraction number = 3.548476e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.567220e-05 │ │ │ │ Vprtstp: contraction number = 1.985960e-01 │ │ │ │ Vnewton: Using errtol_s: 319.364924 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.572419e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.757085e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.691838e+01 │ │ │ │ Vprtstp: contraction number = 7.691838e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.206774e-05 │ │ │ │ Vprtstp: contraction number = 2.167643e-01 │ │ │ │ Vnewton: Using errtol_s: 69.226906 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.588415e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.776286e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.836013e+01 │ │ │ │ Vprtstp: contraction number = 1.836013e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.880520e-06 │ │ │ │ Vprtstp: contraction number = 2.386958e-01 │ │ │ │ Vnewton: Using errtol_s: 16.524170 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.604515e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.795714e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.825966e+00 │ │ │ │ Vprtstp: contraction number = 4.825966e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.571442e-07 │ │ │ │ Vprtstp: contraction number = 2.628499e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.365921e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.437475e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.664172e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.734883e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -22440,27 +22440,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.027416628019E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.032769300439E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.516953015159E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.241420e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.303730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.626421e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.821682e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:21:36 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:50:00 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -22813,129 +22813,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.311240 │ │ │ │ +Vacc_SASA: Time elapsed: 7.442335 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.576577e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.723706e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.646110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.469150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.118730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.447160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.994269e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013206e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087105e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107825e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.285632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.341073e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.446668e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.533880e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.609257e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.733123e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.772718e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.934153e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.936934e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.130058e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.100286e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.327829e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.263969e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.525334e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.390988e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.462764e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.669097e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.740880e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -22944,17 +22944,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.578940273076E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.464055888829E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 7.268608527503E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.788300e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.624000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -23000,138 +23000,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.246197 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.276534 │ │ │ │ +Vacc_SASA: Time elapsed: 7.391184 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.709473e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.785999e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.639560e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.463290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.210760e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.444720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.446611e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.745761e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 7187187.181934 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.534554e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.837562e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.181171e+05 │ │ │ │ Vprtstp: contraction number = 6.181171e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.078820 │ │ │ │ Vnewton: Attempting damping, relres = 0.536981 │ │ │ │ Vnewton: Damping accepted, relres = 0.078820 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.881989e-02 │ │ │ │ Vprtstp: contraction number = 7.881989e-02 │ │ │ │ Vnewton: Using errtol_s: 566493.329521 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.729894e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.065015e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.371738e+04 │ │ │ │ Vprtstp: contraction number = 8.371738e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.055690e-02 │ │ │ │ Vprtstp: contraction number = 1.339370e-01 │ │ │ │ Vnewton: Using errtol_s: 75874.442084 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.890867e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.268950e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.390337e+04 │ │ │ │ Vprtstp: contraction number = 1.390337e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.741620e-03 │ │ │ │ Vprtstp: contraction number = 1.649745e-01 │ │ │ │ Vnewton: Using errtol_s: 12517.346695 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.053035e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.471588e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.648048e+03 │ │ │ │ Vprtstp: contraction number = 2.648048e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.316551e-04 │ │ │ │ Vprtstp: contraction number = 1.904291e-01 │ │ │ │ Vnewton: Using errtol_s: 2383.666964 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.214138e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.677816e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.422627e+02 │ │ │ │ Vprtstp: contraction number = 5.422627e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.790546e-05 │ │ │ │ Vprtstp: contraction number = 2.047472e-01 │ │ │ │ Vnewton: Using errtol_s: 488.049223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.374871e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.882288e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.184576e+02 │ │ │ │ Vprtstp: contraction number = 1.184576e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.483378e-05 │ │ │ │ Vprtstp: contraction number = 2.184475e-01 │ │ │ │ Vnewton: Using errtol_s: 106.613126 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.536592e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.088594e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.976808e+01 │ │ │ │ Vprtstp: contraction number = 2.976808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.727649e-06 │ │ │ │ Vprtstp: contraction number = 2.512947e-01 │ │ │ │ Vnewton: Using errtol_s: 26.791312 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.700120e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.287770e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.888808e+00 │ │ │ │ Vprtstp: contraction number = 8.888808e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.113097e-06 │ │ │ │ Vprtstp: contraction number = 2.986056e-01 │ │ │ │ Vnewton: Using errtol_s: 8.000035 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.860218e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.497485e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.963970e+00 │ │ │ │ Vprtstp: contraction number = 2.963970e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.711568e-07 │ │ │ │ Vprtstp: contraction number = 3.334452e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.540810e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.612940e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.916964e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.988738e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -23140,15 +23140,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.679263931619E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.125861211589E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.606777456856E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.154560e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.273570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -23171,129 +23171,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.346901 │ │ │ │ +Vacc_SASA: Time elapsed: 7.477160 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.661483e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.804883e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.612250e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.472750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.204140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.409940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.940973e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.630563e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.031580e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.722325e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.230865e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.954709e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.393441e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.140208e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.555452e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.331406e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.717302e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.525770e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.879839e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.717318e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.041554e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.913116e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.203802e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.108438e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.388478e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.461245e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.632542e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.703895e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -23302,17 +23302,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.880126377174E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.532414743910E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.786700e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.730900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -23358,127 +23358,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.000694544 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.264023 │ │ │ │ +Vacc_SASA: Time elapsed: 7.378318 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.739781e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.854256e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.622650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.477140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.101470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.418560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.287478e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.233350e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 947577.428093 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.375634e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.327519e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.028571e+05 │ │ │ │ Vprtstp: contraction number = 1.028571e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.100178 │ │ │ │ Vnewton: Attempting damping, relres = 0.546680 │ │ │ │ Vnewton: Damping accepted, relres = 0.100178 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.001782e-01 │ │ │ │ Vprtstp: contraction number = 1.001782e-01 │ │ │ │ Vnewton: Using errtol_s: 94926.584698 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.574439e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.558867e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.470559e+04 │ │ │ │ Vprtstp: contraction number = 1.470559e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.405726e-02 │ │ │ │ Vprtstp: contraction number = 1.403226e-01 │ │ │ │ Vnewton: Using errtol_s: 13320.343474 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.737963e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.748382e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.349875e+03 │ │ │ │ Vprtstp: contraction number = 2.349875e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.232971e-03 │ │ │ │ Vprtstp: contraction number = 1.588482e-01 │ │ │ │ Vnewton: Using errtol_s: 2115.913123 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.901297e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.944390e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.041926e+02 │ │ │ │ Vprtstp: contraction number = 4.041926e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.839085e-04 │ │ │ │ Vprtstp: contraction number = 1.719272e-01 │ │ │ │ Vnewton: Using errtol_s: 363.783073 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.064488e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013109e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.386262e+01 │ │ │ │ Vprtstp: contraction number = 7.386262e+01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.015424e-05 │ │ │ │ Vprtstp: contraction number = 1.827368e-01 │ │ │ │ Vnewton: Using errtol_s: 66.476570 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.227613e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032016e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.423266e+01 │ │ │ │ Vprtstp: contraction number = 1.423266e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.351805e-05 │ │ │ │ Vprtstp: contraction number = 1.926905e-01 │ │ │ │ Vnewton: Using errtol_s: 12.809401 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.392123e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.050961e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.877145e+00 │ │ │ │ Vprtstp: contraction number = 2.877145e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.732685e-06 │ │ │ │ Vprtstp: contraction number = 2.021508e-01 │ │ │ │ Vnewton: Using errtol_s: 2.589431 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.556920e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070470e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.073349e-01 │ │ │ │ Vprtstp: contraction number = 6.073349e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.768409e-07 │ │ │ │ Vprtstp: contraction number = 2.110894e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.395005e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.465980e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624039e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.695780e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -23487,17 +23487,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.348045314741E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.080172074466E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.211710e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.339300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -23518,129 +23518,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 15.356742 │ │ │ │ +Vacc_SASA: Time elapsed: 16.546967 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.724650e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.850238e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.614410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.557910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.275920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.397980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.149549e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.279672e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158561e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289003e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.178700e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.313246e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.195335e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.334381e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212212e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.355009e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228718e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.375992e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.245349e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.397244e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.262056e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.418398e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.278482e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.439438e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.415569e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.488737e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.751777e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.824120e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -23649,17 +23649,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.727728107537E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.464487511349E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 7.268391520583E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.357000e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.131300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -23705,138 +23705,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.239586 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.247050 │ │ │ │ +Vacc_SASA: Time elapsed: 16.734464 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.909986e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.974246e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.637160e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.620900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.401650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.635230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.490796e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.661214e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8056801.731105 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.499919e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.670621e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.019948e+05 │ │ │ │ Vprtstp: contraction number = 7.019948e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.080001 │ │ │ │ Vnewton: Attempting damping, relres = 0.537427 │ │ │ │ Vnewton: Damping accepted, relres = 0.080001 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.000142e-02 │ │ │ │ Vprtstp: contraction number = 8.000142e-02 │ │ │ │ Vnewton: Using errtol_s: 644555.552257 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.519836e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.694395e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.545628e+04 │ │ │ │ Vprtstp: contraction number = 9.545628e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.074028e-02 │ │ │ │ Vprtstp: contraction number = 1.342512e-01 │ │ │ │ Vnewton: Using errtol_s: 86532.331514 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.535872e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.714714e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.576216e+04 │ │ │ │ Vprtstp: contraction number = 1.576216e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.761379e-03 │ │ │ │ Vprtstp: contraction number = 1.639975e-01 │ │ │ │ Vnewton: Using errtol_s: 14191.084898 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.551960e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.735058e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.960538e+03 │ │ │ │ Vprtstp: contraction number = 2.960538e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.307659e-04 │ │ │ │ Vprtstp: contraction number = 1.877880e-01 │ │ │ │ Vnewton: Using errtol_s: 2664.915408 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.567951e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.755494e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.967294e+02 │ │ │ │ Vprtstp: contraction number = 5.967294e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.666049e-05 │ │ │ │ Vprtstp: contraction number = 2.015337e-01 │ │ │ │ Vnewton: Using errtol_s: 537.070343 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.584006e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.780944e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.275865e+02 │ │ │ │ Vprtstp: contraction number = 1.275865e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.425245e-05 │ │ │ │ Vprtstp: contraction number = 2.138065e-01 │ │ │ │ Vnewton: Using errtol_s: 114.829153 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.599942e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.802899e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.141071e+01 │ │ │ │ Vprtstp: contraction number = 3.141071e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.508796e-06 │ │ │ │ Vprtstp: contraction number = 2.461890e-01 │ │ │ │ Vnewton: Using errtol_s: 28.269675 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.616179e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.826826e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.244202e+00 │ │ │ │ Vprtstp: contraction number = 9.244202e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.032654e-06 │ │ │ │ Vprtstp: contraction number = 2.943044e-01 │ │ │ │ Vnewton: Using errtol_s: 8.319891 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.632177e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.846759e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.069585e+00 │ │ │ │ Vprtstp: contraction number = 3.069585e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.428937e-07 │ │ │ │ Vprtstp: contraction number = 3.320508e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.537783e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.612041e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.019042e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.094343e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, -41.2575) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 16.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, -41.2575) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 27.9102) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -23845,27 +23845,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.898743294947E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.125893253171E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.606732677067E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.159080e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.246880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.654304e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.873509e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:23:24 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:52:50 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -24218,129 +24218,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.277758 │ │ │ │ +Vacc_SASA: Time elapsed: 7.341010 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.549841e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.619389e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.597870e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.483650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.164880e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.576780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.955960e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004112e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.084693e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097951e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.281692e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329171e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.443887e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521137e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.603141e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.718210e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.765056e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910387e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.926405e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.104534e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.087675e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.303789e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.248829e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.499881e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.375511e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.447167e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.649814e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.723516e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24349,17 +24349,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.439783180216E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.890574221449E+02 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.267284045292E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.056600e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.652400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -24405,127 +24405,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00201979 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.191480 │ │ │ │ +Vacc_SASA: Time elapsed: 7.425545 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.746083e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.055320e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.589400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.519440e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.163830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.842980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.329969e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.649192e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1602777.342155 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.417030e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.744857e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.455767e+05 │ │ │ │ Vprtstp: contraction number = 1.455767e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.082108 │ │ │ │ Vnewton: Attempting damping, relres = 0.538752 │ │ │ │ Vnewton: Damping accepted, relres = 0.082108 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.210786e-02 │ │ │ │ Vprtstp: contraction number = 8.210786e-02 │ │ │ │ Vnewton: Using errtol_s: 131600.616465 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.615386e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.996516e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.947215e+04 │ │ │ │ Vprtstp: contraction number = 1.947215e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.093564e-02 │ │ │ │ Vprtstp: contraction number = 1.331863e-01 │ │ │ │ Vnewton: Using errtol_s: 17527.393818 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.778223e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.207768e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.986234e+03 │ │ │ │ Vprtstp: contraction number = 2.986234e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.676878e-03 │ │ │ │ Vprtstp: contraction number = 1.533407e-01 │ │ │ │ Vnewton: Using errtol_s: 2687.662365 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.942109e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.418794e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.993905e+02 │ │ │ │ Vprtstp: contraction number = 4.993905e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.804220e-04 │ │ │ │ Vprtstp: contraction number = 1.672286e-01 │ │ │ │ Vnewton: Using errtol_s: 449.454038 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.109389e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.632026e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.039598e+01 │ │ │ │ Vprtstp: contraction number = 9.039598e+01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.075969e-05 │ │ │ │ Vprtstp: contraction number = 1.810118e-01 │ │ │ │ Vnewton: Using errtol_s: 81.356480 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.272734e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.849854e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.755931e+01 │ │ │ │ Vprtstp: contraction number = 1.755931e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.860000e-06 │ │ │ │ Vprtstp: contraction number = 1.942486e-01 │ │ │ │ Vnewton: Using errtol_s: 15.803384 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.435859e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.056780e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.630601e+00 │ │ │ │ Vprtstp: contraction number = 3.630601e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.038674e-06 │ │ │ │ Vprtstp: contraction number = 2.067621e-01 │ │ │ │ Vnewton: Using errtol_s: 3.267541 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.598765e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.262408e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.904977e-01 │ │ │ │ Vprtstp: contraction number = 7.904977e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.438845e-07 │ │ │ │ Vprtstp: contraction number = 2.177319e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.392929e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.464523e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.777823e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.854113e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24534,17 +24534,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.337843047091E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.452499065480E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.155272443356E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.276030e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.322820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -24565,129 +24565,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.301730 │ │ │ │ +Vacc_SASA: Time elapsed: 7.476716 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.594773e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.805950e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.585820e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.501750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.164000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.338260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.669593e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.396236e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.762763e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.490116e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.961893e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.720385e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.126098e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.908376e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.288935e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.101217e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.452662e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.298020e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.615015e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.485454e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.778117e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.682801e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.942773e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.877315e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.396671e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.467868e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.639306e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.711287e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24696,17 +24696,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.047547930931E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.326714299389E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.630706107593E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.015100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.969400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -24752,138 +24752,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.208695 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.298262 │ │ │ │ +Vacc_SASA: Time elapsed: 7.470907 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.587405e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.829441e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.621580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.417060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.210780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.266900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.109600e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.102201e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6744887.867090 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.197446e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.195313e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.873341e+05 │ │ │ │ Vprtstp: contraction number = 5.873341e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.079798 │ │ │ │ Vnewton: Attempting damping, relres = 0.537526 │ │ │ │ Vnewton: Damping accepted, relres = 0.079798 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.979817e-02 │ │ │ │ Vprtstp: contraction number = 7.979817e-02 │ │ │ │ Vnewton: Using errtol_s: 538229.715979 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.392618e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.428538e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.003940e+04 │ │ │ │ Vprtstp: contraction number = 8.003940e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.075173e-02 │ │ │ │ Vprtstp: contraction number = 1.347366e-01 │ │ │ │ Vnewton: Using errtol_s: 72519.230886 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.552838e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.631215e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.324771e+04 │ │ │ │ Vprtstp: contraction number = 1.324771e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.768162e-03 │ │ │ │ Vprtstp: contraction number = 1.644537e-01 │ │ │ │ Vnewton: Using errtol_s: 11926.055102 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.713902e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.835052e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.493439e+03 │ │ │ │ Vprtstp: contraction number = 2.493439e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.328041e-04 │ │ │ │ Vprtstp: contraction number = 1.882203e-01 │ │ │ │ Vnewton: Using errtol_s: 2244.726103 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.874865e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.004011e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.093161e+02 │ │ │ │ Vprtstp: contraction number = 5.093161e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.796477e-05 │ │ │ │ Vprtstp: contraction number = 2.042186e-01 │ │ │ │ Vnewton: Using errtol_s: 458.414752 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.036642e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024311e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115992e+02 │ │ │ │ Vprtstp: contraction number = 1.115992e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.489139e-05 │ │ │ │ Vprtstp: contraction number = 2.191046e-01 │ │ │ │ Vnewton: Using errtol_s: 100.440778 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.197751e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044566e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.141695e+01 │ │ │ │ Vprtstp: contraction number = 3.141695e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.192112e-06 │ │ │ │ Vprtstp: contraction number = 2.815124e-01 │ │ │ │ Vnewton: Using errtol_s: 28.275326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.358667e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064795e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.143181e+01 │ │ │ │ Vprtstp: contraction number = 1.143181e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.525422e-06 │ │ │ │ Vprtstp: contraction number = 3.638791e-01 │ │ │ │ Vnewton: Using errtol_s: 10.288800 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.521479e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085221e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.900145e+00 │ │ │ │ Vprtstp: contraction number = 4.900145e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 6.538480e-07 │ │ │ │ Vprtstp: contraction number = 4.286342e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.536988e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.608988e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.911721e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.981654e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24892,17 +24892,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.068941239771E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.027128342703E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.130929384938E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.174570e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.221040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -24923,129 +24923,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 15.382226 │ │ │ │ +Vacc_SASA: Time elapsed: 16.648117 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.727641e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.858982e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.599120e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.497580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.039680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.405490e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.145921e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.296122e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154729e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.305416e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174582e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329274e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190690e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.349161e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206777e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.369418e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222837e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.389578e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.239022e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.409469e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255193e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.429312e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271287e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.449809e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.378304e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.448338e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.694825e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.767548e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -25054,17 +25054,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.318490670487E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.359627523071E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.777157121148E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.852000e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.991700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -25110,138 +25110,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.208525 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.211142 │ │ │ │ +Vacc_SASA: Time elapsed: 16.367154 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.917205e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.944671e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.605500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.455330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.410460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.725650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.484211e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.669024e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8257970.099902 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.493102e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.678246e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.174738e+05 │ │ │ │ Vprtstp: contraction number = 7.174738e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.079654 │ │ │ │ Vnewton: Attempting damping, relres = 0.537366 │ │ │ │ Vnewton: Damping accepted, relres = 0.079654 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.965353e-02 │ │ │ │ Vprtstp: contraction number = 7.965353e-02 │ │ │ │ Vnewton: Using errtol_s: 657776.459467 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.512403e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.702116e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.738355e+04 │ │ │ │ Vprtstp: contraction number = 9.738355e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.068030e-02 │ │ │ │ Vprtstp: contraction number = 1.340844e-01 │ │ │ │ Vnewton: Using errtol_s: 88197.583593 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.528679e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.721014e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.590859e+04 │ │ │ │ Vprtstp: contraction number = 1.590859e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.734478e-03 │ │ │ │ Vprtstp: contraction number = 1.623998e-01 │ │ │ │ Vnewton: Using errtol_s: 14323.269837 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.544604e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.741031e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.927974e+03 │ │ │ │ Vprtstp: contraction number = 2.927974e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.191803e-04 │ │ │ │ Vprtstp: contraction number = 1.840209e-01 │ │ │ │ Vnewton: Using errtol_s: 2635.781086 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.560583e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.760575e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.843569e+02 │ │ │ │ Vprtstp: contraction number = 5.843569e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.369066e-05 │ │ │ │ Vprtstp: contraction number = 1.995445e-01 │ │ │ │ Vnewton: Using errtol_s: 525.955563 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.576417e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.779839e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.235877e+02 │ │ │ │ Vprtstp: contraction number = 1.235877e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.346947e-05 │ │ │ │ Vprtstp: contraction number = 2.114827e-01 │ │ │ │ Vnewton: Using errtol_s: 111.230501 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.592581e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.799427e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.351690e+01 │ │ │ │ Vprtstp: contraction number = 3.351690e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.652870e-06 │ │ │ │ Vprtstp: contraction number = 2.711962e-01 │ │ │ │ Vnewton: Using errtol_s: 30.165292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.608595e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.819795e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.181991e+01 │ │ │ │ Vprtstp: contraction number = 1.181991e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.288222e-06 │ │ │ │ Vprtstp: contraction number = 3.526602e-01 │ │ │ │ Vnewton: Using errtol_s: 10.638098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.625741e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.840582e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.017523e+00 │ │ │ │ Vprtstp: contraction number = 5.017523e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.468381e-07 │ │ │ │ Vprtstp: contraction number = 4.244906e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.539826e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.613734e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.884189e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.959869e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -25250,27 +25250,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.367295559146E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.051945297594E+05 kT │ │ │ │ Vpmg_energy: dielEnergy = 5.247887391423E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.170510e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.215730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.647745e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.867555e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:25:13 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:55:40 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -25623,129 +25623,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.263596 │ │ │ │ +Vacc_SASA: Time elapsed: 7.368655 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.568598e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.624812e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.620620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.463150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.213470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.286150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.995897e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005064e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088501e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099019e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.284614e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.334786e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.446088e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.524068e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.607686e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.719389e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.767376e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.910541e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.928220e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.102246e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.090638e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.282012e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.252385e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.473866e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.376364e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.448361e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.621594e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.692083e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -25754,15 +25754,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.504309500280E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.755208046486E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 8.724652508101E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.017100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.695400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -25810,127 +25810,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00330279 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.229289 │ │ │ │ +Vacc_SASA: Time elapsed: 7.357943 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.072816e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.264728e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.577290e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.521220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.050860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.647700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.365991e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.641070e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2662068.021804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.452479e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.739363e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.456208e+05 │ │ │ │ Vprtstp: contraction number = 2.456208e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.083386 │ │ │ │ Vnewton: Attempting damping, relres = 0.539586 │ │ │ │ Vnewton: Damping accepted, relres = 0.083386 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.338571e-02 │ │ │ │ Vprtstp: contraction number = 8.338571e-02 │ │ │ │ Vnewton: Using errtol_s: 221978.424581 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.650068e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.988708e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.405567e+04 │ │ │ │ Vprtstp: contraction number = 3.405567e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.151500e-02 │ │ │ │ Vprtstp: contraction number = 1.380932e-01 │ │ │ │ Vnewton: Using errtol_s: 30653.716000 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.811985e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.193711e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.435916e+03 │ │ │ │ Vprtstp: contraction number = 5.435916e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.837816e-03 │ │ │ │ Vprtstp: contraction number = 1.596019e-01 │ │ │ │ Vnewton: Using errtol_s: 4892.390079 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.973248e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.405850e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.557902e+02 │ │ │ │ Vprtstp: contraction number = 9.557902e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.231381e-04 │ │ │ │ Vprtstp: contraction number = 1.758273e-01 │ │ │ │ Vnewton: Using errtol_s: 860.215698 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.135229e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.609919e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.830694e+02 │ │ │ │ Vprtstp: contraction number = 1.830694e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.189280e-05 │ │ │ │ Vprtstp: contraction number = 1.915367e-01 │ │ │ │ Vnewton: Using errtol_s: 164.762841 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.297288e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.807214e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.747370e+01 │ │ │ │ Vprtstp: contraction number = 3.747370e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.266923e-05 │ │ │ │ Vprtstp: contraction number = 2.046964e-01 │ │ │ │ Vnewton: Using errtol_s: 33.726360 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.457827e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.019389e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.392089e+00 │ │ │ │ Vprtstp: contraction number = 8.392089e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.837224e-06 │ │ │ │ Vprtstp: contraction number = 2.239460e-01 │ │ │ │ Vnewton: Using errtol_s: 7.552883 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.620077e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.223358e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.064121e+00 │ │ │ │ Vprtstp: contraction number = 2.064121e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.978444e-07 │ │ │ │ Vprtstp: contraction number = 2.459603e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.378300e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.448444e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.744150e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.818595e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -25939,15 +25939,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.015842175556E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.339968414661E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.688675679646E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.260680e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.311190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -25970,129 +25970,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.273339 │ │ │ │ +Vacc_SASA: Time elapsed: 7.596209 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.577250e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.937145e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.598590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.476730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.070420e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.612940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.689116e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.369444e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.776547e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.464222e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.974652e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.700377e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.135572e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.882105e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.297855e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.069401e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.459340e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.254140e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.620957e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.435274e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.781663e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.623181e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.941367e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.802975e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.375731e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.446984e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.555037e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.629053e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -26101,17 +26101,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.301986990892E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.769795919653E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.974000e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.823100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -26157,127 +26157,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0030506 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.265586 │ │ │ │ +Vacc_SASA: Time elapsed: 7.383990 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.716104e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.790317e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.601700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.432000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.098670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.203820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.020675e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.886158e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1183078.697095 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.109214e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.977209e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.216317e+05 │ │ │ │ Vprtstp: contraction number = 1.216317e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.092815 │ │ │ │ Vnewton: Attempting damping, relres = 0.543699 │ │ │ │ Vnewton: Damping accepted, relres = 0.092815 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.281548e-02 │ │ │ │ Vprtstp: contraction number = 9.281548e-02 │ │ │ │ Vnewton: Using errtol_s: 109808.011526 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.307093e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.203321e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.637169e+04 │ │ │ │ Vprtstp: contraction number = 1.637169e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.245819e-02 │ │ │ │ Vprtstp: contraction number = 1.342253e-01 │ │ │ │ Vnewton: Using errtol_s: 14739.016153 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.468234e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.387890e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.481814e+03 │ │ │ │ Vprtstp: contraction number = 2.481814e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.888035e-03 │ │ │ │ Vprtstp: contraction number = 1.515497e-01 │ │ │ │ Vnewton: Using errtol_s: 2233.693882 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.629345e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.580111e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.090266e+02 │ │ │ │ Vprtstp: contraction number = 4.090266e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.111589e-04 │ │ │ │ Vprtstp: contraction number = 1.648057e-01 │ │ │ │ Vnewton: Using errtol_s: 368.125449 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.790351e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.775637e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.284721e+01 │ │ │ │ Vprtstp: contraction number = 7.284721e+01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.541690e-05 │ │ │ │ Vprtstp: contraction number = 1.780984e-01 │ │ │ │ Vnewton: Using errtol_s: 65.562559 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.951797e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.962371e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.403461e+01 │ │ │ │ Vprtstp: contraction number = 1.403461e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.067651e-05 │ │ │ │ Vprtstp: contraction number = 1.926581e-01 │ │ │ │ Vnewton: Using errtol_s: 12.631156 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.118110e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.015177e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.928656e+00 │ │ │ │ Vprtstp: contraction number = 2.928656e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.227908e-06 │ │ │ │ Vprtstp: contraction number = 2.086737e-01 │ │ │ │ Vnewton: Using errtol_s: 2.635791 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.281220e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034301e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.633899e-01 │ │ │ │ Vprtstp: contraction number = 6.633899e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.046587e-07 │ │ │ │ Vprtstp: contraction number = 2.265168e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.383703e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.454140e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.605020e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.674161e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -26286,17 +26286,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.998704747523E-02 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.756383859488E-01 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.263710e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.326830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -26317,129 +26317,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.159480 │ │ │ │ +Vacc_SASA: Time elapsed: 16.236296 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.805806e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.823283e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.605510e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.599900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.175540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.531260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.129789e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.240611e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.138475e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.250170e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158364e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.273732e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174532e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292448e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190546e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.311422e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206678e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329733e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222705e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.349292e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238938e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.368665e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255013e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.388613e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.377094e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.448941e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.642297e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.717349e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -26448,17 +26448,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.337014891966E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.757508966493E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 8.741342460079E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.457400e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.869500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -26504,127 +26504,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0127136 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.156572 │ │ │ │ +Vacc_SASA: Time elapsed: 16.813596 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.852837e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.927681e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.638150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.486470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.101600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.399200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.461239e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.606293e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3725039.964738 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.469981e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.615353e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.491722e+05 │ │ │ │ Vprtstp: contraction number = 3.491722e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.084831 │ │ │ │ Vnewton: Attempting damping, relres = 0.540016 │ │ │ │ Vnewton: Damping accepted, relres = 0.084831 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.483081e-02 │ │ │ │ Vprtstp: contraction number = 8.483081e-02 │ │ │ │ Vnewton: Using errtol_s: 315998.155182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.489494e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.640601e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.811279e+04 │ │ │ │ Vprtstp: contraction number = 4.811279e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.162816e-02 │ │ │ │ Vprtstp: contraction number = 1.370747e-01 │ │ │ │ Vnewton: Using errtol_s: 43315.357930 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.505365e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.662082e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.589005e+03 │ │ │ │ Vprtstp: contraction number = 7.589005e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.833655e-03 │ │ │ │ Vprtstp: contraction number = 1.576909e-01 │ │ │ │ Vnewton: Using errtol_s: 6830.439897 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521269e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682549e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.299757e+03 │ │ │ │ Vprtstp: contraction number = 1.299757e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.140354e-04 │ │ │ │ Vprtstp: contraction number = 1.712619e-01 │ │ │ │ Vnewton: Using errtol_s: 1169.794412 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.537410e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.701734e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.408127e+02 │ │ │ │ Vprtstp: contraction number = 2.408127e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.818247e-05 │ │ │ │ Vprtstp: contraction number = 1.852736e-01 │ │ │ │ Vnewton: Using errtol_s: 216.732029 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.553507e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.721326e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.749053e+01 │ │ │ │ Vprtstp: contraction number = 4.749053e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.147411e-05 │ │ │ │ Vprtstp: contraction number = 1.972090e-01 │ │ │ │ Vnewton: Using errtol_s: 42.741516 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.569479e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740547e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.028045e+01 │ │ │ │ Vprtstp: contraction number = 1.028045e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.483842e-06 │ │ │ │ Vprtstp: contraction number = 2.164736e-01 │ │ │ │ Vnewton: Using errtol_s: 9.252409 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.585477e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.760538e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.462555e+00 │ │ │ │ Vprtstp: contraction number = 2.462555e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.949733e-07 │ │ │ │ Vprtstp: contraction number = 2.395375e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.365228e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.436587e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.694682e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.766763e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -47.9645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, -2.4645, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -47.9645, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 6.29637, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -26633,27 +26633,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.090781383417E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.340160252589E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 6.690276945765E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.276870e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.324700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.607352e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.785447e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:26:59 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 20:58:30 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -27006,129 +27006,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.312375 │ │ │ │ +Vacc_SASA: Time elapsed: 7.387227 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.611430e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.635517e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.591190e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.413210e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.216530e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.112080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002672e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.992076e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089417e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095196e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.286883e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.324803e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.447925e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.519343e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.609680e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.698562e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.771363e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.895231e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.930744e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.072665e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.090585e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.265082e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.252461e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.445319e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.373153e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.445589e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.599053e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.666565e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -27137,17 +27137,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.018818357311E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.967662971668E+00 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.521900e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.469700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -27193,127 +27193,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.000195471 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.259902 │ │ │ │ +Vacc_SASA: Time elapsed: 7.416361 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.726342e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.885287e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.614150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.450950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.144030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.382140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.333123e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.571043e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1020818.402503 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.420618e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.663473e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.825199e+04 │ │ │ │ Vprtstp: contraction number = 9.825199e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.087060 │ │ │ │ Vnewton: Attempting damping, relres = 0.541082 │ │ │ │ Vnewton: Damping accepted, relres = 0.087060 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.706019e-02 │ │ │ │ Vprtstp: contraction number = 8.706019e-02 │ │ │ │ Vnewton: Using errtol_s: 88872.645048 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.620722e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.892268e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.300904e+04 │ │ │ │ Vprtstp: contraction number = 1.300904e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.147153e-02 │ │ │ │ Vprtstp: contraction number = 1.317655e-01 │ │ │ │ Vnewton: Using errtol_s: 11710.349561 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.783735e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.084541e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.956340e+03 │ │ │ │ Vprtstp: contraction number = 1.956340e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.724829e-03 │ │ │ │ Vprtstp: contraction number = 1.503573e-01 │ │ │ │ Vnewton: Using errtol_s: 1760.737119 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.944840e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.278333e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.204124e+02 │ │ │ │ Vprtstp: contraction number = 3.204124e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.824911e-04 │ │ │ │ Vprtstp: contraction number = 1.637792e-01 │ │ │ │ Vnewton: Using errtol_s: 288.372159 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.108006e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.459494e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.671470e+01 │ │ │ │ Vprtstp: contraction number = 5.671470e+01 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.000230e-05 │ │ │ │ Vprtstp: contraction number = 1.770048e-01 │ │ │ │ Vnewton: Using errtol_s: 51.043267 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.271514e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.654885e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.076760e+01 │ │ │ │ Vprtstp: contraction number = 1.076760e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.493208e-06 │ │ │ │ Vprtstp: contraction number = 1.898554e-01 │ │ │ │ Vnewton: Using errtol_s: 9.690841 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.435799e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.854370e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.170593e+00 │ │ │ │ Vprtstp: contraction number = 2.170593e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.913693e-06 │ │ │ │ Vprtstp: contraction number = 2.015855e-01 │ │ │ │ Vnewton: Using errtol_s: 1.953533 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.598914e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.049106e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.603679e-01 │ │ │ │ Vprtstp: contraction number = 4.603679e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.058813e-07 │ │ │ │ Vprtstp: contraction number = 2.120932e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.390782e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.462258e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.618476e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.689532e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -27322,17 +27322,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.464558654899E-03 kT │ │ │ │ Vpmg_energy: qfEnergy = 0.000000000000E+00 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.022303323465E+00 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.284980e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.317060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -27353,129 +27353,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.319086 │ │ │ │ +Vacc_SASA: Time elapsed: 7.567974 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.604992e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.894341e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.590840e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.480550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.127070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.533690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.671365e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.168389e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.759581e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.263320e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.956192e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.495694e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.115096e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.688690e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.274691e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.885997e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.435938e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.082205e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.595709e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.278010e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.757271e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.472780e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.918057e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.660746e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.371148e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.441985e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.643803e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.716580e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -27484,17 +27484,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.242044176092E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.791375610764E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.948343269624E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.447100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.414000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -27540,127 +27540,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0380116 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.306188 │ │ │ │ +Vacc_SASA: Time elapsed: 7.574099 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.494315e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.802499e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.638030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.490620e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.186250e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.370110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.076923e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.876844e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6064250.335946 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.165137e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.974356e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.053112e+05 │ │ │ │ Vprtstp: contraction number = 5.053112e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.075900 │ │ │ │ Vnewton: Attempting damping, relres = 0.535745 │ │ │ │ Vnewton: Damping accepted, relres = 0.075900 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.590004e-02 │ │ │ │ Vprtstp: contraction number = 7.590004e-02 │ │ │ │ Vnewton: Using errtol_s: 460276.842537 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.363114e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.216526e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.689298e+04 │ │ │ │ Vprtstp: contraction number = 6.689298e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 9.982301e-03 │ │ │ │ Vprtstp: contraction number = 1.315191e-01 │ │ │ │ Vnewton: Using errtol_s: 60535.174769 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.522375e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.420081e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.083906e+04 │ │ │ │ Vprtstp: contraction number = 1.083906e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.608994e-03 │ │ │ │ Vprtstp: contraction number = 1.611846e-01 │ │ │ │ Vnewton: Using errtol_s: 9757.339468 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.682477e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.624578e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.965105e+03 │ │ │ │ Vprtstp: contraction number = 1.965105e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.916449e-04 │ │ │ │ Vprtstp: contraction number = 1.812592e-01 │ │ │ │ Vnewton: Using errtol_s: 1768.607683 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.841308e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.827125e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.700829e+02 │ │ │ │ Vprtstp: contraction number = 3.700829e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.492457e-05 │ │ │ │ Vprtstp: contraction number = 1.883269e-01 │ │ │ │ Vnewton: Using errtol_s: 333.076316 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.001117e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002618e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.574998e+01 │ │ │ │ Vprtstp: contraction number = 6.574998e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.758048e-06 │ │ │ │ Vprtstp: contraction number = 1.776627e-01 │ │ │ │ Vnewton: Using errtol_s: 59.175244 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.159905e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022606e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.293454e+01 │ │ │ │ Vprtstp: contraction number = 1.293454e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.919626e-06 │ │ │ │ Vprtstp: contraction number = 1.967224e-01 │ │ │ │ Vnewton: Using errtol_s: 11.641095 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.319313e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042601e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.078562e+00 │ │ │ │ Vprtstp: contraction number = 3.078562e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.568945e-07 │ │ │ │ Vprtstp: contraction number = 2.380122e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.367288e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.439224e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.709495e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.780724e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -27669,17 +27669,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.156457994238E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.809362574174E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.917972751481E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.185890e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.191570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -27700,129 +27700,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.369514 │ │ │ │ +Vacc_SASA: Time elapsed: 15.713626 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.824364e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.756408e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.593500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.426890e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.286020e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.092200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.135630e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.242554e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.144509e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.251623e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.164514e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.274611e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180764e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.293602e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.196973e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.312577e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.213228e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.331747e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229629e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350784e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.245977e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.369880e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.262316e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.388898e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.392924e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.465566e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.614518e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.682164e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -27831,17 +27831,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.221311774650E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 9.790964149822E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.950799444075E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.260800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.293600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -27887,127 +27887,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0371815 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.285093 │ │ │ │ +Vacc_SASA: Time elapsed: 16.697543 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.899828e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.995962e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.593990e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.515720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.133590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.596400e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.473287e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.613334e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 6913573.322497 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.482103e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.625219e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.778762e+05 │ │ │ │ Vprtstp: contraction number = 5.778762e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.075994 │ │ │ │ Vnewton: Attempting damping, relres = 0.535763 │ │ │ │ Vnewton: Damping accepted, relres = 0.075994 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.599436e-02 │ │ │ │ Vprtstp: contraction number = 7.599436e-02 │ │ │ │ Vnewton: Using errtol_s: 525392.598640 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.501813e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.653337e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.670486e+04 │ │ │ │ Vprtstp: contraction number = 7.670486e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.002063e-02 │ │ │ │ Vprtstp: contraction number = 1.318602e-01 │ │ │ │ Vnewton: Using errtol_s: 69278.365005 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.517784e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.673831e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.241801e+04 │ │ │ │ Vprtstp: contraction number = 1.241801e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.616751e-03 │ │ │ │ Vprtstp: contraction number = 1.613422e-01 │ │ │ │ Vnewton: Using errtol_s: 11177.524829 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.533626e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.698342e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.271971e+03 │ │ │ │ Vprtstp: contraction number = 2.271971e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.957685e-04 │ │ │ │ Vprtstp: contraction number = 1.829401e-01 │ │ │ │ Vnewton: Using errtol_s: 2044.817292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.549517e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.718991e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.414335e+02 │ │ │ │ Vprtstp: contraction number = 4.414335e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.746599e-05 │ │ │ │ Vprtstp: contraction number = 1.942938e-01 │ │ │ │ Vnewton: Using errtol_s: 397.295336 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.565168e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.740352e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.690501e+01 │ │ │ │ Vprtstp: contraction number = 8.690501e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.131327e-05 │ │ │ │ Vprtstp: contraction number = 1.968689e-01 │ │ │ │ Vnewton: Using errtol_s: 78.215105 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.581054e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762293e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.879618e+01 │ │ │ │ Vprtstp: contraction number = 1.879618e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.446866e-06 │ │ │ │ Vprtstp: contraction number = 2.162828e-01 │ │ │ │ Vnewton: Using errtol_s: 16.916585 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.596825e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.782074e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.583329e+00 │ │ │ │ Vprtstp: contraction number = 4.583329e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.966529e-07 │ │ │ │ Vprtstp: contraction number = 2.438437e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.356780e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.427657e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.854756e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.939006e+01 │ │ │ │ Vpmg_setPart: lower corner = (-53.482, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (2.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-53.482, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (13.3006, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -28016,27 +28016,27 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.139698158758E+00 kT │ │ │ │ Vpmg_energy: qfEnergy = 7.809316280828E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.918099666156E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.199420e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.229300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.618721e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.809218e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:28:46 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:01:44 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol1.pqr │ │ │ │ @@ -28389,129 +28389,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.296696 │ │ │ │ +Vacc_SASA: Time elapsed: 8.257999 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.607705e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.525569e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.600070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.444720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.183700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.807460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002782e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101312e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4300910.832168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091613e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188804e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.776390e+05 │ │ │ │ Vprtstp: contraction number = 1.776390e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041319 │ │ │ │ Vnewton: Attempting damping, relres = 0.513474 │ │ │ │ Vnewton: Damping accepted, relres = 0.041319 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.131938e-02 │ │ │ │ Vprtstp: contraction number = 4.131938e-02 │ │ │ │ Vnewton: Using errtol_s: 177710.973970 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.396870e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.677180e+04 │ │ │ │ Vprtstp: contraction number = 2.677180e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.962101e-03 │ │ │ │ Vprtstp: contraction number = 1.442931e-01 │ │ │ │ Vnewton: Using errtol_s: 25642.465478 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.450764e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.594618e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.966549e+03 │ │ │ │ Vprtstp: contraction number = 4.966549e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.056655e-03 │ │ │ │ Vprtstp: contraction number = 1.772286e-01 │ │ │ │ Vnewton: Using errtol_s: 4544.578762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612703e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.793743e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.011325e+03 │ │ │ │ Vprtstp: contraction number = 1.011325e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.118038e-04 │ │ │ │ Vprtstp: contraction number = 2.004475e-01 │ │ │ │ Vnewton: Using errtol_s: 910.949292 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.773208e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.989952e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.253595e+02 │ │ │ │ Vprtstp: contraction number = 2.253595e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.715911e-05 │ │ │ │ Vprtstp: contraction number = 2.226547e-01 │ │ │ │ Vnewton: Using errtol_s: 202.827138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.935548e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.186995e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.445207e+01 │ │ │ │ Vprtstp: contraction number = 5.445207e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.139456e-05 │ │ │ │ Vprtstp: contraction number = 2.416194e-01 │ │ │ │ Vnewton: Using errtol_s: 49.006980 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.097208e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.390344e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420316e+01 │ │ │ │ Vprtstp: contraction number = 1.420316e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.972126e-06 │ │ │ │ Vprtstp: contraction number = 2.608373e-01 │ │ │ │ Vnewton: Using errtol_s: 12.782849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.258852e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.589066e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.022184e+00 │ │ │ │ Vprtstp: contraction number = 4.022184e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.416744e-07 │ │ │ │ Vprtstp: contraction number = 2.831893e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.380084e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.452075e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.641866e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.707481e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -28520,17 +28520,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.085287424313E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.020959449622E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.003436009271E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.597000e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.821000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 39.7309 │ │ │ │ Vpbe_ctor2: solute dimensions = 68.682 x 69.075 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -28576,127 +28576,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0111702 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.226711 │ │ │ │ +Vacc_SASA: Time elapsed: 7.527065 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.128121e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.477575e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.634230e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.559580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.168880e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.812690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.380626e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.781549e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2843800.208997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.468548e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.875893e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.648041e+05 │ │ │ │ Vprtstp: contraction number = 2.648041e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.084229 │ │ │ │ Vnewton: Attempting damping, relres = 0.539926 │ │ │ │ Vnewton: Damping accepted, relres = 0.084229 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.422893e-02 │ │ │ │ Vprtstp: contraction number = 8.422893e-02 │ │ │ │ Vnewton: Using errtol_s: 239530.237257 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.667554e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.114381e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.601789e+04 │ │ │ │ Vprtstp: contraction number = 3.601789e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.140061e-02 │ │ │ │ Vprtstp: contraction number = 1.353527e-01 │ │ │ │ Vnewton: Using errtol_s: 32421.054732 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.830860e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.323851e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.547762e+03 │ │ │ │ Vprtstp: contraction number = 5.547762e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.755765e-03 │ │ │ │ Vprtstp: contraction number = 1.540062e-01 │ │ │ │ Vnewton: Using errtol_s: 4993.043762 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.993111e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.531817e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.234937e+02 │ │ │ │ Vprtstp: contraction number = 9.234937e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.922661e-04 │ │ │ │ Vprtstp: contraction number = 1.664609e-01 │ │ │ │ Vnewton: Using errtol_s: 831.146494 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.156542e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.736560e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.647026e+02 │ │ │ │ Vprtstp: contraction number = 1.647026e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.212477e-05 │ │ │ │ Vprtstp: contraction number = 1.783469e-01 │ │ │ │ Vnewton: Using errtol_s: 148.232430 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.319768e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.945016e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.095227e+01 │ │ │ │ Vprtstp: contraction number = 3.095227e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.795714e-06 │ │ │ │ Vprtstp: contraction number = 1.879282e-01 │ │ │ │ Vnewton: Using errtol_s: 27.857053 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.483086e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.152579e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.500935e+00 │ │ │ │ Vprtstp: contraction number = 6.500935e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.057403e-06 │ │ │ │ Vprtstp: contraction number = 2.100309e-01 │ │ │ │ Vnewton: Using errtol_s: 5.850843 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.646599e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.357752e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.529139e+00 │ │ │ │ Vprtstp: contraction number = 1.529139e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.839389e-07 │ │ │ │ Vprtstp: contraction number = 2.352183e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.392314e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.464025e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.741185e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.818146e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -28705,15 +28705,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.004865379330E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 1.781523307319E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 8.939732950056E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.255190e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.312540e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -28736,129 +28736,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.322851 │ │ │ │ +Vacc_SASA: Time elapsed: 7.511768 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.613522e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.852820e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.601460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.466100e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.159520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.674550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.721262e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.498877e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4276578.139223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.810596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.593489e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.716926e+05 │ │ │ │ Vprtstp: contraction number = 1.716926e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.040940 │ │ │ │ Vnewton: Attempting damping, relres = 0.513162 │ │ │ │ Vnewton: Damping accepted, relres = 0.040940 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.093968e-02 │ │ │ │ Vprtstp: contraction number = 4.093968e-02 │ │ │ │ Vnewton: Using errtol_s: 175081.721880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.005683e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.830589e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.487025e+04 │ │ │ │ Vprtstp: contraction number = 2.487025e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.724811e-03 │ │ │ │ Vprtstp: contraction number = 1.398353e-01 │ │ │ │ Vnewton: Using errtol_s: 24482.603484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.168744e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.018421e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.528470e+03 │ │ │ │ Vprtstp: contraction number = 4.528470e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.801406e-04 │ │ │ │ Vprtstp: contraction number = 1.712092e-01 │ │ │ │ Vnewton: Using errtol_s: 4191.647712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.331269e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.218295e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.122748e+02 │ │ │ │ Vprtstp: contraction number = 9.122748e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923658e-04 │ │ │ │ Vprtstp: contraction number = 1.962635e-01 │ │ │ │ Vnewton: Using errtol_s: 822.667398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.493184e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.421034e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052635e+02 │ │ │ │ Vprtstp: contraction number = 2.052635e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.319998e-05 │ │ │ │ Vprtstp: contraction number = 2.245720e-01 │ │ │ │ Vnewton: Using errtol_s: 184.748098 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.655435e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.621446e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.154123e+01 │ │ │ │ Vprtstp: contraction number = 5.154123e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.084685e-05 │ │ │ │ Vprtstp: contraction number = 2.510845e-01 │ │ │ │ Vnewton: Using errtol_s: 46.387392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.818248e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.819790e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.435770e+01 │ │ │ │ Vprtstp: contraction number = 1.435770e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.021563e-06 │ │ │ │ Vprtstp: contraction number = 2.785660e-01 │ │ │ │ Vnewton: Using errtol_s: 12.921949 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.979708e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.017944e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.361187e+00 │ │ │ │ Vprtstp: contraction number = 4.361187e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.178062e-07 │ │ │ │ Vprtstp: contraction number = 3.037522e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.383067e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.454242e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.669332e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.743661e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -28867,15 +28867,15 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.162784451104E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.383505562700E+02 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.754184182339E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.354600e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.618300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 40.4102 │ │ │ │ Vpbe_ctor2: solute dimensions = 61.161 x 72.117 x 70.346 │ │ │ │ Vpbe_ctor2: solute charge = -12 │ │ │ │ @@ -28923,138 +28923,138 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00475113 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 7.304815 │ │ │ │ +Vacc_SASA: Time elapsed: 7.416083 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.877562e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.053357e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.636710e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.606450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.280250e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.846870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.078022e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.164066e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1712482.416854 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.165123e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.259431e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.778057e+05 │ │ │ │ Vprtstp: contraction number = 1.778057e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.095206 │ │ │ │ Vnewton: Attempting damping, relres = 0.544528 │ │ │ │ Vnewton: Damping accepted, relres = 0.095206 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.520604e-02 │ │ │ │ Vprtstp: contraction number = 9.520604e-02 │ │ │ │ Vnewton: Using errtol_s: 163038.671160 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.366628e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.488354e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.588526e+04 │ │ │ │ Vprtstp: contraction number = 2.588526e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.365073e-02 │ │ │ │ Vprtstp: contraction number = 1.433809e-01 │ │ │ │ Vnewton: Using errtol_s: 23376.634124 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.531329e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.685873e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.392675e+03 │ │ │ │ Vprtstp: contraction number = 4.392675e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.309227e-03 │ │ │ │ Vprtstp: contraction number = 1.691651e-01 │ │ │ │ Vnewton: Using errtol_s: 3954.509988 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.694609e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.877908e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.232796e+02 │ │ │ │ Vprtstp: contraction number = 8.232796e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 4.326939e-04 │ │ │ │ Vprtstp: contraction number = 1.873761e-01 │ │ │ │ Vnewton: Using errtol_s: 740.980697 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.858321e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007349e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.669237e+02 │ │ │ │ Vprtstp: contraction number = 1.669237e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 8.772776e-05 │ │ │ │ Vprtstp: contraction number = 2.027479e-01 │ │ │ │ Vnewton: Using errtol_s: 150.232247 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.022955e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027018e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.642088e+01 │ │ │ │ Vprtstp: contraction number = 3.642088e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.914112e-05 │ │ │ │ Vprtstp: contraction number = 2.181877e-01 │ │ │ │ Vnewton: Using errtol_s: 32.778836 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.186190e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.046462e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.545476e+00 │ │ │ │ Vprtstp: contraction number = 8.545476e+00 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.491102e-06 │ │ │ │ Vprtstp: contraction number = 2.346311e-01 │ │ │ │ Vnewton: Using errtol_s: 7.690933 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.350411e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066010e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.153814e+00 │ │ │ │ Vprtstp: contraction number = 2.153814e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.131943e-06 │ │ │ │ Vprtstp: contraction number = 2.520414e-01 │ │ │ │ Vnewton: Using errtol_s: 1.938433 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.515212e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085419e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.814982e-01 │ │ │ │ Vprtstp: contraction number = 5.814982e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.056081e-07 │ │ │ │ Vprtstp: contraction number = 2.699853e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.565162e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.638038e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.847669e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.924842e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -29063,17 +29063,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.651168945816E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 3.320671858523E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.644537494834E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.307170e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.315310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -29094,129 +29094,129 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.295632 │ │ │ │ +Vacc_SASA: Time elapsed: 16.643540 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.818076e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.852634e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.628440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.417280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.152890e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.519800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154907e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.295306e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 8699406.430616 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.163688e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.304971e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528464e+05 │ │ │ │ Vprtstp: contraction number = 3.528464e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.041605 │ │ │ │ Vnewton: Attempting damping, relres = 0.513349 │ │ │ │ Vnewton: Damping accepted, relres = 0.041605 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160535e-02 │ │ │ │ Vprtstp: contraction number = 4.160535e-02 │ │ │ │ Vnewton: Using errtol_s: 361941.817774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183595e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329569e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.210930e+04 │ │ │ │ Vprtstp: contraction number = 5.210930e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.921711e-03 │ │ │ │ Vprtstp: contraction number = 1.423305e-01 │ │ │ │ Vnewton: Using errtol_s: 51515.371182 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.199860e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.349314e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.570568e+03 │ │ │ │ Vprtstp: contraction number = 9.570568e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.018950e-03 │ │ │ │ Vprtstp: contraction number = 1.720701e-01 │ │ │ │ Vnewton: Using errtol_s: 8864.257334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.216527e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.368772e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.944504e+03 │ │ │ │ Vprtstp: contraction number = 1.944504e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.015521e-04 │ │ │ │ Vprtstp: contraction number = 1.978037e-01 │ │ │ │ Vnewton: Using errtol_s: 1753.383252 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.235293e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.389191e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.357668e+02 │ │ │ │ Vprtstp: contraction number = 4.357668e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.508379e-05 │ │ │ │ Vprtstp: contraction number = 2.236831e-01 │ │ │ │ Vnewton: Using errtol_s: 392.202227 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.254280e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.410006e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.074784e+02 │ │ │ │ Vprtstp: contraction number = 1.074784e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.111924e-05 │ │ │ │ Vprtstp: contraction number = 2.466350e-01 │ │ │ │ Vnewton: Using errtol_s: 96.730784 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.273574e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.430396e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.903808e+01 │ │ │ │ Vprtstp: contraction number = 2.903808e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.004146e-06 │ │ │ │ Vprtstp: contraction number = 2.701755e-01 │ │ │ │ Vnewton: Using errtol_s: 26.134288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.292034e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.450983e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.552738e+00 │ │ │ │ Vprtstp: contraction number = 8.552738e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.848266e-07 │ │ │ │ Vprtstp: contraction number = 2.945351e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.505730e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.577200e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.718424e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.790361e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-75.482, -62.9645, -64.2575) │ │ │ │ Vpmg_setPart: actual maxima = (80.518, 58.0355, 97.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -29225,17 +29225,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 2.317973104173E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.391935061774E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.197593144317E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.367900e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.332700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 56.367 │ │ │ │ Vpbe_ctor2: solute dimensions = 94.322 x 73.942 x 97.846 │ │ │ │ Vpbe_ctor2: solute charge = -24 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.073486 │ │ │ │ @@ -29281,127 +29281,127 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0257349 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 16.298637 │ │ │ │ +Vacc_SASA: Time elapsed: 16.619535 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.885452e+01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.925608e+01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.595890e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.777300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.359470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 6.056530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.502708e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.669318e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 4500132.646352 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.511506e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.678693e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.278020e+05 │ │ │ │ Vprtstp: contraction number = 4.278020e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.086415 │ │ │ │ Vnewton: Attempting damping, relres = 0.540695 │ │ │ │ Vnewton: Damping accepted, relres = 0.086415 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.641451e-02 │ │ │ │ Vprtstp: contraction number = 8.641451e-02 │ │ │ │ Vnewton: Using errtol_s: 388876.774521 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.531343e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.703069e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.967321e+04 │ │ │ │ Vprtstp: contraction number = 5.967321e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 1.194851e-02 │ │ │ │ Vprtstp: contraction number = 1.382697e-01 │ │ │ │ Vnewton: Using errtol_s: 53769.886692 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.547461e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.722206e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.609884e+03 │ │ │ │ Vprtstp: contraction number = 9.609884e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.922151e-03 │ │ │ │ Vprtstp: contraction number = 1.608695e-01 │ │ │ │ Vnewton: Using errtol_s: 8649.935921 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.563712e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.742698e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.688280e+03 │ │ │ │ Vprtstp: contraction number = 1.688280e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.376534e-04 │ │ │ │ Vprtstp: contraction number = 1.756643e-01 │ │ │ │ Vnewton: Using errtol_s: 1519.485051 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.579848e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.762199e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.185424e+02 │ │ │ │ Vprtstp: contraction number = 3.185424e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.370679e-05 │ │ │ │ Vprtstp: contraction number = 1.886751e-01 │ │ │ │ Vnewton: Using errtol_s: 286.689023 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.596129e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.782842e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.336866e+01 │ │ │ │ Vprtstp: contraction number = 6.336866e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.267337e-05 │ │ │ │ Vprtstp: contraction number = 1.989328e-01 │ │ │ │ Vnewton: Using errtol_s: 57.031849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612268e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.803708e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.358194e+01 │ │ │ │ Vprtstp: contraction number = 1.358194e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.716310e-06 │ │ │ │ Vprtstp: contraction number = 2.143321e-01 │ │ │ │ Vnewton: Using errtol_s: 12.223755 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.628395e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.824346e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.189745e+00 │ │ │ │ Vprtstp: contraction number = 3.189745e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.379304e-07 │ │ │ │ Vprtstp: contraction number = 2.348518e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.382804e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.456610e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.705061e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.787058e+01 │ │ │ │ Vpmg_setPart: lower corner = (2.518, -2.4645, 16.7425) │ │ │ │ Vpmg_setPart: upper corner = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: actual minima = (-8.26461, -11.2254, 5.5748) │ │ │ │ Vpmg_setPart: actual maxima = (58.518, 43.0355, 74.7425) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ @@ -29410,17 +29410,17 @@ │ │ │ │ Vpmg_setPart: bflag[DOWN] = 1 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 3.132873625516E-01 kT │ │ │ │ Vpmg_energy: qfEnergy = 2.116420853422E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.060038494093E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.262980e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.285360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: printing only subset of domain │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.650703e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.850693e+02 │ │ │ ├── ./usr/share/apbs/examples/alkanes/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:30:35 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:05:01 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path 2-methylbutane.pdb │ │ │ │ @@ -302,130 +302,130 @@ │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (13.5347, 12.2207, 11.3787) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-6.76736, -6.11036, -5.68936) │ │ │ │ Vclist_assignAtoms: Have 6745 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.035335 │ │ │ │ -initAPOL: Time elapsed: 7.107459 │ │ │ │ +Vacc_SASA: Time elapsed: 0.036061 │ │ │ │ +initAPOL: Time elapsed: 7.281695 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 15 x 12 x 11 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (13.0267, 11.7717, 11.1107) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-2.59636, -5.18336, -14.1304) │ │ │ │ Vclist_assignAtoms: Have 4888 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.028590 │ │ │ │ -initAPOL: Time elapsed: 5.824950 │ │ │ │ +Vacc_SASA: Time elapsed: 0.028246 │ │ │ │ +initAPOL: Time elapsed: 5.997025 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 14 x 12 x 15 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (12.7417, 11.4947, 13.2787) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-5.24736, -5.15936, -5.87136) │ │ │ │ Vclist_assignAtoms: Have 6902 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.037917 │ │ │ │ -initAPOL: Time elapsed: 7.538482 │ │ │ │ +Vacc_SASA: Time elapsed: 0.037287 │ │ │ │ +initAPOL: Time elapsed: 7.747837 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 14 x 12 x 13 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (12.4767, 11.4917, 12.3367) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-4.91836, -5.22036, -4.87936) │ │ │ │ Vclist_assignAtoms: Have 4977 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.026374 │ │ │ │ -initAPOL: Time elapsed: 5.413352 │ │ │ │ +Vacc_SASA: Time elapsed: 0.026068 │ │ │ │ +initAPOL: Time elapsed: 5.590699 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 9 x 9 x 10 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (10.0327, 10.2387, 10.6647) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-4.79536, -5.14036, -4.56736) │ │ │ │ Vclist_assignAtoms: Have 1946 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.015251 │ │ │ │ -initAPOL: Time elapsed: 3.326363 │ │ │ │ +Vacc_SASA: Time elapsed: 0.014840 │ │ │ │ +initAPOL: Time elapsed: 3.493075 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 19 x 15 x 12 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (15.0957, 13.1957, 11.4487) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-2.59636, -6.60736, -14.1304) │ │ │ │ Vclist_assignAtoms: Have 9434 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.041819 │ │ │ │ -initAPOL: Time elapsed: 8.552576 │ │ │ │ +Vacc_SASA: Time elapsed: 0.043570 │ │ │ │ +initAPOL: Time elapsed: 8.763385 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 13 x 12 x 14 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (12.0577, 11.5517, 12.5037) │ │ │ │ Vclist_setupGrid: Grid lower corner = (12.5656, 12.8626, 12.9606) │ │ │ │ Vclist_assignAtoms: Have 5377 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.032635 │ │ │ │ -initAPOL: Time elapsed: 6.376478 │ │ │ │ +Vacc_SASA: Time elapsed: 0.031445 │ │ │ │ +initAPOL: Time elapsed: 6.262404 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 9 x 9 x 8 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (10.1767, 10.1117, 9.66772) │ │ │ │ Vclist_setupGrid: Grid lower corner = (12.9396, 12.7376, 12.9816) │ │ │ │ Vclist_assignAtoms: Have 1014 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.008930 │ │ │ │ -initAPOL: Time elapsed: 2.182165 │ │ │ │ +Vacc_SASA: Time elapsed: 0.009133 │ │ │ │ +initAPOL: Time elapsed: 2.248791 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 13 x 13 x 14 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (12.2347, 12.1667, 12.6837) │ │ │ │ Vclist_setupGrid: Grid lower corner = (12.5496, 12.8526, 12.8586) │ │ │ │ Vclist_assignAtoms: Have 6725 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.037017 │ │ │ │ -initAPOL: Time elapsed: 7.519642 │ │ │ │ +Vacc_SASA: Time elapsed: 0.038255 │ │ │ │ +initAPOL: Time elapsed: 7.795208 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 17 x 14 x 11 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (14.1127, 12.8537, 11.1297) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-2.59636, -6.26536, -14.1304) │ │ │ │ Vclist_assignAtoms: Have 6650 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.034051 │ │ │ │ -initAPOL: Time elapsed: 7.132282 │ │ │ │ +Vacc_SASA: Time elapsed: 0.033595 │ │ │ │ +initAPOL: Time elapsed: 7.574703 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 10 x 14 x 12 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.05 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (10.9097, 12.4407, 11.4747) │ │ │ │ Vclist_setupGrid: Grid lower corner = (12.9086, 12.7426, 12.8736) │ │ │ │ Vclist_assignAtoms: Have 3766 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 109.953 │ │ │ │ Vacc_storeParms: Using 11012-point reference sphere │ │ │ │ -Vacc_SASA: Time elapsed: 0.021239 │ │ │ │ -initAPOL: Time elapsed: 4.840589 │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.583955e+01 │ │ │ │ +Vacc_SASA: Time elapsed: 0.022830 │ │ │ │ +initAPOL: Time elapsed: 4.994611 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.778771e+01 │ │ │ ├── ./usr/share/apbs/examples/born/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:30:09 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:30:25 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -194,32 +194,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002997 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000622 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.942700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.039500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.942600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.084300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.423200e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.810610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.078300e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.292080e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -242,33 +242,33 @@ │ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.668195e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.905504e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.855067e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.121505e+00 │ │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.750853990251E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.715000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.354000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -315,30 +315,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.111569 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000499 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000519 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.213540e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.270410e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.590100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.076600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.396380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.838330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.336648e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.593760e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.284366e-01 │ │ │ │ Vprtstp: contraction number = 1.284366e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -370,33 +370,33 @@ │ │ │ │ Vprtstp: contraction number = 3.689006e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.340984e-06 │ │ │ │ Vprtstp: contraction number = 3.689051e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.946966e-07 │ │ │ │ Vprtstp: contraction number = 3.689058e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.503409e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.732714e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.817024e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.087775e+00 │ │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.775144565213E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.986000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.247000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -443,30 +443,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.339539 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001489 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000597 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.032710e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.154110e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.794900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.059600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.396030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.857160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.485733e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.109265e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.377836e-01 │ │ │ │ Vprtstp: contraction number = 1.377836e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -501,33 +501,33 @@ │ │ │ │ Vprtstp: contraction number = 3.896678e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.022958e-06 │ │ │ │ Vprtstp: contraction number = 3.896627e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 3.986147e-07 │ │ │ │ Vprtstp: contraction number = 3.896686e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.733117e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.964851e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.186216e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.458063e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 3.817909770059E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.069000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.108000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ WARNING │ │ │ │ Vgrid_readGZ: gzip read/write support is disabled in this build │ │ │ │ Vgrid_readGZ: configure and compile without the --disable-zlib flag. │ │ │ │ WARNING │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ @@ -552,28 +552,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.797100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.226600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.826700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.045000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.378140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.854250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.149734e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.261297e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -590,31 +590,31 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.909262e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.138349e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.236308e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.510122e+00 │ │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 9.607786035504E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.202000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.066000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -661,28 +661,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 8.7631 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.107600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.575800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.137200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.199400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.386100e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.863020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.373513e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521027e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114981e-01 │ │ │ │ Vprtstp: contraction number = 1.114981e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -699,31 +699,31 @@ │ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473476e-06 │ │ │ │ Vprtstp: contraction number = 1.075295e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.593050e-07 │ │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.901024e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.137529e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.197692e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.470960e+00 │ │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.961195484638E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.977000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.453000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -770,28 +770,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 26.656 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.587400e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.745400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.861400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.191300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.271780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.842290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.592085e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.776967e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114975e-01 │ │ │ │ Vprtstp: contraction number = 1.114975e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -808,39 +808,39 @@ │ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473471e-06 │ │ │ │ Vprtstp: contraction number = 1.075296e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.593045e-07 │ │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.551421e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.749534e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.189098e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.461561e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 4.003287887017E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.797000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.128000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 9.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.747670e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.996848e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:30:18 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:30:51 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -1028,32 +1028,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002754 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000598 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.608520e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.715600e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.727800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.108800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.132100e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.954040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.581570e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.677690e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1073,33 +1073,33 @@ │ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.881312e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.058689e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.519817e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.798038e+00 │ │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.691034776619E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.802000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.173000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1146,30 +1146,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.111618 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002348 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000518 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.424570e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.503590e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.514900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.052700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.222580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.830240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.672136e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.512845e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.204709e-01 │ │ │ │ Vprtstp: contraction number = 1.204709e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1186,33 +1186,33 @@ │ │ │ │ Vprtstp: contraction number = 1.476379e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 5.011380e-06 │ │ │ │ Vprtstp: contraction number = 1.603001e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.492596e-07 │ │ │ │ Vprtstp: contraction number = 1.694662e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.706462e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.886520e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.237518e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.501154e+00 │ │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.775933047078E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.111000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.563000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1259,30 +1259,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.339781 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001083 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000528 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.320170e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.510860e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.902400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.161500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.388620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.008940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.132285e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.600195e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.298995e-01 │ │ │ │ Vprtstp: contraction number = 1.298995e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1302,31 +1302,31 @@ │ │ │ │ Vprtstp: contraction number = 1.916174e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.164097e-06 │ │ │ │ Vprtstp: contraction number = 1.993376e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.370219e-07 │ │ │ │ Vprtstp: contraction number = 2.019420e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.111501e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.322426e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.508973e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.794062e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 3.818523837085E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.845000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.408000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -1349,28 +1349,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.755600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.157400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.569500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.845600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.345370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.850110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.514525e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.421520e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1387,31 +1387,31 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.513603e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.736333e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.228479e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.498033e+00 │ │ │ │ Vpmg_setPart: lower corner = (-25, -25, -25) │ │ │ │ Vpmg_setPart: upper corner = (25, 25, 25) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 9.607786035504E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.764000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.243000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -1458,28 +1458,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 8.7631 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.940400e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.621800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.770700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.977900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.274720e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.862470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.318493e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200792e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114981e-01 │ │ │ │ Vprtstp: contraction number = 1.114981e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1496,33 +1496,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473476e-06 │ │ │ │ Vprtstp: contraction number = 1.075295e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.593050e-07 │ │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.802815e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.013606e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.235310e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.505550e+00 │ │ │ │ Vpmg_setPart: lower corner = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: upper corner = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: actual minima = (-12.2474, -12.2474, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (12.2474, 12.2474, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.961195484638E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.767000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.236000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1567,28 +1567,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 26.656 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.967800e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.636200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.349500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.978000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.252630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.863980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141293e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.460185e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114975e-01 │ │ │ │ Vprtstp: contraction number = 1.114975e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1605,39 +1605,39 @@ │ │ │ │ Vprtstp: contraction number = 1.068029e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473471e-06 │ │ │ │ Vprtstp: contraction number = 1.075296e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.593045e-07 │ │ │ │ Vprtstp: contraction number = 1.081151e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.866434e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.078243e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.190077e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.461016e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 4.003287887017E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.832000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.059000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.328444e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.680352e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:30:26 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:31:14 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -1885,32 +1885,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001669 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001101 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.991500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.721400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.723500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.073800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.341540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.807460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.980460e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.279180e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1933,31 +1933,31 @@ │ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.565552e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.789858e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.789614e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.054577e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.937713497535E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.839000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.230000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -2006,30 +2006,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0318856 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000542 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000506 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.487150e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.553970e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.723200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.238100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.347450e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.986110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.253872e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.577698e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.311479e-01 │ │ │ │ Vprtstp: contraction number = 1.311479e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2061,31 +2061,31 @@ │ │ │ │ Vprtstp: contraction number = 3.924056e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.308381e-06 │ │ │ │ Vprtstp: contraction number = 3.934819e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 9.098344e-07 │ │ │ │ Vprtstp: contraction number = 3.941440e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.338989e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.563284e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.715816e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.002087e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.569607552225E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.944000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.109000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -2134,30 +2134,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0917244 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000497 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000578 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.235260e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.414180e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.576100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.201100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.259520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.892520e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.242441e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.028939e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.316256e-01 │ │ │ │ Vprtstp: contraction number = 1.316256e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2195,31 +2195,31 @@ │ │ │ │ Vprtstp: contraction number = 4.543160e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.790206e-06 │ │ │ │ Vprtstp: contraction number = 4.616591e-01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.377288e-07 │ │ │ │ Vprtstp: contraction number = 4.679511e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.818314e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.029600e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.314584e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.592997e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198283392867E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.717000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.137000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -2242,28 +2242,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.628800e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.214100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.762400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.030200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.319060e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.834380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.132761e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265441e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2280,33 +2280,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.969975e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.190416e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.222143e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.489984e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.302000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.039000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2351,28 +2351,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.50448 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.195000e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.249800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.207300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.992400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.426020e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.870150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.363893e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.523659e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2392,31 +2392,31 @@ │ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.308914e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.549562e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.505669e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.774348e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.191000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.370000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -2463,28 +2463,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.21011 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.853900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.006200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.056000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.206700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.554490e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.880280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.630022e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.811563e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2516,39 +2516,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.551082e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.809302e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.815125e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.091338e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.121000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.472000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.985594e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.194421e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:30:37 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:31:42 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -2796,32 +2796,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001658 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000615 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.859900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.007800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.887600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.996400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.369330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.850000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.995780e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.352720e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2844,33 +2844,33 @@ │ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.619446e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.849121e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.870157e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.139896e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.937713497535E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.993000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.142000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2917,30 +2917,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.031798 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000553 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000527 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.624130e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.565120e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.730600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.951700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.587360e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.778400e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.359248e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.644878e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.311630e-01 │ │ │ │ Vprtstp: contraction number = 1.311630e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2972,31 +2972,31 @@ │ │ │ │ Vprtstp: contraction number = 3.943689e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.411496e-06 │ │ │ │ Vprtstp: contraction number = 3.954554e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 9.552609e-07 │ │ │ │ Vprtstp: contraction number = 3.961279e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.603218e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.862766e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.756115e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.019217e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.569480660622E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.009000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.177000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -3045,30 +3045,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0914959 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000515 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000573 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.289900e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.377180e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.655100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.674800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.355810e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.851570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.633279e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.130601e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.316347e-01 │ │ │ │ Vprtstp: contraction number = 1.316347e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3106,31 +3106,31 @@ │ │ │ │ Vprtstp: contraction number = 4.560576e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.840082e-06 │ │ │ │ Vprtstp: contraction number = 4.634922e-01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.644979e-07 │ │ │ │ Vprtstp: contraction number = 4.698149e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.004226e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.232136e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.414779e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.691036e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198276421620E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.103000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.260000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -3153,28 +3153,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.990900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.219000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.727300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.000100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.555680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.923990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.194684e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.286830e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3191,33 +3191,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.070631e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.328446e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.250430e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.526948e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.754000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.073000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3262,28 +3262,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.350600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.942200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.915900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.127600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.446080e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.819170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.435631e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.548513e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3303,33 +3303,33 @@ │ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.347312e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.595883e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.569198e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.837431e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.244000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.275000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3374,28 +3374,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.239600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.707100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.938300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.909400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.645450e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.826090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.706626e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.841290e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3427,39 +3427,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.524914e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.790728e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.862249e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.127542e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.036000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.583000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.059806e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.229046e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:30:49 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:32:10 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -3707,32 +3707,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001708 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000653 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.075600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.973900e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.099400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.232000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.654410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.767010e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.357670e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.250550e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3755,33 +3755,33 @@ │ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.840205e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.104610e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.775509e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.033688e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.937713497591E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.096000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.091000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3828,30 +3828,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.031798 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001032 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000509 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.577480e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.466070e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.871200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.698500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.585870e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.773960e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.614807e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.522080e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.311246e-01 │ │ │ │ Vprtstp: contraction number = 1.311246e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3883,33 +3883,33 @@ │ │ │ │ Vprtstp: contraction number = 3.922726e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.295236e-06 │ │ │ │ Vprtstp: contraction number = 3.933610e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 9.043960e-07 │ │ │ │ Vprtstp: contraction number = 3.940319e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.631565e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.895201e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.786629e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.044058e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.569607562894E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.021000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.538000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3956,30 +3956,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0914865 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000507 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000530 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.313330e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.311740e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.796400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.090800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.507340e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.807940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.945475e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.024791e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.312535e-01 │ │ │ │ Vprtstp: contraction number = 1.312535e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4017,33 +4017,33 @@ │ │ │ │ Vprtstp: contraction number = 4.543257e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.762407e-06 │ │ │ │ Vprtstp: contraction number = 4.617179e-01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.248702e-07 │ │ │ │ Vprtstp: contraction number = 4.680361e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.153242e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.404724e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.243418e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.511580e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198283391562E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.024000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.029000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -4064,28 +4064,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.182400e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.931200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.852700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.614500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.564340e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.629090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.241041e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255014e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4102,33 +4102,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.059615e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.318615e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.114509e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.356225e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.844000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.259000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -4173,28 +4173,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.480500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.530600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.840500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.554700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.415580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.742080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.479427e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.500916e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4214,31 +4214,31 @@ │ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.330332e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.563872e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.490537e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.741602e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.144000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.309000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -4285,28 +4285,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.114000e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.460000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.851500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.867500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.395650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.766220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.745462e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.785012e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4338,39 +4338,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.486988e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.720207e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.803243e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.061171e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.118000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.239000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.094852e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.166070e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:31:01 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:32:37 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -4618,32 +4618,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001677 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000658 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.017700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.744800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.037600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.629900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.386290e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.265190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.030010e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.827690e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252488e-01 │ │ │ │ Vprtstp: contraction number = 1.252488e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4666,33 +4666,33 @@ │ │ │ │ Vprtstp: contraction number = 2.345457e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.154547e-06 │ │ │ │ Vprtstp: contraction number = 2.398447e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.798201e-07 │ │ │ │ Vprtstp: contraction number = 2.423636e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.626594e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.859927e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.895969e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.215966e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.937713497591E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.788000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.295000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -4739,30 +4739,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0317109 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001653 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000540 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.509440e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.567990e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.664600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.995300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.470590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.852010e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.346602e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.724753e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.311373e-01 │ │ │ │ Vprtstp: contraction number = 1.311373e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4794,31 +4794,31 @@ │ │ │ │ Vprtstp: contraction number = 3.942499e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.398436e-06 │ │ │ │ Vprtstp: contraction number = 3.953474e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 9.498453e-07 │ │ │ │ Vprtstp: contraction number = 3.960269e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.518314e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.766333e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.918309e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.188702e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.569480671365E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.931000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.373000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -4867,30 +4867,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0912591 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000524 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000516 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.295570e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.348740e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.762500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.908100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.455710e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.856310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.554912e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.365610e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.312625e-01 │ │ │ │ Vprtstp: contraction number = 1.312625e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -4928,33 +4928,33 @@ │ │ │ │ Vprtstp: contraction number = 4.561186e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 1.813861e-06 │ │ │ │ Vprtstp: contraction number = 4.635791e-01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 8.523872e-07 │ │ │ │ Vprtstp: contraction number = 4.699296e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.046387e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.291735e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.341019e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.611447e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198276420222E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.018000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.338000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -4975,28 +4975,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.136000e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.406200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.831800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.958700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.468750e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.837020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.189397e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.302170e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5013,33 +5013,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.034789e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.276655e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.260094e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.529398e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.943000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.228000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -5084,28 +5084,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.49076 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.331300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.501300e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.956100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.003100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.354010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.853780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.424678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.564325e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5125,33 +5125,33 @@ │ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.290968e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.518752e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.604328e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.872147e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.163000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.153000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -5196,28 +5196,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.17281 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.907300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.732700e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.747000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.971000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.472320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.845860e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.687207e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.860847e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5249,39 +5249,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.510733e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.755804e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.842378e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.109858e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.920000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.309000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.040126e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.246093e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:31:12 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:33:07 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -5529,32 +5529,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001948 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001253 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.855560e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.862330e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.048000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.017800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.625040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.900390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.674590e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.818030e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5574,31 +5574,31 @@ │ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.374880e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.636655e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.570983e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.842778e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.922758694117E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.132000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.295000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -5647,30 +5647,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0319041 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001649 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000573 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.757390e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.879970e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.798800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.007300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.545930e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.844220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.388286e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.626379e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.251607e-01 │ │ │ │ Vprtstp: contraction number = 1.251607e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5693,33 +5693,33 @@ │ │ │ │ Vprtstp: contraction number = 2.197650e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.342799e-06 │ │ │ │ Vprtstp: contraction number = 2.223851e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.012580e-07 │ │ │ │ Vprtstp: contraction number = 2.243508e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.633807e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.886693e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.831107e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.098431e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.571571268982E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.101000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.235000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -5766,30 +5766,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0918985 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000506 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000559 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.490580e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.743250e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.808400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.834600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.703310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.898270e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.846781e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.317383e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.287586e-01 │ │ │ │ Vprtstp: contraction number = 1.287586e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5821,33 +5821,33 @@ │ │ │ │ Vprtstp: contraction number = 3.624968e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.194036e-06 │ │ │ │ Vprtstp: contraction number = 3.635428e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.993852e-07 │ │ │ │ Vprtstp: contraction number = 3.643446e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.698960e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.959376e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.691578e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.960721e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198500974871E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.085000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.374000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -5868,28 +5868,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.891500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.035000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.792500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.684100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.551360e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.784250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.085466e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.130873e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -5906,33 +5906,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.160254e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.418390e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.158640e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.416843e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.163000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.422000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -5977,28 +5977,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.50448 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.606600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.943400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.855600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.105600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.547920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.905200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.336554e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.384087e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6018,33 +6018,33 @@ │ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.523225e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.781755e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.554892e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.830061e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.013000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.396000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -6089,28 +6089,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.21011 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.129700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.913300e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.624400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.970800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.454120e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.844870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.622293e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.675901e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6142,39 +6142,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.752391e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.989960e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.746931e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.013154e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.087000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.971000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.998241e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.051447e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:31:24 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:33:34 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -6422,32 +6422,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001688 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001154 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.745700e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.612680e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.024300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.552000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.489670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.706500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.308830e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.309160e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6467,33 +6467,33 @@ │ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.459280e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.692101e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.439250e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.683622e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.922758694117E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.049000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.445000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -6540,30 +6540,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0318166 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001030 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001048 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.817820e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.899730e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.754700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.112900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.464790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.863640e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.422276e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.448238e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.251837e-01 │ │ │ │ Vprtstp: contraction number = 1.251837e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6586,33 +6586,33 @@ │ │ │ │ Vprtstp: contraction number = 2.194352e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.332747e-06 │ │ │ │ Vprtstp: contraction number = 2.220306e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.985011e-07 │ │ │ │ Vprtstp: contraction number = 2.239743e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.715604e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.948553e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.874546e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.143491e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.571611855754E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.957000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.275000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -6659,30 +6659,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0916405 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000631 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001044 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.611740e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.653230e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.043400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.818900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.651690e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.795700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.973253e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.164453e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.287503e-01 │ │ │ │ Vprtstp: contraction number = 1.287503e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6714,31 +6714,31 @@ │ │ │ │ Vprtstp: contraction number = 3.625355e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.195364e-06 │ │ │ │ Vprtstp: contraction number = 3.635887e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.999739e-07 │ │ │ │ Vprtstp: contraction number = 3.643923e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.619838e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.877624e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.895091e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.155040e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198504468748E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.037000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.168000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -6761,28 +6761,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.435400e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.294500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.049700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.138200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.577260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.830920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090202e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.137332e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6799,33 +6799,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.340499e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.595272e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.268951e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.538075e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508821E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.955000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.264000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -6870,28 +6870,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.678100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.374300e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.086900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.894700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.404400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.799980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.357151e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.399564e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114250e-01 │ │ │ │ Vprtstp: contraction number = 1.114250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -6911,33 +6911,33 @@ │ │ │ │ Vprtstp: contraction number = 1.974463e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739617e-06 │ │ │ │ Vprtstp: contraction number = 2.010776e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.579966e-07 │ │ │ │ Vprtstp: contraction number = 2.036768e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.426904e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.661894e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.630880e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.892617e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -11.8833, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 7.06083, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934179E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.931000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.417000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -6982,28 +6982,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.374700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.773200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.842900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.010400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.578950e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 2.005370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.635873e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.700766e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114069e-01 │ │ │ │ Vprtstp: contraction number = 1.114069e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7035,39 +7035,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639461e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623548e-06 │ │ │ │ Vprtstp: contraction number = 3.646489e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928874e-07 │ │ │ │ Vprtstp: contraction number = 3.651801e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.483636e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.744773e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.962139e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.248069e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, -6, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 0, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -6, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 1.17757, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 1 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313627E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.959000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.237000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.984698e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.098115e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:31:35 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:34:01 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -7315,32 +7315,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002110 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000609 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.767360e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.782370e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.850700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.177500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.419110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.884660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.249570e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.771460e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7360,33 +7360,33 @@ │ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.405712e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.631185e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.616165e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.888769e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.922758694192E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.982000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.292000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -7433,30 +7433,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0318166 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000548 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000538 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.748650e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.773570e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.683600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.313600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.430510e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.678050e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.349263e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.631540e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252629e-01 │ │ │ │ Vprtstp: contraction number = 1.252629e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7479,31 +7479,31 @@ │ │ │ │ Vprtstp: contraction number = 2.198448e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.343869e-06 │ │ │ │ Vprtstp: contraction number = 2.224198e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.015100e-07 │ │ │ │ Vprtstp: contraction number = 2.243596e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.655263e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.881981e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.843762e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.086993e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.571571270505E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.076000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.345000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -7552,30 +7552,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0916602 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000518 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000558 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.355790e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.800480e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.447100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.676000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.252300e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.863140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.759974e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.336878e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.283061e-01 │ │ │ │ Vprtstp: contraction number = 1.283061e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7607,33 +7607,33 @@ │ │ │ │ Vprtstp: contraction number = 3.626484e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.188308e-06 │ │ │ │ Vprtstp: contraction number = 3.636628e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.975574e-07 │ │ │ │ Vprtstp: contraction number = 3.644631e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.479161e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.683975e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.825734e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.092382e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198500974608E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.040000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.283000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -7654,28 +7654,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.825500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.750400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.861400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.548000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.424400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.775170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052143e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.145722e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7692,31 +7692,31 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.055627e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.288853e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.213063e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.467644e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.131000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.305000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -7763,28 +7763,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.4976 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.376300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.281900e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.964000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.135600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.347290e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.790640e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.289466e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.402545e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7804,31 +7804,31 @@ │ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.385449e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.612147e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.580145e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.844259e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-11.8833, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (7.06083, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.191000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.038000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -7875,28 +7875,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.19142 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.012100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.194600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.019100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.436300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.557330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.830770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.565546e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.695445e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -7928,39 +7928,39 @@ │ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.582649e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.862592e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.822640e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.083802e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (0, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-6, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (1.17757, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 1 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.918000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.327000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.924305e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.078405e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 15:31:46 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 19:34:28 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion.xml │ │ │ │ @@ -8208,32 +8208,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001892 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001211 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.731040e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.774310e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.718100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.933400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.356070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.813990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.095520e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.606160e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.315574e-01 │ │ │ │ Vprtstp: contraction number = 1.315574e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -8253,33 +8253,33 @@ │ │ │ │ Vprtstp: contraction number = 2.039480e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.384411e-06 │ │ │ │ Vprtstp: contraction number = 2.095783e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.318373e-07 │ │ │ │ Vprtstp: contraction number = 2.125342e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.347578e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.564065e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.583496e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.845052e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.922758694192E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.962000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.293000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -8326,30 +8326,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0317294 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002103 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000526 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.698280e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.817340e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.673700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.823700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.386410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.788120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.267260e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.602212e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.252944e-01 │ │ │ │ Vprtstp: contraction number = 1.252944e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -8372,33 +8372,33 @@ │ │ │ │ Vprtstp: contraction number = 2.195054e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.334000e-06 │ │ │ │ Vprtstp: contraction number = 2.220609e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.987906e-07 │ │ │ │ Vprtstp: contraction number = 2.239810e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.601996e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.825223e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.798712e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.056954e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.571611857350E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.103000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.309000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -8445,30 +8445,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0914032 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001075 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000545 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.453030e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.626950e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.772000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.790800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.371530e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.776660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648155e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.233946e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.282975e-01 │ │ │ │ Vprtstp: contraction number = 1.282975e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -8500,31 +8500,31 @@ │ │ │ │ Vprtstp: contraction number = 3.626822e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.189511e-06 │ │ │ │ Vprtstp: contraction number = 3.637026e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.980984e-07 │ │ │ │ Vprtstp: contraction number = 3.645099e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.495379e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.713977e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.542900e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.797813e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.198504468496E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.031000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.008000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -8547,28 +8547,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.855100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.088800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.810800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.808500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.407570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.784360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042507e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108009e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114962e-01 │ │ │ │ Vprtstp: contraction number = 1.114962e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -8585,33 +8585,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068021e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473387e-06 │ │ │ │ Vprtstp: contraction number = 1.075288e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.592943e-07 │ │ │ │ Vprtstp: contraction number = 1.081144e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.924416e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.156714e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.015574e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.276366e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-25, -25, -25) │ │ │ │ Vpmg_setPart: actual maxima = (25, 25, 25) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.401946508931E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.971000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.230000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -8656,28 +8656,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2.49076 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.268800e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.357800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.882300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.789300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.186620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.802580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.262684e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.344871e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115250e-01 │ │ │ │ Vprtstp: contraction number = 1.115250e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -8697,33 +8697,33 @@ │ │ │ │ Vprtstp: contraction number = 1.974179e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.739799e-06 │ │ │ │ Vprtstp: contraction number = 2.010662e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.580347e-07 │ │ │ │ Vprtstp: contraction number = 2.036772e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.036308e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.223960e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.390861e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.652113e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-7.06083, -7.06083, -12.2474) │ │ │ │ Vpmg_setPart: actual maxima = (11.8833, 11.8833, 12.2474) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.099156934185E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.148000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.185000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.200000e-05 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3 │ │ │ │ Vpbe_ctor2: solute dimensions = 6 x 6 x 6 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -8768,28 +8768,28 @@ │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 7.17281 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.085400e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.563000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.265400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.386800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.440090e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.586330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.500294e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.616776e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.116239e-01 │ │ │ │ Vprtstp: contraction number = 1.116239e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -8821,29 +8821,29 @@ │ │ │ │ Vprtstp: contraction number = 3.639660e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.623522e-06 │ │ │ │ Vprtstp: contraction number = 3.646624e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 5.928877e-07 │ │ │ │ Vprtstp: contraction number = 3.651861e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.407376e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.650250e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.837684e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.072792e+00 │ │ │ │ Vpmg_setPart: lower corner = (0, 0, -6) │ │ │ │ Vpmg_setPart: upper corner = (6, 6, 6) │ │ │ │ Vpmg_setPart: actual minima = (-1.17757, -1.17757, -6) │ │ │ │ Vpmg_setPart: actual maxima = (6, 6, 6) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 1 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 1 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.244769313634E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.919000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.326000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.841634e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.001375e+01 │ │ │ ├── ./usr/share/apbs/examples/hca-bind/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:34:26 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:11:51 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path acet.pqr │ │ │ │ @@ -289,32 +289,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.016624 │ │ │ │ +Vacc_SASA: Time elapsed: 0.013031 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.361500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.575300e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.343900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.770500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.492840e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.722570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.867570e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.575410e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.087255e-01 │ │ │ │ Vprtstp: contraction number = 1.087255e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -331,32 +331,32 @@ │ │ │ │ Vprtstp: contraction number = 1.074047e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.481057e-06 │ │ │ │ Vprtstp: contraction number = 1.080656e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.608051e-07 │ │ │ │ Vprtstp: contraction number = 1.085746e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.717546e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.978412e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.068047e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.320167e+00 │ │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.785902379684E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.500000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.580000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -402,30 +402,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.104294 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.014525 │ │ │ │ +Vacc_SASA: Time elapsed: 0.012203 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.552800e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.850400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.035900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.646200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.232950e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.726680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.509364e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.874334e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.287269e-01 │ │ │ │ Vprtstp: contraction number = 1.287269e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -451,32 +451,32 @@ │ │ │ │ Vprtstp: contraction number = 3.073619e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.517211e-06 │ │ │ │ Vprtstp: contraction number = 3.092055e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 4.703221e-07 │ │ │ │ Vprtstp: contraction number = 3.099912e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.493711e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.694443e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.919060e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.170445e+00 │ │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.473001739532E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.020000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -522,30 +522,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.504504 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.015830 │ │ │ │ +Vacc_SASA: Time elapsed: 0.012172 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.812200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.938600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.925600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.593800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.239390e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.700710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.306019e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.141836e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.402627e-01 │ │ │ │ Vprtstp: contraction number = 1.402627e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -574,30 +574,30 @@ │ │ │ │ Vprtstp: contraction number = 3.281873e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.285796e-06 │ │ │ │ Vprtstp: contraction number = 3.294777e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.250794e-07 │ │ │ │ Vprtstp: contraction number = 3.305964e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.687911e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.884020e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.241812e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.492137e+00 │ │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.210605041355E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.530000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -620,32 +620,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 4.079204 │ │ │ │ +Vacc_SASA: Time elapsed: 4.011897 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.251493e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.169495e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.308800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.893400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.429410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.751190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.247146e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.381809e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.838248e-02 │ │ │ │ Vprtstp: contraction number = 7.838248e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -707,30 +707,30 @@ │ │ │ │ Vprtstp: contraction number = 6.567898e-01 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 1.365716e-06 │ │ │ │ Vprtstp: contraction number = 6.589433e-01 │ │ │ │ Vprtstp: iteration = 22 │ │ │ │ Vprtstp: relative residual = 9.028429e-07 │ │ │ │ Vprtstp: contraction number = 6.610767e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.411119e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.628214e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.085693e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.341045e+00 │ │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.689092374656E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.070000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.530000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -778,30 +778,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 4518.73 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2191.64 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.945899 │ │ │ │ +Vacc_SASA: Time elapsed: 3.993294 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.205979e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.249000e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.965400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.569700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.251470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.752770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.229863e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.441793e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.397950e-01 │ │ │ │ Vprtstp: contraction number = 1.397950e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -842,30 +842,30 @@ │ │ │ │ Vprtstp: contraction number = 5.527064e-01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 1.277233e-06 │ │ │ │ Vprtstp: contraction number = 5.598610e-01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 7.227170e-07 │ │ │ │ Vprtstp: contraction number = 5.658458e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.704640e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.905125e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.743384e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.996915e+00 │ │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.222630775541E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.160000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.910000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -913,30 +913,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 110988 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 56275.9 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.956525 │ │ │ │ +Vacc_SASA: Time elapsed: 3.772951 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.194939e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.987333e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.057200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.584200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.255240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.666010e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.040402e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.240597e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115653e-01 │ │ │ │ Vprtstp: contraction number = 1.115653e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -962,30 +962,30 @@ │ │ │ │ Vprtstp: contraction number = 3.498142e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.355176e-06 │ │ │ │ Vprtstp: contraction number = 3.685616e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.245419e-07 │ │ │ │ Vprtstp: contraction number = 3.925575e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.395320e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.591419e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.782061e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.029049e+00 │ │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.441218006192E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.090000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.440000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ │ @@ -1008,32 +1008,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 4.002417 │ │ │ │ +Vacc_SASA: Time elapsed: 3.817879 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.192440e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.989466e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.101400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.424800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.271470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.642310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.719815e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.942957e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.658858e-02 │ │ │ │ Vprtstp: contraction number = 7.658858e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1095,32 +1095,32 @@ │ │ │ │ Vprtstp: contraction number = 6.561084e-01 │ │ │ │ Vprtstp: iteration = 21 │ │ │ │ Vprtstp: relative residual = 1.508067e-06 │ │ │ │ Vprtstp: contraction number = 6.580134e-01 │ │ │ │ Vprtstp: iteration = 22 │ │ │ │ Vprtstp: relative residual = 9.954065e-07 │ │ │ │ Vprtstp: contraction number = 6.600544e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.565590e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 5.762433e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.077829e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.321009e+00 │ │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.698545237167E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.250000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.080000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1166,30 +1166,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 4519.43 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2191.49 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.983945 │ │ │ │ +Vacc_SASA: Time elapsed: 3.855844 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.225292e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.081303e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.901900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.578200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.265540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.692910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.719725e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.984868e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.396668e-01 │ │ │ │ Vprtstp: contraction number = 1.396668e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1230,32 +1230,32 @@ │ │ │ │ Vprtstp: contraction number = 5.525486e-01 │ │ │ │ Vprtstp: iteration = 14 │ │ │ │ Vprtstp: relative residual = 1.290655e-06 │ │ │ │ Vprtstp: contraction number = 5.600207e-01 │ │ │ │ Vprtstp: iteration = 15 │ │ │ │ Vprtstp: relative residual = 7.308313e-07 │ │ │ │ Vprtstp: contraction number = 5.662486e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.699961e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.898564e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.989630e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.239152e+00 │ │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.237049215096E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.420000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.240000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1301,30 +1301,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 110994 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 56275.1 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 4.004734 │ │ │ │ +Vacc_SASA: Time elapsed: 3.931378 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.242248e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.159583e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.215800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.546600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.225190e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.674100e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.534265e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.825513e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.163858e-01 │ │ │ │ Vprtstp: contraction number = 1.163858e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1353,38 +1353,38 @@ │ │ │ │ Vprtstp: contraction number = 3.950088e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.396547e-06 │ │ │ │ Vprtstp: contraction number = 4.328810e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.612158e-07 │ │ │ │ Vprtstp: contraction number = 4.734646e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.003913e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.197395e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.172673e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.419781e+00 │ │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.492900778210E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.400000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.960000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.839945e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.148348e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:35:07 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:13:10 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path acet.pqr │ │ │ │ @@ -1669,32 +1669,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.015129 │ │ │ │ +Vacc_SASA: Time elapsed: 0.014816 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.762590e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.660580e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.140800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.809900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.459190e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.784990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.769120e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.015060e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.084928e-01 │ │ │ │ Vprtstp: contraction number = 1.084928e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1711,32 +1711,32 @@ │ │ │ │ Vprtstp: contraction number = 1.067805e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.430429e-06 │ │ │ │ Vprtstp: contraction number = 1.075005e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.545898e-07 │ │ │ │ Vprtstp: contraction number = 1.080723e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.865063e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.097309e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.002564e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.260201e+00 │ │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.520701614302E+02 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.000000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.800000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1782,30 +1782,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.105108 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.013001 │ │ │ │ +Vacc_SASA: Time elapsed: 0.012940 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.290420e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.088380e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.870300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.763800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.275470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.708020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.868587e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.067397e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.225646e-01 │ │ │ │ Vprtstp: contraction number = 1.225646e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1822,32 +1822,32 @@ │ │ │ │ Vprtstp: contraction number = 1.454441e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 5.669194e-06 │ │ │ │ Vprtstp: contraction number = 1.566066e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 9.449546e-07 │ │ │ │ Vprtstp: contraction number = 1.666823e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.809564e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.998119e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.767438e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.013297e+00 │ │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.468387819400E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.160000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 6.35359 │ │ │ │ Vpbe_ctor2: solute dimensions = 7.389 x 11.027 x 9.931 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1893,30 +1893,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.520445 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.015645 │ │ │ │ +Vacc_SASA: Time elapsed: 0.012695 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.278510e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.987810e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.193000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.459100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.408270e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.597550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.142802e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.272950e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.305252e-01 │ │ │ │ Vprtstp: contraction number = 1.305252e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1936,32 +1936,32 @@ │ │ │ │ Vprtstp: contraction number = 1.733670e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.357163e-06 │ │ │ │ Vprtstp: contraction number = 1.824572e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.550194e-07 │ │ │ │ Vprtstp: contraction number = 1.879063e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.080057e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.308027e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.132611e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.363433e+00 │ │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.211840549614E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.420000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1982,32 +1982,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 4.039728 │ │ │ │ +Vacc_SASA: Time elapsed: 3.931671 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.332712e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.193845e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.159800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.860200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.251240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.765380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.175338e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.186423e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.136636e-02 │ │ │ │ Vprtstp: contraction number = 5.136636e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2027,32 +2027,32 @@ │ │ │ │ Vprtstp: contraction number = 2.406804e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.980432e-06 │ │ │ │ Vprtstp: contraction number = 2.704556e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.800745e-07 │ │ │ │ Vprtstp: contraction number = 2.929030e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.981345e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.170376e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.511507e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.767662e+00 │ │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.766185147917E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.770000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.950000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2098,30 +2098,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 4619.67 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2259.75 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.963000 │ │ │ │ +Vacc_SASA: Time elapsed: 3.957408 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.342189e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.324081e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.163500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.992400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.234580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.688910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.827390e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.895811e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.613067e-02 │ │ │ │ Vprtstp: contraction number = 9.613067e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2141,32 +2141,32 @@ │ │ │ │ Vprtstp: contraction number = 1.833548e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.811522e-06 │ │ │ │ Vprtstp: contraction number = 1.939744e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.707504e-07 │ │ │ │ Vprtstp: contraction number = 2.046624e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.961059e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.148237e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.366214e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.614378e+00 │ │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.226315327863E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.340000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.750000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2212,30 +2212,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 111278 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 55995.6 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.939701 │ │ │ │ +Vacc_SASA: Time elapsed: 3.859052 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.306458e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.201318e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.172100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.601400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.248070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.655500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.474442e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.578032e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.009208e-01 │ │ │ │ Vprtstp: contraction number = 1.009208e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2252,32 +2252,32 @@ │ │ │ │ Vprtstp: contraction number = 1.451140e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 3.266673e-06 │ │ │ │ Vprtstp: contraction number = 1.668260e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.985159e-07 │ │ │ │ Vprtstp: contraction number = 1.832188e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.743949e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.937277e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.893937e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.137389e+00 │ │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.444499098932E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.100000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.420000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2298,32 +2298,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.982894 │ │ │ │ +Vacc_SASA: Time elapsed: 3.843403 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.289038e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.130741e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.994100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.565200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.215100e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.646240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.096979e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.205756e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.894768e-02 │ │ │ │ Vprtstp: contraction number = 4.894768e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2343,30 +2343,30 @@ │ │ │ │ Vprtstp: contraction number = 2.414708e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.098574e-06 │ │ │ │ Vprtstp: contraction number = 2.683582e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.050680e-07 │ │ │ │ Vprtstp: contraction number = 2.883234e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.950246e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.133478e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.181265e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.424952e+00 │ │ │ │ Vpmg_setPart: lower corner = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: upper corner = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: actual minima = (-54.0285, -44.1015, -32.821) │ │ │ │ Vpmg_setPart: actual maxima = (41.9715, 51.8985, 63.179) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.771575298437E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.420000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.270000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ │ @@ -2414,30 +2414,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 4620.09 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 2259.49 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 4.008386 │ │ │ │ +Vacc_SASA: Time elapsed: 3.930569 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.359385e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.306220e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.875700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.471600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.229700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.739030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.748067e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.881602e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.547807e-02 │ │ │ │ Vprtstp: contraction number = 9.547807e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2457,32 +2457,32 @@ │ │ │ │ Vprtstp: contraction number = 1.878215e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.896640e-06 │ │ │ │ Vprtstp: contraction number = 1.994763e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.991489e-07 │ │ │ │ Vprtstp: contraction number = 2.104505e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.991059e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.182814e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.245175e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.505404e+00 │ │ │ │ Vpmg_setPart: lower corner = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: upper corner = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: actual minima = (-24.6188, -14.6918, -3.41132) │ │ │ │ Vpmg_setPart: actual maxima = (12.5618, 22.4888, 33.7693) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.240652812594E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.690000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.770000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 31.0304 │ │ │ │ Vpbe_ctor2: solute dimensions = 49.637 x 47.533 x 56.913 │ │ │ │ Vpbe_ctor2: solute charge = -1.01863e-14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2528,30 +2528,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 111288 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 55994.2 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 4.000602 │ │ │ │ +Vacc_SASA: Time elapsed: 4.037771 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.358173e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.391913e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.129800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.314800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.212250e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.761540e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.402385e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.572182e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.031999e-01 │ │ │ │ Vprtstp: contraction number = 1.031999e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2568,28 +2568,28 @@ │ │ │ │ Vprtstp: contraction number = 1.434980e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 3.331639e-06 │ │ │ │ Vprtstp: contraction number = 1.622112e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.872183e-07 │ │ │ │ Vprtstp: contraction number = 1.762551e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.705228e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.889650e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.970014e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.227885e+00 │ │ │ │ Vpmg_setPart: lower corner = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: upper corner = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: actual minima = (-13.2285, -3.3015, 7.979) │ │ │ │ Vpmg_setPart: actual maxima = (1.1715, 11.0985, 22.379) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.496181357535E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 3.560000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.560000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.578003e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.774072e+01 │ │ │ ├── ./usr/share/apbs/examples/ion-pmf/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:36:09 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:15:35 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path ion-pmf.pdb │ │ │ │ @@ -161,28 +161,28 @@ │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefSpline... │ │ │ │ Vpmg_fillco: filling coefficient arrays │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.088900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.580000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.945000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.325300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.240230e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.930340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.615970e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.429830e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.194542e-01 │ │ │ │ Vprtstp: contraction number = 1.194542e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -202,33 +202,33 @@ │ │ │ │ Vprtstp: contraction number = 1.749569e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.117484e-06 │ │ │ │ Vprtstp: contraction number = 1.874072e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.180018e-07 │ │ │ │ Vprtstp: contraction number = 1.950826e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.955718e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.154469e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.598426e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.882163e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.324828953427E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.010000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.280000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.682600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.812700e-02 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 4 │ │ │ │ Vpbe_ctor2: solute dimensions = 8 x 4 x 4 │ │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -249,28 +249,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.739600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.471500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.946000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.043200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.240540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.865240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.489124e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.289743e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.110640e-01 │ │ │ │ Vprtstp: contraction number = 1.110640e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -287,50 +287,50 @@ │ │ │ │ Vprtstp: contraction number = 1.067494e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.466502e-06 │ │ │ │ Vprtstp: contraction number = 1.074548e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.584103e-07 │ │ │ │ Vprtstp: contraction number = 1.080191e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.710915e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.907710e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.267616e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.540554e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 7.232617942545E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.931000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.442000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vpmg_dbForce: No force for uniform dielectric! │ │ │ │ Vpmg_dbForce: No force for uniform dielectric! │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-04 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.460000e-04 │ │ │ │ APOL: Setting up hash table and accessibility object... │ │ │ │ Vclist_ctor2: Using 16 x 8 x 8 hash table │ │ │ │ Vclist_ctor2: automatic domain setup. │ │ │ │ Vclist_ctor2: Using 1.8 max radius │ │ │ │ Vclist_setupGrid: Grid lengths = (14.792, 10.792, 10.792) │ │ │ │ Vclist_setupGrid: Grid lower corner = (-8.396, -5.396, -5.396) │ │ │ │ Vclist_assignAtoms: Have 720 atom entries │ │ │ │ Vacc_storeParms: Surf. density = 100 │ │ │ │ Vacc_storeParms: Max area = 181.458 │ │ │ │ Vacc_storeParms: Using 18030-point reference sphere │ │ │ │ forceAPOL: Trying atom surf... │ │ │ │ -forceAPOL: atom surf: Time elapsed: 0.006010 │ │ │ │ -forceAPOL: Time elapsed: 12.617797 │ │ │ │ -Vacc_SASA: Time elapsed: 0.000005 │ │ │ │ -initAPOL: Time elapsed: 36.197309 │ │ │ │ +forceAPOL: atom surf: Time elapsed: 0.006462 │ │ │ │ +forceAPOL: Time elapsed: 12.900314 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000004 │ │ │ │ +initAPOL: Time elapsed: 36.884813 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ @@ -339,8 +339,8 @@ │ │ │ │ printForce: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.039484e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 4.244181e+01 │ │ │ ├── ./usr/share/apbs/examples/ionize/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:35:42 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:14:08 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path acetic-acid.xml │ │ │ │ @@ -481,32 +481,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.007433 │ │ │ │ +Vacc_SASA: Time elapsed: 0.004390 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.223500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.114500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.799100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.173600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.526800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.837510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.598510e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.538720e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.188999e-01 │ │ │ │ Vprtstp: contraction number = 3.188999e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -535,30 +535,30 @@ │ │ │ │ Vprtstp: contraction number = 2.912126e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.816386e-06 │ │ │ │ Vprtstp: contraction number = 2.924708e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.271441e-07 │ │ │ │ Vprtstp: contraction number = 2.936899e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.653586e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.915379e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.403729e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.674656e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 4.781227236323E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.320000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.500000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ │ @@ -606,30 +606,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0505207 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.005124 │ │ │ │ +Vacc_SASA: Time elapsed: 0.003822 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.054100e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.011260e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.859400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.222700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.237600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.807040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.326618e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.139248e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.598074e-01 │ │ │ │ Vprtstp: contraction number = 2.598074e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -661,32 +661,32 @@ │ │ │ │ Vprtstp: contraction number = 3.326351e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 2.087103e-06 │ │ │ │ Vprtstp: contraction number = 3.343120e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 7.014192e-07 │ │ │ │ Vprtstp: contraction number = 3.360731e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.899303e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.098562e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.762945e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.033274e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.039953678525E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.000000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -707,28 +707,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.489300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.990100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.974400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.476900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.229920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.888460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.477684e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.227642e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.679930e-01 │ │ │ │ Vprtstp: contraction number = 1.679930e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -745,30 +745,30 @@ │ │ │ │ Vprtstp: contraction number = 1.043091e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.862252e-06 │ │ │ │ Vprtstp: contraction number = 1.059323e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.994142e-07 │ │ │ │ Vprtstp: contraction number = 1.070823e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.728116e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.926122e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.158213e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.435625e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 4.800125490193E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.140000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ │ @@ -814,28 +814,28 @@ │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 1.14339 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.624900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.929900e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.847200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.161700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.234910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.825060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.490470e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073490e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.651787e-01 │ │ │ │ Vprtstp: contraction number = 1.651787e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -852,32 +852,32 @@ │ │ │ │ Vprtstp: contraction number = 1.055047e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.934803e-06 │ │ │ │ Vprtstp: contraction number = 1.064764e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.073576e-07 │ │ │ │ Vprtstp: contraction number = 1.071724e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.771809e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.971437e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.201849e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.470955e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.058572238076E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.040000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -898,32 +898,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.006369 │ │ │ │ +Vacc_SASA: Time elapsed: 0.003605 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.384900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.405200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.964100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.277400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.248790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.856930e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053712e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.328719e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.669750e-01 │ │ │ │ Vprtstp: contraction number = 1.669750e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -952,32 +952,32 @@ │ │ │ │ Vprtstp: contraction number = 3.348642e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.783762e-06 │ │ │ │ Vprtstp: contraction number = 3.348981e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 9.322590e-07 │ │ │ │ Vprtstp: contraction number = 3.348918e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.644592e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.846834e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.333714e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.609879e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 6.748221698410E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.090000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.040000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -1023,30 +1023,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.600233 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.005270 │ │ │ │ +Vacc_SASA: Time elapsed: 0.003481 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.056760e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.029380e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.841200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.217900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.234900e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.834560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.348985e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.700612e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.532338e-01 │ │ │ │ Vprtstp: contraction number = 1.532338e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1078,32 +1078,32 @@ │ │ │ │ Vprtstp: contraction number = 3.529902e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.276975e-06 │ │ │ │ Vprtstp: contraction number = 3.528897e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.504551e-07 │ │ │ │ Vprtstp: contraction number = 3.527516e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.884966e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.078745e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.776216e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.048687e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.143395002184E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.080000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.260000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1124,28 +1124,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.351200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.811400e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.930000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.282700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.215240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.888440e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.661891e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.111068e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.140338e-01 │ │ │ │ Vprtstp: contraction number = 1.140338e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1162,30 +1162,30 @@ │ │ │ │ Vprtstp: contraction number = 1.066400e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.493481e-06 │ │ │ │ Vprtstp: contraction number = 1.074330e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.613267e-07 │ │ │ │ Vprtstp: contraction number = 1.080206e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.702399e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.894267e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.188087e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.468172e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 6.912847895210E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.100000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.000000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ @@ -1231,28 +1231,28 @@ │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 22.4432 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.417700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.054000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.716000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.215100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.215790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.860090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.859363e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.365298e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.151233e-01 │ │ │ │ Vprtstp: contraction number = 1.151233e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1269,32 +1269,32 @@ │ │ │ │ Vprtstp: contraction number = 1.065071e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.498104e-06 │ │ │ │ Vprtstp: contraction number = 1.072349e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.614370e-07 │ │ │ │ Vprtstp: contraction number = 1.077609e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.728095e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.917589e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.225224e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.499040e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.159793508256E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.210000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.190000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -1315,32 +1315,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000275 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000277 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.157000e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.990500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.946600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.363600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.254160e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.914480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.057198e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.620871e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.470644e-01 │ │ │ │ Vprtstp: contraction number = 1.470644e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1366,32 +1366,32 @@ │ │ │ │ Vprtstp: contraction number = 2.846821e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.962532e-06 │ │ │ │ Vprtstp: contraction number = 2.852652e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 5.602483e-07 │ │ │ │ Vprtstp: contraction number = 2.854722e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.403070e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.602975e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.172854e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.454033e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.170869129315E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.800000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -1437,30 +1437,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.650584 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000270 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000286 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.528200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.300500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.927100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.009000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.272500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.804920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.326764e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.974229e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.382011e-01 │ │ │ │ Vprtstp: contraction number = 1.382011e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1489,32 +1489,32 @@ │ │ │ │ Vprtstp: contraction number = 3.143969e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.077403e-06 │ │ │ │ Vprtstp: contraction number = 3.146378e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.391862e-07 │ │ │ │ Vprtstp: contraction number = 3.148184e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.701951e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.900644e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.423293e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.691431e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.162367825044E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.200000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1535,28 +1535,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.677900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.112800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.951100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.129700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.227410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.890940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.621237e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.348445e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.118955e-01 │ │ │ │ Vprtstp: contraction number = 1.118955e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1573,32 +1573,32 @@ │ │ │ │ Vprtstp: contraction number = 1.069169e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.490424e-06 │ │ │ │ Vprtstp: contraction number = 1.076150e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.611536e-07 │ │ │ │ Vprtstp: contraction number = 1.081260e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.666165e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.863412e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.096653e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.375055e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.417301695136E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.200000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.600000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1642,28 +1642,28 @@ │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 27.9953 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.492300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.140800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.779000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.066000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.212540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.856020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.815253e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.593540e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.111894e-01 │ │ │ │ Vprtstp: contraction number = 1.111894e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1680,44 +1680,44 @@ │ │ │ │ Vprtstp: contraction number = 1.067651e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.469870e-06 │ │ │ │ Vprtstp: contraction number = 1.074950e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.588283e-07 │ │ │ │ Vprtstp: contraction number = 1.080560e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.700862e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.891074e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.036402e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.308037e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.406572492944E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.400000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.600000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.985629e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.798180e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:35:56 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:14:54 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path acetic-acid.xml │ │ │ │ @@ -2194,32 +2194,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.007306 │ │ │ │ +Vacc_SASA: Time elapsed: 0.005289 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.822720e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.716900e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.058600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.759400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.219910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.727920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.990150e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.571110e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.596091e-01 │ │ │ │ Vprtstp: contraction number = 2.596091e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2239,32 +2239,32 @@ │ │ │ │ Vprtstp: contraction number = 1.697798e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.455171e-06 │ │ │ │ Vprtstp: contraction number = 1.730577e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.805682e-07 │ │ │ │ Vprtstp: contraction number = 1.752050e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.962820e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.147472e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.288815e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.539100e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 4.781452735910E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.260000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -2310,30 +2310,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0553032 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.005243 │ │ │ │ +Vacc_SASA: Time elapsed: 0.003474 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.316010e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.182970e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.765600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.731600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.273200e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.739020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.798034e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.227421e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.192618e-01 │ │ │ │ Vprtstp: contraction number = 2.192618e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2353,32 +2353,32 @@ │ │ │ │ Vprtstp: contraction number = 1.807641e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.267839e-06 │ │ │ │ Vprtstp: contraction number = 1.838237e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.807397e-07 │ │ │ │ Vprtstp: contraction number = 1.861749e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.990981e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.186793e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.383558e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.636019e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.040239618722E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.040000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.700000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2399,28 +2399,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.716800e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.659600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.855000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.685500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.251950e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.724190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.052086e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.908600e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.679930e-01 │ │ │ │ Vprtstp: contraction number = 1.679930e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2437,32 +2437,32 @@ │ │ │ │ Vprtstp: contraction number = 1.043091e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.862252e-06 │ │ │ │ Vprtstp: contraction number = 1.059323e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.994142e-07 │ │ │ │ Vprtstp: contraction number = 1.070823e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.655930e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.863017e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.067936e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.318620e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 4.800125490193E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.010000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.700000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1.66533e-16 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2506,28 +2506,28 @@ │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 1.14339 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.447300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.716100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.146900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.764500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.208540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.757400e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.984547e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.310353e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.651787e-01 │ │ │ │ Vprtstp: contraction number = 1.651787e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2544,32 +2544,32 @@ │ │ │ │ Vprtstp: contraction number = 1.055047e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.934803e-06 │ │ │ │ Vprtstp: contraction number = 1.064764e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.073576e-07 │ │ │ │ Vprtstp: contraction number = 1.071724e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.691783e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.884996e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.112606e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.370637e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.058572238076E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.030000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.370000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -2590,32 +2590,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.005965 │ │ │ │ +Vacc_SASA: Time elapsed: 0.003484 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.915560e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.825770e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.835500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.789700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.231730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.831680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.070290e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087852e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.505354e-01 │ │ │ │ Vprtstp: contraction number = 1.505354e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2635,30 +2635,30 @@ │ │ │ │ Vprtstp: contraction number = 1.898671e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.115563e-06 │ │ │ │ Vprtstp: contraction number = 1.948490e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.143002e-07 │ │ │ │ Vprtstp: contraction number = 1.971715e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.905209e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.098857e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.358547e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.621957e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 6.749438220873E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.020000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.510000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ @@ -2706,30 +2706,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.607375 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.005276 │ │ │ │ +Vacc_SASA: Time elapsed: 0.003555 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.322280e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.309120e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.181100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.801400e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.209350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.747200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140539e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.373103e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.420228e-01 │ │ │ │ Vprtstp: contraction number = 1.420228e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2749,32 +2749,32 @@ │ │ │ │ Vprtstp: contraction number = 1.900725e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.720330e-06 │ │ │ │ Vprtstp: contraction number = 1.966740e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.430374e-07 │ │ │ │ Vprtstp: contraction number = 1.996219e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.925765e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.114654e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.330294e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.584031e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.143498275233E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.900000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.910000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2795,28 +2795,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.626600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.860700e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.859100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.877700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.247010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.742000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.358657e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.636720e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.140338e-01 │ │ │ │ Vprtstp: contraction number = 1.140338e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2833,32 +2833,32 @@ │ │ │ │ Vprtstp: contraction number = 1.066400e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.493481e-06 │ │ │ │ Vprtstp: contraction number = 1.074330e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.613267e-07 │ │ │ │ Vprtstp: contraction number = 1.080206e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.760203e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.960726e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.124489e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.382517e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 6.912847895210E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.430000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 3.17612 │ │ │ │ Vpbe_ctor2: solute dimensions = 4.116 x 5.186 x 5.967 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2902,28 +2902,28 @@ │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 22.4432 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.439700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.834700e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.116600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.820200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.222440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.745870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.562463e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.882792e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.151233e-01 │ │ │ │ Vprtstp: contraction number = 1.151233e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2940,32 +2940,32 @@ │ │ │ │ Vprtstp: contraction number = 1.065071e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.498104e-06 │ │ │ │ Vprtstp: contraction number = 1.072349e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.614370e-07 │ │ │ │ Vprtstp: contraction number = 1.077609e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.687974e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.882656e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.122038e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.380966e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.159793508256E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.400000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.250000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.128839 │ │ │ │ @@ -2986,32 +2986,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000273 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000264 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.660720e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.545910e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.849100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.744800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.243520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.750360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.768438e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.136851e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.382442e-01 │ │ │ │ Vprtstp: contraction number = 1.382442e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3031,30 +3031,30 @@ │ │ │ │ Vprtstp: contraction number = 1.741425e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.778515e-06 │ │ │ │ Vprtstp: contraction number = 1.810766e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.297938e-07 │ │ │ │ Vprtstp: contraction number = 1.854322e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.919185e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.116274e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.394092e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.649534e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.171449807940E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.700000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.240000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -3102,30 +3102,30 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.654498 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000280 │ │ │ │ +Vacc_SASA: Time elapsed: 0.000272 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.057640e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.082790e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.184100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.953600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.226230e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.793680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.000511e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.424168e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.297624e-01 │ │ │ │ Vprtstp: contraction number = 1.297624e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3145,32 +3145,32 @@ │ │ │ │ Vprtstp: contraction number = 1.701143e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.306208e-06 │ │ │ │ Vprtstp: contraction number = 1.773242e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.371381e-07 │ │ │ │ Vprtstp: contraction number = 1.815470e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.940621e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.127733e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.417799e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.679802e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.163593499843E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.800000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.500000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3191,28 +3191,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.908500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.251100e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.874300e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.070100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.249790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.829070e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219013e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.697106e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.118955e-01 │ │ │ │ Vprtstp: contraction number = 1.118955e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3229,32 +3229,32 @@ │ │ │ │ Vprtstp: contraction number = 1.069169e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.490424e-06 │ │ │ │ Vprtstp: contraction number = 1.076150e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.611536e-07 │ │ │ │ Vprtstp: contraction number = 1.081260e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.703700e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.900393e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.133186e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.403033e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: upper corner = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: actual minima = (-6, -6.1535, -4.713) │ │ │ │ Vpmg_setPart: actual maxima = (6, 5.8465, 7.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 3.417301695136E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.050000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.330000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.15 │ │ │ │ Vpbe_ctor2: solute dimensions = 2.3 x 2.3 x 2.3 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3298,28 +3298,28 @@ │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ VPMG::extEnergy: extQmEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 27.9953 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.383900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.744800e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.122900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.208200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.226230e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.803540e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.417721e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.945203e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.111894e-01 │ │ │ │ Vprtstp: contraction number = 1.111894e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3336,34 +3336,34 @@ │ │ │ │ Vprtstp: contraction number = 1.067651e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.469870e-06 │ │ │ │ Vprtstp: contraction number = 1.074950e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.588283e-07 │ │ │ │ Vprtstp: contraction number = 1.080560e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.646765e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.847357e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.186423e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.457157e+00 │ │ │ │ Vpmg_setPart: lower corner = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: upper corner = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: actual minima = (-3, -3.1535, -1.713) │ │ │ │ Vpmg_setPart: actual maxima = (3, 2.8465, 4.287) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 5.406572492944E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.080000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.020000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 2.582820e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 3.164899e+01 │ │ │ ├── ./usr/share/apbs/examples/pka-lig/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:36:47 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:16:45 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ │ @@ -340,31 +340,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.041508 │ │ │ │ +Vacc_SASA: Time elapsed: 0.039790 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.038970e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.719500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.614520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.686350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.474610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.225350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111041e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.191868e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.561608e-01 │ │ │ │ Vprtstp: contraction number = 1.561608e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -390,32 +390,32 @@ │ │ │ │ Vprtstp: contraction number = 2.750705e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.932473e-06 │ │ │ │ Vprtstp: contraction number = 2.767817e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 5.373027e-07 │ │ │ │ Vprtstp: contraction number = 2.780389e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.821031e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.595711e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 8.629908e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.487422e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.795090079491E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.430000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -461,29 +461,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.123733 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.042025 │ │ │ │ +Vacc_SASA: Time elapsed: 0.037595 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.646520e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.861110e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.618140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.689160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.501780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.044190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099811e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097681e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.152775e-01 │ │ │ │ Vprtstp: contraction number = 2.152775e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -515,30 +515,30 @@ │ │ │ │ Vprtstp: contraction number = 3.353090e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.328976e-06 │ │ │ │ Vprtstp: contraction number = 3.371305e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.496116e-07 │ │ │ │ Vprtstp: contraction number = 3.383143e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.039387e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.116875e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.032714e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.116649e+01 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.468794426258E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.370000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.670000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -561,31 +561,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.336827 │ │ │ │ +Vacc_SASA: Time elapsed: 5.397659 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.563195e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.655250e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.609670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.739060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.423890e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.203390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.774767e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.784923e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.188493e-01 │ │ │ │ Vprtstp: contraction number = 1.188493e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -638,30 +638,30 @@ │ │ │ │ Vprtstp: contraction number = 6.152114e-01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.141886e-06 │ │ │ │ Vprtstp: contraction number = 6.186689e-01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 7.101689e-07 │ │ │ │ Vprtstp: contraction number = 6.219261e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.642024e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.718626e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.679591e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.765628e+01 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.467100888191E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.376000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.600000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -709,29 +709,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 119417 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 58605.1 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.238257 │ │ │ │ +Vacc_SASA: Time elapsed: 5.315570 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.694111e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.799062e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.587260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.724600e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.495060e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.160340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.066648e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.133507e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.393577e-01 │ │ │ │ Vprtstp: contraction number = 1.393577e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -766,30 +766,30 @@ │ │ │ │ Vprtstp: contraction number = 4.796270e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.074713e-06 │ │ │ │ Vprtstp: contraction number = 4.999984e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 5.553244e-07 │ │ │ │ Vprtstp: contraction number = 5.167187e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.115905e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.193562e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.172243e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.258107e+01 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.427017897319E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.300000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.130000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -812,31 +812,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.379895 │ │ │ │ +Vacc_SASA: Time elapsed: 5.536424 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.625412e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.813901e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.603150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.747660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.475050e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.478670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.824348e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.979060e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189544e-01 │ │ │ │ Vprtstp: contraction number = 1.189544e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -889,32 +889,32 @@ │ │ │ │ Vprtstp: contraction number = 6.138674e-01 │ │ │ │ Vprtstp: iteration = 18 │ │ │ │ Vprtstp: relative residual = 1.173454e-06 │ │ │ │ Vprtstp: contraction number = 6.173088e-01 │ │ │ │ Vprtstp: iteration = 19 │ │ │ │ Vprtstp: relative residual = 7.281097e-07 │ │ │ │ Vprtstp: contraction number = 6.204841e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.616784e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.693325e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.759659e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.848472e+01 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.485227452845E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.683000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.897000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -960,29 +960,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 119415 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 58604.6 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.399612 │ │ │ │ +Vacc_SASA: Time elapsed: 5.503965 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.841578e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.008532e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.598570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.653240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.510760e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.353600e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.104456e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.429904e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.423446e-01 │ │ │ │ Vprtstp: contraction number = 1.423446e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1017,38 +1017,38 @@ │ │ │ │ Vprtstp: contraction number = 4.820331e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 1.206020e-06 │ │ │ │ Vprtstp: contraction number = 5.012326e-01 │ │ │ │ Vprtstp: iteration = 13 │ │ │ │ Vprtstp: relative residual = 6.232432e-07 │ │ │ │ Vprtstp: contraction number = 5.167767e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.129497e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.205857e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.199194e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.285957e+01 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.511771058265E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.590000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.230000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.024235e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.064118e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:37:48 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:19:26 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ │ @@ -1384,31 +1384,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.041247 │ │ │ │ +Vacc_SASA: Time elapsed: 0.040143 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.306800e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.896640e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.654620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.728630e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.430440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.148400e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.506499e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.662025e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.452428e-01 │ │ │ │ Vprtstp: contraction number = 1.452428e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1428,30 +1428,30 @@ │ │ │ │ Vprtstp: contraction number = 1.683190e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.126022e-06 │ │ │ │ Vprtstp: contraction number = 1.729184e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.755158e-07 │ │ │ │ Vprtstp: contraction number = 1.766283e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.919402e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.670182e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.420372e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.258353e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.796545857614E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.800000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.570000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ │ @@ -1499,29 +1499,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.131443 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.041656 │ │ │ │ +Vacc_SASA: Time elapsed: 0.038482 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.099910e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.844200e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.619920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.664830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.489350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.187890e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.915780e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073177e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.793309e-01 │ │ │ │ Vprtstp: contraction number = 1.793309e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1541,32 +1541,32 @@ │ │ │ │ Vprtstp: contraction number = 1.800338e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.360443e-06 │ │ │ │ Vprtstp: contraction number = 1.860813e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.400789e-07 │ │ │ │ Vprtstp: contraction number = 1.904746e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.096758e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.849964e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.447776e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.282597e+00 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.475324562943E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.570000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.460000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1587,31 +1587,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.346108 │ │ │ │ +Vacc_SASA: Time elapsed: 5.362296 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.985448e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.104898e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.603780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.664370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.577130e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.111070e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.377616e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.514094e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.027357e-02 │ │ │ │ Vprtstp: contraction number = 9.027357e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1631,32 +1631,32 @@ │ │ │ │ Vprtstp: contraction number = 1.817922e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.545186e-06 │ │ │ │ Vprtstp: contraction number = 1.999061e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.371519e-07 │ │ │ │ Vprtstp: contraction number = 2.181950e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.945156e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.696805e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.299205e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.128313e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.474786197493E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.392000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.604000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1702,29 +1702,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 120029 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 58911.7 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.212784 │ │ │ │ +Vacc_SASA: Time elapsed: 5.305931 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.075007e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.261969e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.620690e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.626040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.491240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.099620e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.757678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.955510e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.164650e-01 │ │ │ │ Vprtstp: contraction number = 1.164650e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1744,30 +1744,30 @@ │ │ │ │ Vprtstp: contraction number = 1.751675e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.167167e-06 │ │ │ │ Vprtstp: contraction number = 1.847486e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.216013e-07 │ │ │ │ Vprtstp: contraction number = 1.898626e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.777525e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.530160e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.989374e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.813502e+00 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.434258164340E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 4.890000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.220000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -1790,31 +1790,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.360147 │ │ │ │ +Vacc_SASA: Time elapsed: 5.366498 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.029862e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.134767e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.663390e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.708950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.930760e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.288770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.121343e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.356347e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.976616e-02 │ │ │ │ Vprtstp: contraction number = 8.976616e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1834,32 +1834,32 @@ │ │ │ │ Vprtstp: contraction number = 1.851080e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.610068e-06 │ │ │ │ Vprtstp: contraction number = 2.038795e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.565510e-07 │ │ │ │ Vprtstp: contraction number = 2.214509e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.872108e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.674393e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.338229e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.191719e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.493215172512E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.515000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.680000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1905,29 +1905,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 120027 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 58911 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 5.367362 │ │ │ │ +Vacc_SASA: Time elapsed: 5.708533 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.238500e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.648687e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.642100e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.716350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.577780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.412150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.511853e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.844570e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.180177e-01 │ │ │ │ Vprtstp: contraction number = 1.180177e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1947,38 +1947,38 @@ │ │ │ │ Vprtstp: contraction number = 1.739107e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.163103e-06 │ │ │ │ Vprtstp: contraction number = 1.834388e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.205019e-07 │ │ │ │ Vprtstp: contraction number = 1.895807e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.069977e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.836353e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.081945e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.947345e+00 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.519180536568E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.220000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.360000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.226929e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.563530e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:38:36 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:20:56 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ │ @@ -2314,31 +2314,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.032368 │ │ │ │ +Vacc_SASA: Time elapsed: 0.032811 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.740420e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.531160e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.636570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.636480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.485160e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.169340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.166131e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.226176e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.599213e-01 │ │ │ │ Vprtstp: contraction number = 1.599213e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2367,32 +2367,32 @@ │ │ │ │ Vprtstp: contraction number = 2.963523e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.017970e-06 │ │ │ │ Vprtstp: contraction number = 2.969958e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.027030e-07 │ │ │ │ Vprtstp: contraction number = 2.973596e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.561757e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.032553e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.010390e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.094570e+01 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.810710599589E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.270000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.480000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2438,29 +2438,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.127039 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.034165 │ │ │ │ +Vacc_SASA: Time elapsed: 0.031276 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.122666e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.126859e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.693400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.663630e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.595570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.144660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.266848e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.332585e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.128592e-01 │ │ │ │ Vprtstp: contraction number = 2.128592e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2492,32 +2492,32 @@ │ │ │ │ Vprtstp: contraction number = 3.367480e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 1.365284e-06 │ │ │ │ Vprtstp: contraction number = 3.379196e-01 │ │ │ │ Vprtstp: iteration = 12 │ │ │ │ Vprtstp: relative residual = 4.626034e-07 │ │ │ │ Vprtstp: contraction number = 3.388332e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.049408e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.128509e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.131560e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.215728e+01 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.488596110069E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.020000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.720000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2538,31 +2538,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.418805 │ │ │ │ +Vacc_SASA: Time elapsed: 3.483881 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.894225e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.959902e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.591410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.765760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.393750e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.301320e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.884316e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.050656e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.008467e-01 │ │ │ │ Vprtstp: contraction number = 1.008467e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2591,30 +2591,30 @@ │ │ │ │ Vprtstp: contraction number = 4.011046e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.434965e-06 │ │ │ │ Vprtstp: contraction number = 4.261259e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.351498e-07 │ │ │ │ Vprtstp: contraction number = 4.426237e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.234542e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.994635e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.045518e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.133095e+01 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.502732517701E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.486000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.820000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -2662,29 +2662,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 122258 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 60015.6 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.374070 │ │ │ │ +Vacc_SASA: Time elapsed: 3.499295 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.555294e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.749548e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.602940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.654360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.447580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.301900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.442266e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.760166e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.444678e-01 │ │ │ │ Vprtstp: contraction number = 1.444678e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2713,32 +2713,32 @@ │ │ │ │ Vprtstp: contraction number = 3.502797e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.520619e-06 │ │ │ │ Vprtstp: contraction number = 3.554465e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.554489e-07 │ │ │ │ Vprtstp: contraction number = 3.652782e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.373622e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.013502e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.828439e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.068905e+01 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.462158714651E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.140000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.950000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2759,31 +2759,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.434351 │ │ │ │ +Vacc_SASA: Time elapsed: 3.521848 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.858264e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.016150e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.614600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.694070e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.560050e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.260170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.946096e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.333756e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.951095e-02 │ │ │ │ Vprtstp: contraction number = 9.951095e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2812,32 +2812,32 @@ │ │ │ │ Vprtstp: contraction number = 3.973081e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.298337e-06 │ │ │ │ Vprtstp: contraction number = 4.223462e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.734047e-07 │ │ │ │ Vprtstp: contraction number = 4.416455e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.431089e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.021034e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.981520e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.084325e+01 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.522103263384E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.479000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.653000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -2883,29 +2883,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 122254 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 60014.8 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.450534 │ │ │ │ +Vacc_SASA: Time elapsed: 3.532214 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.375232e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.502728e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.625590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.682890e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.495310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.165560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.507242e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.969954e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.413483e-01 │ │ │ │ Vprtstp: contraction number = 1.413483e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -2934,38 +2934,38 @@ │ │ │ │ Vprtstp: contraction number = 3.543205e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.106047e-06 │ │ │ │ Vprtstp: contraction number = 3.675340e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.216013e-07 │ │ │ │ Vprtstp: contraction number = 3.811783e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.660131e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.043723e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 9.608998e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.045788e+01 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.548006855100E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.320000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.120000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.480388e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.941150e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:39:24 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:22:36 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr │ │ │ │ @@ -3301,31 +3301,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.033547 │ │ │ │ +Vacc_SASA: Time elapsed: 0.033820 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.952720e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.587270e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.606990e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.666820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.396500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.122440e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.556304e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.717690e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.452175e-01 │ │ │ │ Vprtstp: contraction number = 1.452175e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3345,30 +3345,30 @@ │ │ │ │ Vprtstp: contraction number = 1.752116e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.443360e-06 │ │ │ │ Vprtstp: contraction number = 1.802654e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 4.491907e-07 │ │ │ │ Vprtstp: contraction number = 1.838414e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.822867e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.559175e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.328044e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.157851e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.816452194100E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.300000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.430000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 10.66 │ │ │ │ Vpbe_ctor2: solute dimensions = 17.188 x 12.75 x 15.33 │ │ │ │ Vpbe_ctor2: solute charge = 1.11022e-16 │ │ │ │ @@ -3416,29 +3416,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.133537 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.032536 │ │ │ │ +Vacc_SASA: Time elapsed: 0.032283 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.538192e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.636489e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.677850e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.659240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.502720e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.237080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070721e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.154650e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.775500e-01 │ │ │ │ Vprtstp: contraction number = 1.775500e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3458,32 +3458,32 @@ │ │ │ │ Vprtstp: contraction number = 1.827663e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.496113e-06 │ │ │ │ Vprtstp: contraction number = 1.891043e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.759954e-07 │ │ │ │ Vprtstp: contraction number = 1.933563e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.916030e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.679555e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.211744e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.049011e+00 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.493961459749E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.280000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.620000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3504,31 +3504,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.411850 │ │ │ │ +Vacc_SASA: Time elapsed: 3.486283 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.257191e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.447987e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.581130e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.617900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.477130e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.141550e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.365517e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.506177e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.789951e-02 │ │ │ │ Vprtstp: contraction number = 8.789951e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3545,32 +3545,32 @@ │ │ │ │ Vprtstp: contraction number = 1.398889e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 4.364929e-06 │ │ │ │ Vprtstp: contraction number = 1.509054e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.472971e-07 │ │ │ │ Vprtstp: contraction number = 1.941148e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.127080e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.875333e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.341120e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.168265e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.503907197961E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.409000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.735000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3616,29 +3616,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 122356 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 60065 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.372793 │ │ │ │ +Vacc_SASA: Time elapsed: 3.442233 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.974155e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.177411e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.624250e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.661820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.488280e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.257040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.653880e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.845381e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.361361e-01 │ │ │ │ Vprtstp: contraction number = 1.361361e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3658,32 +3658,32 @@ │ │ │ │ Vprtstp: contraction number = 1.780896e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.357861e-06 │ │ │ │ Vprtstp: contraction number = 1.814853e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.460991e-07 │ │ │ │ Vprtstp: contraction number = 1.812402e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.969743e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.724292e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.244454e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.089106e+00 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.463376211100E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.150000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.060000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3704,31 +3704,31 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.441333 │ │ │ │ +Vacc_SASA: Time elapsed: 3.529340 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.454266e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.508476e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.647460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.646880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.830000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.294080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.979895e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.207984e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.694592e-02 │ │ │ │ Vprtstp: contraction number = 8.694592e-02 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3745,32 +3745,32 @@ │ │ │ │ Vprtstp: contraction number = 1.389852e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 4.160523e-06 │ │ │ │ Vprtstp: contraction number = 1.496124e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.105844e-07 │ │ │ │ Vprtstp: contraction number = 1.948275e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 5.950645e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 6.759781e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.272040e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.115923e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: upper corner = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: actual minima = (-6.031, -67.507, -7.978) │ │ │ │ Vpmg_setPart: actual maxima = (63.969, 2.493, 62.022) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.523234125638E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.467000e-03 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.745000e-03 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 37.837 │ │ │ │ Vpbe_ctor2: solute dimensions = 60.969 x 56.587 x 62.12 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -3816,29 +3816,29 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 122353 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 60064.1 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 3.443573 │ │ │ │ +Vacc_SASA: Time elapsed: 3.503320 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.799989e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 5.978742e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (097, 097, 097) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.618480e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 1.668090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (049, 049, 049) │ │ │ │ Vbuildops: Galer: (025, 025, 025) │ │ │ │ Vbuildops: Galer: (013, 013, 013) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.569050e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.191240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.234098e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.519804e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.348493e-01 │ │ │ │ Vprtstp: contraction number = 1.348493e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -3858,28 +3858,28 @@ │ │ │ │ Vprtstp: contraction number = 1.735657e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.117086e-06 │ │ │ │ Vprtstp: contraction number = 1.891826e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.184693e-07 │ │ │ │ Vprtstp: contraction number = 1.955708e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 6.891393e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.654653e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 7.288627e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.127158e+00 │ │ │ │ Vpmg_setPart: lower corner = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: upper corner = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: actual minima = (12.822, -45.153, 9.545) │ │ │ │ Vpmg_setPart: actual maxima = (36.822, -21.153, 33.545) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.549194232887E+05 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 5.250000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 6.230000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.930529e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.259033e+01 │ │ │ ├── ./usr/share/apbs/examples/point-pmf/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:07 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:23:59 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ │ @@ -184,28 +184,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.982100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.932500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.087200e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.769600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.229660e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.726230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.492990e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.958360e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -222,33 +222,33 @@ │ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.708286e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.903418e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.201098e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.453404e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.691000e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.750100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -269,28 +269,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.975500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.041000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.921400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.233500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.261070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.894470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.227632e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.833041e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.116487e-01 │ │ │ │ Vprtstp: contraction number = 1.116487e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -307,33 +307,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068390e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.476968e-06 │ │ │ │ Vprtstp: contraction number = 1.075610e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.596976e-07 │ │ │ │ Vprtstp: contraction number = 1.081253e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.680020e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.884697e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.283497e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.561129e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.241648379021E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.674400e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.782300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 7.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 0.5 │ │ │ │ Vpbe_ctor2: solute dimensions = 1 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -354,28 +354,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.079000e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.377500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.879400e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.848200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.254080e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.836660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.175738e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.444990e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.110273e-01 │ │ │ │ Vprtstp: contraction number = 1.110273e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -392,39 +392,39 @@ │ │ │ │ Vprtstp: contraction number = 1.067630e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.464818e-06 │ │ │ │ Vprtstp: contraction number = 1.074713e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.582462e-07 │ │ │ │ Vprtstp: contraction number = 1.080314e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.710579e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.912400e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.265545e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.533153e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.660589930493E+02 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.681800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.790700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.906724e+00 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.736463e+00 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:10 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:24:08 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ │ @@ -604,28 +604,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.975500e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.912000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.124100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.990000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.222280e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.844080e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.521010e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.105030e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -642,31 +642,31 @@ │ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.714325e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.912997e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.293148e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.562341e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.673200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.764000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ @@ -689,28 +689,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.024200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.371000e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.905800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.033500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.260850e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.860130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.238517e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.934860e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115116e-01 │ │ │ │ Vprtstp: contraction number = 1.115116e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -727,33 +727,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068563e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.477070e-06 │ │ │ │ Vprtstp: contraction number = 1.075813e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.597562e-07 │ │ │ │ Vprtstp: contraction number = 1.081575e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.720992e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.927251e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.261219e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.531956e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.209948502984E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.655500e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.792200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1 │ │ │ │ Vpbe_ctor2: solute dimensions = 2 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -774,28 +774,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.060700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.369200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.902000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.890200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.257130e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.863000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.231123e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.526904e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.112280e-01 │ │ │ │ Vprtstp: contraction number = 1.112280e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -812,39 +812,39 @@ │ │ │ │ Vprtstp: contraction number = 1.067265e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.466596e-06 │ │ │ │ Vprtstp: contraction number = 1.074314e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.583845e-07 │ │ │ │ Vprtstp: contraction number = 1.079946e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.684262e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.889998e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.266671e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.536847e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.681569832028E+02 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.685800e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.815900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.936139e+00 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.822775e+00 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:13 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:24:18 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ │ @@ -1024,28 +1024,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.028100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.962700e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.159800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.081100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.222090e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.854520e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.476710e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.194070e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1062,33 +1062,33 @@ │ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.737602e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.933040e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.292836e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.566919e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.692100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.780300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1109,28 +1109,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.918700e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.353200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.884900e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.016000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.272610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.854900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.255980e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.944701e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.122494e-01 │ │ │ │ Vprtstp: contraction number = 1.122494e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1147,33 +1147,33 @@ │ │ │ │ Vprtstp: contraction number = 1.068256e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.484900e-06 │ │ │ │ Vprtstp: contraction number = 1.075504e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.605755e-07 │ │ │ │ Vprtstp: contraction number = 1.081389e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.740992e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.946736e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.295453e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.567302e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.079207063662E+02 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.678900e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.774000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 1.5 │ │ │ │ Vpbe_ctor2: solute dimensions = 3 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1194,28 +1194,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.837600e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.391700e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.877700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.878200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.268190e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.815370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.263702e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.566376e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117126e-01 │ │ │ │ Vprtstp: contraction number = 1.117126e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1232,39 +1232,39 @@ │ │ │ │ Vprtstp: contraction number = 1.067223e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.472511e-06 │ │ │ │ Vprtstp: contraction number = 1.074345e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.590395e-07 │ │ │ │ Vprtstp: contraction number = 1.080057e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.677200e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.879982e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.273181e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.538736e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.915601904303E+02 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.673100e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.744700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.960697e+00 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.866326e+00 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:16 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:24:27 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path mol0.pqr │ │ │ │ @@ -1444,28 +1444,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.118300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.062600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.045700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.942900e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.270590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.851730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.598990e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.149270e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117158e-01 │ │ │ │ Vprtstp: contraction number = 1.117158e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1482,33 +1482,33 @@ │ │ │ │ Vprtstp: contraction number = 1.067217e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.472908e-06 │ │ │ │ Vprtstp: contraction number = 1.074130e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.590269e-07 │ │ │ │ Vprtstp: contraction number = 1.079680e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.737913e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.942798e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.178700e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.449023e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 7.887170085535E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.665700e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.725800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 0 │ │ │ │ Vpbe_ctor2: solute dimensions = 0 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1529,28 +1529,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.947000e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.179500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.889100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.789300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.239610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.784520e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.259641e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.810100e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.115116e-01 │ │ │ │ Vprtstp: contraction number = 1.115116e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1567,31 +1567,31 @@ │ │ │ │ Vprtstp: contraction number = 1.068563e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.477070e-06 │ │ │ │ Vprtstp: contraction number = 1.075813e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.597562e-07 │ │ │ │ Vprtstp: contraction number = 1.081575e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.698705e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.895716e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.139475e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.398107e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 8.209948502984E+01 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.657200e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.713600e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2 │ │ │ │ Vpbe_ctor2: solute dimensions = 4 x 0 x 0 │ │ │ │ Vpbe_ctor2: solute charge = 2 │ │ │ │ @@ -1614,28 +1614,28 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.966900e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.265600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.776100e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.829500e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.238420e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.755930e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.226535e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.265208e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.113661e-01 │ │ │ │ Vprtstp: contraction number = 1.113661e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1652,29 +1652,29 @@ │ │ │ │ Vprtstp: contraction number = 1.067553e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.470482e-06 │ │ │ │ Vprtstp: contraction number = 1.074604e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.588507e-07 │ │ │ │ Vprtstp: contraction number = 1.080263e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.649699e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.853068e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.115356e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.372292e+00 │ │ │ │ Vpmg_setPart: lower corner = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: upper corner = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: actual minima = (-6.72, -6.72, -6.72) │ │ │ │ Vpmg_setPart: actual maxima = (6.72, 6.72, 6.72) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.645453654146E+02 kT │ │ │ │ Vpmg_qmEnergy: Zero energy for zero ionic strength! │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.667500e-02 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.714300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 5.896894e+00 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 7.405678e+00 │ │ │ ├── ./usr/share/apbs/examples/protein-rna/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:28 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:24:48 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -274,151 +274,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.902195 │ │ │ │ +Vacc_SASA: Time elapsed: 0.914771 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.640195e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.633093e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.380650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.435950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.302650e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.084310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.352123e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.416095e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3489953.107213 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.147534e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.253931e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.541420e+05 │ │ │ │ Vprtstp: contraction number = 4.541420e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.152961 │ │ │ │ Vnewton: Attempting damping, relres = 0.557868 │ │ │ │ Vnewton: Damping accepted, relres = 0.152961 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.529613e-01 │ │ │ │ Vprtstp: contraction number = 1.529613e-01 │ │ │ │ Vnewton: Using errtol_s: 533827.862441 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.906533e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.347204e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.616204e+04 │ │ │ │ Vprtstp: contraction number = 7.616204e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.889845e-02 │ │ │ │ Vprtstp: contraction number = 1.889265e-01 │ │ │ │ Vnewton: Using errtol_s: 100854.249053 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.331627e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.141940e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.621156e+04 │ │ │ │ Vprtstp: contraction number = 1.621156e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.485254e-03 │ │ │ │ Vprtstp: contraction number = 2.244153e-01 │ │ │ │ Vnewton: Using errtol_s: 22633.233232 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.760812e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.909277e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.163481e+03 │ │ │ │ Vprtstp: contraction number = 4.163481e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.448984e-03 │ │ │ │ Vprtstp: contraction number = 2.234275e-01 │ │ │ │ Vnewton: Using errtol_s: 5056.886378 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.187275e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064684e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.135331e+03 │ │ │ │ Vprtstp: contraction number = 1.135331e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.105204e-04 │ │ │ │ Vprtstp: contraction number = 2.143021e-01 │ │ │ │ Vnewton: Using errtol_s: 1083.701574 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060207e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.228533e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.001303e+02 │ │ │ │ Vprtstp: contraction number = 3.001303e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 7.746175e-05 │ │ │ │ Vprtstp: contraction number = 2.494579e-01 │ │ │ │ Vnewton: Using errtol_s: 270.337872 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.202412e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.403876e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.503484e+01 │ │ │ │ Vprtstp: contraction number = 8.503484e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.192913e-05 │ │ │ │ Vprtstp: contraction number = 2.830962e-01 │ │ │ │ Vnewton: Using errtol_s: 76.531632 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.344302e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.574011e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.526272e+01 │ │ │ │ Vprtstp: contraction number = 2.526272e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.514831e-06 │ │ │ │ Vprtstp: contraction number = 2.970857e-01 │ │ │ │ Vnewton: Using errtol_s: 22.736454 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.486408e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.750373e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.640103e+00 │ │ │ │ Vprtstp: contraction number = 7.640103e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.970254e-06 │ │ │ │ Vprtstp: contraction number = 3.024259e-01 │ │ │ │ Vnewton: Using errtol_s: 6.876093 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.628361e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.929808e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.337433e+00 │ │ │ │ Vprtstp: contraction number = 2.337433e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.027844e-07 │ │ │ │ Vprtstp: contraction number = 3.059426e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.502644e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.564600e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.830466e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.900048e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -428,17 +428,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.965827433401E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.569434563500E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.283478359962E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.382210e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.451040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.025 │ │ │ │ Vpbe_ctor2: xkappa = 0.0514861 │ │ │ │ @@ -485,160 +485,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.194992 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.890124 │ │ │ │ +Vacc_SASA: Time elapsed: 0.932910 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.881382e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.980795e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.394330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.502280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.331330e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.194840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.004475e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.358796e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3601925.484823 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.083554e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.442186e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.484865e+05 │ │ │ │ Vprtstp: contraction number = 5.484865e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.170948 │ │ │ │ Vnewton: Attempting damping, relres = 0.567920 │ │ │ │ Vnewton: Damping accepted, relres = 0.170948 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.709480e-01 │ │ │ │ Vprtstp: contraction number = 1.709480e-01 │ │ │ │ Vnewton: Using errtol_s: 615741.974888 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.257265e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.648648e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.034638e+05 │ │ │ │ Vprtstp: contraction number = 1.034638e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.462084e-02 │ │ │ │ Vprtstp: contraction number = 2.025226e-01 │ │ │ │ Vnewton: Using errtol_s: 124701.671212 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.397512e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.811315e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.424561e+04 │ │ │ │ Vprtstp: contraction number = 2.424561e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.233375e-03 │ │ │ │ Vprtstp: contraction number = 2.378156e-01 │ │ │ │ Vnewton: Using errtol_s: 29656.002425 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.538104e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.975631e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.562093e+03 │ │ │ │ Vprtstp: contraction number = 6.562093e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.983416e-03 │ │ │ │ Vprtstp: contraction number = 2.408995e-01 │ │ │ │ Vnewton: Using errtol_s: 7144.117639 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.679427e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.146691e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.862413e+03 │ │ │ │ Vprtstp: contraction number = 1.862413e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.794286e-04 │ │ │ │ Vprtstp: contraction number = 2.417186e-01 │ │ │ │ Vnewton: Using errtol_s: 1726.865972 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.820542e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.317085e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.263950e+02 │ │ │ │ Vprtstp: contraction number = 5.263950e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.315588e-04 │ │ │ │ Vprtstp: contraction number = 2.744075e-01 │ │ │ │ Vnewton: Using errtol_s: 473.865007 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.960452e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.490223e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.568838e+02 │ │ │ │ Vprtstp: contraction number = 1.568838e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.920007e-05 │ │ │ │ Vprtstp: contraction number = 2.979661e-01 │ │ │ │ Vnewton: Using errtol_s: 141.195715 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.100373e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.652722e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.889017e+01 │ │ │ │ Vprtstp: contraction number = 4.889017e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.221601e-05 │ │ │ │ Vprtstp: contraction number = 3.116325e-01 │ │ │ │ Vnewton: Using errtol_s: 44.001172 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.241534e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.831131e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.562922e+01 │ │ │ │ Vprtstp: contraction number = 1.562922e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.905217e-06 │ │ │ │ Vprtstp: contraction number = 3.196802e-01 │ │ │ │ Vnewton: Using errtol_s: 14.066301 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.381765e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.006552e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.094993e+00 │ │ │ │ Vprtstp: contraction number = 5.094993e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.273067e-06 │ │ │ │ Vprtstp: contraction number = 3.259914e-01 │ │ │ │ Vnewton: Using errtol_s: 4.585493 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.522635e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.186121e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.686155e+00 │ │ │ │ Vprtstp: contraction number = 1.686155e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.213135e-07 │ │ │ │ Vprtstp: contraction number = 3.309436e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.625895e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.688171e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.965129e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.036593e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -648,17 +648,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.946137752289E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.954048421546E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475783126623E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.369160e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.387140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -685,151 +685,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.315424 │ │ │ │ +Vacc_SASA: Time elapsed: 0.313279 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.129820e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.397480e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.436840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.255530e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.173570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.064438e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.793334e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 990625.209730 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.144277e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.876934e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.350454e+05 │ │ │ │ Vprtstp: contraction number = 1.350454e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.127353 │ │ │ │ Vnewton: Attempting damping, relres = 0.559577 │ │ │ │ Vnewton: Damping accepted, relres = 0.127353 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.273531e-01 │ │ │ │ Vprtstp: contraction number = 1.273531e-01 │ │ │ │ Vnewton: Using errtol_s: 126159.215622 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.319404e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.078528e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.277893e+04 │ │ │ │ Vprtstp: contraction number = 2.277893e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.085042e-02 │ │ │ │ Vprtstp: contraction number = 1.637213e-01 │ │ │ │ Vnewton: Using errtol_s: 20654.953727 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.462081e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.247646e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.649050e+03 │ │ │ │ Vprtstp: contraction number = 4.649050e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.224159e-03 │ │ │ │ Vprtstp: contraction number = 2.025935e-01 │ │ │ │ Vnewton: Using errtol_s: 4184.558722 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.604456e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.415113e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.091881e+03 │ │ │ │ Vprtstp: contraction number = 1.091881e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 9.919956e-04 │ │ │ │ Vprtstp: contraction number = 2.348386e-01 │ │ │ │ Vnewton: Using errtol_s: 982.695801 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.747791e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.582010e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.793836e+02 │ │ │ │ Vprtstp: contraction number = 2.793836e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 2.538250e-04 │ │ │ │ Vprtstp: contraction number = 2.558731e-01 │ │ │ │ Vnewton: Using errtol_s: 251.445454 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.891411e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.751446e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.524959e+01 │ │ │ │ Vprtstp: contraction number = 7.524959e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 6.836556e-05 │ │ │ │ Vprtstp: contraction number = 2.693413e-01 │ │ │ │ Vnewton: Using errtol_s: 67.724647 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.035059e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.920193e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.096668e+01 │ │ │ │ Vprtstp: contraction number = 2.096668e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.904859e-05 │ │ │ │ Vprtstp: contraction number = 2.786284e-01 │ │ │ │ Vnewton: Using errtol_s: 18.870009 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.181508e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.083510e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.985543e+00 │ │ │ │ Vprtstp: contraction number = 5.985543e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 5.437969e-06 │ │ │ │ Vprtstp: contraction number = 2.854789e-01 │ │ │ │ Vnewton: Using errtol_s: 5.386989 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.329698e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.251831e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.740420e+00 │ │ │ │ Vprtstp: contraction number = 1.740420e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.581202e-06 │ │ │ │ Vprtstp: contraction number = 2.907706e-01 │ │ │ │ Vnewton: Using errtol_s: 1.566378 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.473339e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.417828e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.132173e-01 │ │ │ │ Vprtstp: contraction number = 5.132173e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 4.662667e-07 │ │ │ │ Vprtstp: contraction number = 2.948812e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.518782e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.580134e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.733629e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.803722e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -839,17 +839,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.196703875366E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.838438031793E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.417360829181E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.418230e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.450910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.025 │ │ │ │ Vpbe_ctor2: xkappa = 0.0514861 │ │ │ │ @@ -896,149 +896,149 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.017697 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.307894 │ │ │ │ +Vacc_SASA: Time elapsed: 0.296043 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.808160e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.912370e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.370860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.366570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.231150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.988760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.748754e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.700732e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1033125.204115 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.829257e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.782586e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.675387e+05 │ │ │ │ Vprtstp: contraction number = 1.675387e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.150147 │ │ │ │ Vnewton: Attempting damping, relres = 0.571307 │ │ │ │ Vnewton: Damping accepted, relres = 0.150147 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.501469e-01 │ │ │ │ Vprtstp: contraction number = 1.501469e-01 │ │ │ │ Vnewton: Using errtol_s: 155120.525305 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.003768e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.966227e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.209762e+04 │ │ │ │ Vprtstp: contraction number = 3.209762e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.810624e-02 │ │ │ │ Vprtstp: contraction number = 1.871917e-01 │ │ │ │ Vnewton: Using errtol_s: 29037.270087 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.145361e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.129406e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.331420e+03 │ │ │ │ Vprtstp: contraction number = 7.331420e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.387218e-03 │ │ │ │ Vprtstp: contraction number = 2.272526e-01 │ │ │ │ Vnewton: Using errtol_s: 6598.796330 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.287516e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.292745e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.824095e+03 │ │ │ │ Vprtstp: contraction number = 1.824095e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.589055e-03 │ │ │ │ Vprtstp: contraction number = 2.487867e-01 │ │ │ │ Vnewton: Using errtol_s: 1641.692880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.432815e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.454591e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.792383e+02 │ │ │ │ Vprtstp: contraction number = 4.792383e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.174858e-04 │ │ │ │ Vprtstp: contraction number = 2.627258e-01 │ │ │ │ Vnewton: Using errtol_s: 431.315051 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.577670e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.618274e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.310006e+02 │ │ │ │ Vprtstp: contraction number = 1.310006e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.141203e-04 │ │ │ │ Vprtstp: contraction number = 2.733515e-01 │ │ │ │ Vnewton: Using errtol_s: 117.900599 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.720502e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.782916e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.696481e+01 │ │ │ │ Vprtstp: contraction number = 3.696481e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.220165e-05 │ │ │ │ Vprtstp: contraction number = 2.821727e-01 │ │ │ │ Vnewton: Using errtol_s: 33.268335 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.866856e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.936388e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.072629e+01 │ │ │ │ Vprtstp: contraction number = 1.072629e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.344133e-06 │ │ │ │ Vprtstp: contraction number = 2.901756e-01 │ │ │ │ Vnewton: Using errtol_s: 9.653659 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.010405e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.107201e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.196371e+00 │ │ │ │ Vprtstp: contraction number = 3.196371e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.784497e-06 │ │ │ │ Vprtstp: contraction number = 2.979941e-01 │ │ │ │ Vnewton: Using errtol_s: 2.876734 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.159909e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.277170e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.745912e-01 │ │ │ │ Vprtstp: contraction number = 9.745912e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.490085e-07 │ │ │ │ Vprtstp: contraction number = 3.049056e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.521392e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.582314e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.709463e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.777066e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1048,15 +1048,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.190473517167E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.070936043953E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.033615774534E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.399170e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.460770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -1085,151 +1085,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.492814 │ │ │ │ +Vacc_SASA: Time elapsed: 0.498742 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.087635e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.113017e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.372380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.380910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.306620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.810390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.729518e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.891612e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3098216.768197 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.806959e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.973502e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.288533e+05 │ │ │ │ Vprtstp: contraction number = 4.288533e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.287242 │ │ │ │ Vnewton: Attempting damping, relres = 0.564665 │ │ │ │ Vnewton: Damping accepted, relres = 0.287242 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.872423e-01 │ │ │ │ Vprtstp: contraction number = 2.872423e-01 │ │ │ │ Vnewton: Using errtol_s: 889939.028652 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.982706e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.171330e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.459682e+04 │ │ │ │ Vprtstp: contraction number = 8.459682e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 7.479655e-02 │ │ │ │ Vprtstp: contraction number = 2.603953e-01 │ │ │ │ Vnewton: Using errtol_s: 231735.935287 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.126558e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.349101e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.140926e+04 │ │ │ │ Vprtstp: contraction number = 2.140926e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.197950e-02 │ │ │ │ Vprtstp: contraction number = 2.938571e-01 │ │ │ │ Vnewton: Using errtol_s: 68097.244831 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.269503e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.528243e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.306461e+03 │ │ │ │ Vprtstp: contraction number = 6.306461e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 6.113198e-03 │ │ │ │ Vprtstp: contraction number = 2.781319e-01 │ │ │ │ Vnewton: Using errtol_s: 18940.013709 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.413401e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.701940e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.039254e+03 │ │ │ │ Vprtstp: contraction number = 2.039254e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.310252e-03 │ │ │ │ Vprtstp: contraction number = 2.143317e-01 │ │ │ │ Vnewton: Using errtol_s: 4059.444466 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.555029e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.870265e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.729156e+02 │ │ │ │ Vprtstp: contraction number = 5.729156e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.010708e-04 │ │ │ │ Vprtstp: contraction number = 1.534596e-01 │ │ │ │ Vnewton: Using errtol_s: 622.960837 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.696510e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003480e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.140542e+02 │ │ │ │ Vprtstp: contraction number = 1.140542e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.330907e-05 │ │ │ │ Vprtstp: contraction number = 1.656585e-01 │ │ │ │ Vnewton: Using errtol_s: 103.198728 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.839357e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019562e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.743226e+01 │ │ │ │ Vprtstp: contraction number = 2.743226e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.968958e-06 │ │ │ │ Vprtstp: contraction number = 2.392429e-01 │ │ │ │ Vnewton: Using errtol_s: 24.689560 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.982954e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035936e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.960222e+00 │ │ │ │ Vprtstp: contraction number = 7.960222e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.312364e-06 │ │ │ │ Vprtstp: contraction number = 2.901714e-01 │ │ │ │ Vnewton: Using errtol_s: 7.164205 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.125525e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052362e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.414518e+00 │ │ │ │ Vprtstp: contraction number = 2.414518e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.013925e-07 │ │ │ │ Vprtstp: contraction number = 3.033227e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.505599e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.567389e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.761670e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.827662e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1239,17 +1239,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.097220464694E+01 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.877310278267E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.366275092847E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.398720e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.423980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.025 │ │ │ │ Vpbe_ctor2: xkappa = 0.0514861 │ │ │ │ @@ -1296,160 +1296,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.182726 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.503109 │ │ │ │ +Vacc_SASA: Time elapsed: 0.488479 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.310127e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.330810e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.400030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.304510e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.953510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.444477e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087068e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3179322.196917 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.524068e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095255e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.157153e+05 │ │ │ │ Vprtstp: contraction number = 5.157153e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.300823 │ │ │ │ Vnewton: Attempting damping, relres = 0.575285 │ │ │ │ Vnewton: Damping accepted, relres = 0.300823 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.008234e-01 │ │ │ │ Vprtstp: contraction number = 3.008234e-01 │ │ │ │ Vnewton: Using errtol_s: 956414.609494 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.697258e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.113786e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.112831e+05 │ │ │ │ Vprtstp: contraction number = 1.112831e+05 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 7.919694e-02 │ │ │ │ Vprtstp: contraction number = 2.632672e-01 │ │ │ │ Vnewton: Using errtol_s: 251792.580740 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.838644e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.131650e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.912764e+04 │ │ │ │ Vprtstp: contraction number = 2.912764e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.322957e-02 │ │ │ │ Vprtstp: contraction number = 2.933140e-01 │ │ │ │ Vnewton: Using errtol_s: 73854.286564 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.980092e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.149591e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.683374e+03 │ │ │ │ Vprtstp: contraction number = 8.683374e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 6.478032e-03 │ │ │ │ Vprtstp: contraction number = 2.788701e-01 │ │ │ │ Vnewton: Using errtol_s: 20595.750772 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.012138e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.167064e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.778111e+03 │ │ │ │ Vprtstp: contraction number = 2.778111e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.439717e-03 │ │ │ │ Vprtstp: contraction number = 2.222460e-01 │ │ │ │ Vnewton: Using errtol_s: 4577.322906 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026261e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183824e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.948966e+02 │ │ │ │ Vprtstp: contraction number = 7.948966e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.541519e-04 │ │ │ │ Vprtstp: contraction number = 1.765291e-01 │ │ │ │ Vnewton: Using errtol_s: 808.030623 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040382e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200727e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.884080e+02 │ │ │ │ Vprtstp: contraction number = 1.884080e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.345432e-05 │ │ │ │ Vprtstp: contraction number = 2.103243e-01 │ │ │ │ Vnewton: Using errtol_s: 169.948515 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.054528e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.217736e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.248467e+01 │ │ │ │ Vprtstp: contraction number = 5.248467e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.485742e-05 │ │ │ │ Vprtstp: contraction number = 2.779462e-01 │ │ │ │ Vnewton: Using errtol_s: 47.236538 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068557e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233043e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.636645e+01 │ │ │ │ Vprtstp: contraction number = 1.636645e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.633006e-06 │ │ │ │ Vprtstp: contraction number = 3.118310e-01 │ │ │ │ Vnewton: Using errtol_s: 14.729818 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082570e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.249374e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.289991e+00 │ │ │ │ Vprtstp: contraction number = 5.289991e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.497487e-06 │ │ │ │ Vprtstp: contraction number = 3.232214e-01 │ │ │ │ Vnewton: Using errtol_s: 4.760992 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.096621e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.265168e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.736329e+00 │ │ │ │ Vprtstp: contraction number = 1.736329e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.915187e-07 │ │ │ │ Vprtstp: contraction number = 3.282291e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.629034e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.691041e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.914751e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.982273e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1459,29 +1459,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.094905051954E+01 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.139048085008E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.067494556843E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.374510e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.475020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.136779e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.309760e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:41:23 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:27:18 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -1751,151 +1751,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.903286 │ │ │ │ +Vacc_SASA: Time elapsed: 0.895540 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.627838e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.591564e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.392470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.505040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.280440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.133040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.327958e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.379603e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2974958.994733 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.112165e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.207509e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.870275e+05 │ │ │ │ Vprtstp: contraction number = 3.870275e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153059 │ │ │ │ Vnewton: Attempting damping, relres = 0.557808 │ │ │ │ Vnewton: Damping accepted, relres = 0.153059 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.530588e-01 │ │ │ │ Vprtstp: contraction number = 1.530588e-01 │ │ │ │ Vnewton: Using errtol_s: 455343.743026 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.862141e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.218044e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.695400e+04 │ │ │ │ Vprtstp: contraction number = 6.695400e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.920739e-02 │ │ │ │ Vprtstp: contraction number = 1.908246e-01 │ │ │ │ Vnewton: Using errtol_s: 86890.793846 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.273310e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.970586e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.482146e+04 │ │ │ │ Vprtstp: contraction number = 1.482146e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.545819e-03 │ │ │ │ Vprtstp: contraction number = 2.241151e-01 │ │ │ │ Vnewton: Using errtol_s: 19473.541826 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.700668e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.782529e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.884267e+03 │ │ │ │ Vprtstp: contraction number = 3.884267e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.453691e-03 │ │ │ │ Vprtstp: contraction number = 2.220793e-01 │ │ │ │ Vnewton: Using errtol_s: 4324.671146 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.127374e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049472e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.057768e+03 │ │ │ │ Vprtstp: contraction number = 1.057768e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.284783e-04 │ │ │ │ Vprtstp: contraction number = 2.259615e-01 │ │ │ │ Vnewton: Using errtol_s: 977.209364 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.055562e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.217901e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.866048e+02 │ │ │ │ Vprtstp: contraction number = 2.866048e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 8.672414e-05 │ │ │ │ Vprtstp: contraction number = 2.640179e-01 │ │ │ │ Vnewton: Using errtol_s: 258.000773 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.197356e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.382873e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.283684e+01 │ │ │ │ Vprtstp: contraction number = 8.283684e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.506027e-05 │ │ │ │ Vprtstp: contraction number = 2.889653e-01 │ │ │ │ Vnewton: Using errtol_s: 74.553271 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.341506e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.555479e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.472736e+01 │ │ │ │ Vprtstp: contraction number = 2.472736e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.480652e-06 │ │ │ │ Vprtstp: contraction number = 2.985065e-01 │ │ │ │ Vnewton: Using errtol_s: 22.254632 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.484457e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.728457e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.490971e+00 │ │ │ │ Vprtstp: contraction number = 7.490971e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.266207e-06 │ │ │ │ Vprtstp: contraction number = 3.029425e-01 │ │ │ │ Vnewton: Using errtol_s: 6.741874 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.627048e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.901575e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.293363e+00 │ │ │ │ Vprtstp: contraction number = 2.293363e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.938001e-07 │ │ │ │ Vprtstp: contraction number = 3.061503e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.504197e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.566016e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.803827e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.874370e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -1905,15 +1905,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.155593608885E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.568720386421E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.283293314758E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.383150e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.421610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ @@ -1962,160 +1962,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.103051 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.898932 │ │ │ │ +Vacc_SASA: Time elapsed: 0.893705 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.882342e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.911432e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.404660e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.491240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.528370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.985970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.005929e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.318645e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 3077114.923847 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.084584e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.401260e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.742704e+05 │ │ │ │ Vprtstp: contraction number = 4.742704e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.172865 │ │ │ │ Vnewton: Attempting damping, relres = 0.568730 │ │ │ │ Vnewton: Damping accepted, relres = 0.172865 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.728651e-01 │ │ │ │ Vprtstp: contraction number = 1.728651e-01 │ │ │ │ Vnewton: Using errtol_s: 531925.831070 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.258456e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.591555e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.143761e+04 │ │ │ │ Vprtstp: contraction number = 9.143761e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.526713e-02 │ │ │ │ Vprtstp: contraction number = 2.040153e-01 │ │ │ │ Vnewton: Using errtol_s: 108521.009470 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.400163e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.765704e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.196947e+04 │ │ │ │ Vprtstp: contraction number = 2.196947e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.376912e-03 │ │ │ │ Vprtstp: contraction number = 2.375275e-01 │ │ │ │ Vnewton: Using errtol_s: 25776.719868 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.542543e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.925525e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.034692e+03 │ │ │ │ Vprtstp: contraction number = 6.034692e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.018356e-03 │ │ │ │ Vprtstp: contraction number = 2.409428e-01 │ │ │ │ Vnewton: Using errtol_s: 6210.714220 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.685907e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.101960e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.718760e+03 │ │ │ │ Vprtstp: contraction number = 1.718760e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.089360e-04 │ │ │ │ Vprtstp: contraction number = 2.521537e-01 │ │ │ │ Vnewton: Using errtol_s: 1566.054712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.828392e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.276505e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.951703e+02 │ │ │ │ Vprtstp: contraction number = 4.951703e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.448376e-04 │ │ │ │ Vprtstp: contraction number = 2.845889e-01 │ │ │ │ Vnewton: Using errtol_s: 445.681818 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.970611e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.434330e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.503700e+02 │ │ │ │ Vprtstp: contraction number = 1.503700e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.398054e-05 │ │ │ │ Vprtstp: contraction number = 3.036542e-01 │ │ │ │ Vnewton: Using errtol_s: 135.333176 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.111990e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.610795e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.725124e+01 │ │ │ │ Vprtstp: contraction number = 4.725124e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.382013e-05 │ │ │ │ Vprtstp: contraction number = 3.142328e-01 │ │ │ │ Vnewton: Using errtol_s: 42.526127 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.254443e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.778400e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.517823e+01 │ │ │ │ Vprtstp: contraction number = 1.517823e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.439356e-06 │ │ │ │ Vprtstp: contraction number = 3.212239e-01 │ │ │ │ Vnewton: Using errtol_s: 13.660408 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.396535e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.955213e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.961627e+00 │ │ │ │ Vprtstp: contraction number = 4.961627e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.451185e-06 │ │ │ │ Vprtstp: contraction number = 3.268910e-01 │ │ │ │ Vnewton: Using errtol_s: 4.465464 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.539129e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.135290e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.644451e+00 │ │ │ │ Vprtstp: contraction number = 1.644451e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.809720e-07 │ │ │ │ Vprtstp: contraction number = 3.314339e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.642132e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.706638e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.958405e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.027516e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2125,17 +2125,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.136719459534E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.953334472721E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475599755841E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.359760e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.399330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -2162,151 +2162,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.318573 │ │ │ │ +Vacc_SASA: Time elapsed: 0.321395 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.145600e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.444020e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.377800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.461000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.325460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.014620e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.085822e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.733080e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 847635.298627 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.164962e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.816129e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.156652e+05 │ │ │ │ Vprtstp: contraction number = 1.156652e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.129563 │ │ │ │ Vnewton: Attempting damping, relres = 0.559453 │ │ │ │ Vnewton: Damping accepted, relres = 0.129563 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.295633e-01 │ │ │ │ Vprtstp: contraction number = 1.295633e-01 │ │ │ │ Vnewton: Using errtol_s: 109822.397033 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.337277e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.003256e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.025826e+04 │ │ │ │ Vprtstp: contraction number = 2.025826e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.180592e-02 │ │ │ │ Vprtstp: contraction number = 1.683033e-01 │ │ │ │ Vnewton: Using errtol_s: 18483.468929 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.477608e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.165036e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.307643e+03 │ │ │ │ Vprtstp: contraction number = 4.307643e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.574915e-03 │ │ │ │ Vprtstp: contraction number = 2.098015e-01 │ │ │ │ Vnewton: Using errtol_s: 3877.859579 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.617724e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.326165e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.042197e+03 │ │ │ │ Vprtstp: contraction number = 1.042197e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.106587e-03 │ │ │ │ Vprtstp: contraction number = 2.418813e-01 │ │ │ │ Vnewton: Using errtol_s: 937.981802 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.758824e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.490149e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.719312e+02 │ │ │ │ Vprtstp: contraction number = 2.719312e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 2.887307e-04 │ │ │ │ Vprtstp: contraction number = 2.609201e-01 │ │ │ │ Vnewton: Using errtol_s: 244.738306 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.899953e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.657909e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.411670e+01 │ │ │ │ Vprtstp: contraction number = 7.411670e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 7.869545e-05 │ │ │ │ Vprtstp: contraction number = 2.725566e-01 │ │ │ │ Vnewton: Using errtol_s: 66.705044 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.042181e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.823939e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.079247e+01 │ │ │ │ Vprtstp: contraction number = 2.079247e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.207697e-05 │ │ │ │ Vprtstp: contraction number = 2.805368e-01 │ │ │ │ Vnewton: Using errtol_s: 18.713222 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.183311e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.981621e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.958188e+00 │ │ │ │ Vprtstp: contraction number = 5.958188e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.326270e-06 │ │ │ │ Vprtstp: contraction number = 2.865551e-01 │ │ │ │ Vnewton: Using errtol_s: 5.362370 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.324615e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.145275e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.735927e+00 │ │ │ │ Vprtstp: contraction number = 1.735927e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.843168e-06 │ │ │ │ Vprtstp: contraction number = 2.913515e-01 │ │ │ │ Vnewton: Using errtol_s: 1.562335 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.465383e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.296314e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.124069e-01 │ │ │ │ Vprtstp: contraction number = 5.124069e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 5.440621e-07 │ │ │ │ Vprtstp: contraction number = 2.951777e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.486620e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.548651e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.678272e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.747427e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2316,17 +2316,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.454852948136E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.836680918650E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.416367945808E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.418030e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.450650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0728124 │ │ │ │ @@ -2373,149 +2373,149 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0108218 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.313235 │ │ │ │ +Vacc_SASA: Time elapsed: 0.311898 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.853530e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.144000e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.407320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.472790e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.344000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.150420e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.740323e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.590037e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 886073.910303 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.819194e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.674553e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.444647e+05 │ │ │ │ Vprtstp: contraction number = 1.444647e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.152834 │ │ │ │ Vnewton: Attempting damping, relres = 0.571521 │ │ │ │ Vnewton: Damping accepted, relres = 0.152834 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.528340e-01 │ │ │ │ Vprtstp: contraction number = 1.528340e-01 │ │ │ │ Vnewton: Using errtol_s: 135422.205259 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.995407e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.880257e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.834174e+04 │ │ │ │ Vprtstp: contraction number = 2.834174e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.906007e-02 │ │ │ │ Vprtstp: contraction number = 1.901414e-01 │ │ │ │ Vnewton: Using errtol_s: 25749.370228 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.138391e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.044596e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.624232e+03 │ │ │ │ Vprtstp: contraction number = 6.624232e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.729649e-03 │ │ │ │ Vprtstp: contraction number = 2.315772e-01 │ │ │ │ Vnewton: Using errtol_s: 5962.966787 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.280657e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.213142e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.678296e+03 │ │ │ │ Vprtstp: contraction number = 1.678296e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.704684e-03 │ │ │ │ Vprtstp: contraction number = 2.533095e-01 │ │ │ │ Vnewton: Using errtol_s: 1510.476086 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.422169e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.379050e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.484576e+02 │ │ │ │ Vprtstp: contraction number = 4.484576e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.555067e-04 │ │ │ │ Vprtstp: contraction number = 2.672089e-01 │ │ │ │ Vnewton: Using errtol_s: 403.612606 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.564475e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.533488e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.244400e+02 │ │ │ │ Vprtstp: contraction number = 1.244400e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.263959e-04 │ │ │ │ Vprtstp: contraction number = 2.774841e-01 │ │ │ │ Vnewton: Using errtol_s: 111.996087 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.705474e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.682605e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.556127e+01 │ │ │ │ Vprtstp: contraction number = 3.556127e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.612018e-05 │ │ │ │ Vprtstp: contraction number = 2.857702e-01 │ │ │ │ Vnewton: Using errtol_s: 32.005148 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.846857e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.838601e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.042544e+01 │ │ │ │ Vprtstp: contraction number = 1.042544e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.058929e-05 │ │ │ │ Vprtstp: contraction number = 2.931684e-01 │ │ │ │ Vnewton: Using errtol_s: 9.382897 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.988080e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.008366e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.131407e+00 │ │ │ │ Vprtstp: contraction number = 3.131407e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.180622e-06 │ │ │ │ Vprtstp: contraction number = 3.003620e-01 │ │ │ │ Vnewton: Using errtol_s: 2.818266 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.129668e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.173955e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.605131e-01 │ │ │ │ Vprtstp: contraction number = 9.605131e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.756091e-07 │ │ │ │ Vprtstp: contraction number = 3.067353e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.497875e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.560672e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.713053e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.783379e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2525,17 +2525,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.447897988359E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.069186882543E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.032629667471E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.407690e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.437430e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -2562,151 +2562,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.491524 │ │ │ │ +Vacc_SASA: Time elapsed: 0.482807 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.078458e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.087996e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.387540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.336380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.006180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.698081e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.770816e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2425643.021917 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.775919e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.852639e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.395849e+05 │ │ │ │ Vprtstp: contraction number = 3.395849e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.271218 │ │ │ │ Vnewton: Attempting damping, relres = 0.565917 │ │ │ │ Vnewton: Damping accepted, relres = 0.271218 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.712177e-01 │ │ │ │ Vprtstp: contraction number = 2.712177e-01 │ │ │ │ Vnewton: Using errtol_s: 657877.293778 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.948471e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.049129e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.802706e+04 │ │ │ │ Vprtstp: contraction number = 6.802706e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 6.815619e-02 │ │ │ │ Vprtstp: contraction number = 2.512970e-01 │ │ │ │ Vnewton: Using errtol_s: 165322.578504 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.089353e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.229070e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.706699e+04 │ │ │ │ Vprtstp: contraction number = 1.706699e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.896759e-02 │ │ │ │ Vprtstp: contraction number = 2.782960e-01 │ │ │ │ Vnewton: Using errtol_s: 46008.609864 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.229992e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.378930e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.017255e+03 │ │ │ │ Vprtstp: contraction number = 5.017255e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 4.765082e-03 │ │ │ │ Vprtstp: contraction number = 2.512223e-01 │ │ │ │ Vnewton: Using errtol_s: 11558.387363 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.371898e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.541049e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.518068e+03 │ │ │ │ Vprtstp: contraction number = 1.518068e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 8.818480e-04 │ │ │ │ Vprtstp: contraction number = 1.850646e-01 │ │ │ │ Vnewton: Using errtol_s: 2139.048483 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.513696e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.685561e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.762132e+02 │ │ │ │ Vprtstp: contraction number = 3.762132e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.458866e-04 │ │ │ │ Vprtstp: contraction number = 1.654328e-01 │ │ │ │ Vnewton: Using errtol_s: 353.868838 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.655138e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.846030e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.902937e+01 │ │ │ │ Vprtstp: contraction number = 8.902937e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.304341e-05 │ │ │ │ Vprtstp: contraction number = 2.265007e-01 │ │ │ │ Vnewton: Using errtol_s: 80.151522 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.795342e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000621e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.527505e+01 │ │ │ │ Vprtstp: contraction number = 2.527505e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.377960e-06 │ │ │ │ Vprtstp: contraction number = 2.838073e-01 │ │ │ │ Vnewton: Using errtol_s: 22.747583 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.937596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016499e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.628220e+00 │ │ │ │ Vprtstp: contraction number = 7.628220e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.830342e-06 │ │ │ │ Vprtstp: contraction number = 3.018078e-01 │ │ │ │ Vnewton: Using errtol_s: 6.865399 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.080326e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031426e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.330827e+00 │ │ │ │ Vprtstp: contraction number = 2.330827e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.648198e-07 │ │ │ │ Vprtstp: contraction number = 3.055531e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.491474e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.553641e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.667277e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.735152e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2716,17 +2716,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.060833611390E+01 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.876241790075E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.364173698262E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.477060e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.405310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.05 │ │ │ │ Vpbe_ctor2: xkappa = 0.0728124 │ │ │ │ @@ -2773,160 +2773,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0855205 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.490292 │ │ │ │ +Vacc_SASA: Time elapsed: 0.466269 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.300078e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.280789e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.374630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.416670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.249580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.832300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.397941e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064895e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2500270.754638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.476950e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.072939e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.160810e+05 │ │ │ │ Vprtstp: contraction number = 4.160810e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.288431 │ │ │ │ Vnewton: Attempting damping, relres = 0.577725 │ │ │ │ Vnewton: Damping accepted, relres = 0.288431 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.884309e-01 │ │ │ │ Vprtstp: contraction number = 2.884309e-01 │ │ │ │ Vnewton: Using errtol_s: 721155.339967 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.650594e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091974e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.034405e+04 │ │ │ │ Vprtstp: contraction number = 9.034405e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 7.349134e-02 │ │ │ │ Vprtstp: contraction number = 2.547970e-01 │ │ │ │ Vnewton: Using errtol_s: 183748.247493 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.793093e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108953e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.360950e+04 │ │ │ │ Vprtstp: contraction number = 2.360950e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 2.053916e-02 │ │ │ │ Vprtstp: contraction number = 2.794773e-01 │ │ │ │ Vnewton: Using errtol_s: 51353.458771 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.934723e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126233e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.072490e+03 │ │ │ │ Vprtstp: contraction number = 7.072490e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 5.268603e-03 │ │ │ │ Vprtstp: contraction number = 2.565150e-01 │ │ │ │ Vnewton: Using errtol_s: 13172.933437 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007604e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.142634e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.172100e+03 │ │ │ │ Vprtstp: contraction number = 2.172100e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 1.067554e-03 │ │ │ │ Vprtstp: contraction number = 2.026257e-01 │ │ │ │ Vnewton: Using errtol_s: 2669.175106 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.021711e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158545e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.851792e+02 │ │ │ │ Vprtstp: contraction number = 5.851792e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.156116e-04 │ │ │ │ Vprtstp: contraction number = 2.019677e-01 │ │ │ │ Vnewton: Using errtol_s: 539.087280 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035840e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174257e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.590368e+02 │ │ │ │ Vprtstp: contraction number = 1.590368e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.725368e-05 │ │ │ │ Vprtstp: contraction number = 2.655409e-01 │ │ │ │ Vnewton: Using errtol_s: 143.149712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049912e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188274e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.862838e+01 │ │ │ │ Vprtstp: contraction number = 4.862838e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.750434e-05 │ │ │ │ Vprtstp: contraction number = 3.057329e-01 │ │ │ │ Vnewton: Using errtol_s: 43.765584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064255e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.203507e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.560157e+01 │ │ │ │ Vprtstp: contraction number = 1.560157e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.615959e-06 │ │ │ │ Vprtstp: contraction number = 3.208324e-01 │ │ │ │ Vnewton: Using errtol_s: 14.041419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078359e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.219158e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.091636e+00 │ │ │ │ Vprtstp: contraction number = 5.091636e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.832791e-06 │ │ │ │ Vprtstp: contraction number = 3.263540e-01 │ │ │ │ Vnewton: Using errtol_s: 4.582473 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.092382e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.234805e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.679382e+00 │ │ │ │ Vprtstp: contraction number = 1.679382e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.045119e-07 │ │ │ │ Vprtstp: contraction number = 3.298314e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.633119e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.694380e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.821006e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.887389e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -2936,29 +2936,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.058843361489E+01 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.137979732190E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.067286106944E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.406250e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.414530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.132829e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.275985e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:42:17 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:29:47 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -3228,151 +3228,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.893772 │ │ │ │ +Vacc_SASA: Time elapsed: 0.893024 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.619081e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.598492e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.389340e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.411840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.285380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.872800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.315195e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.348084e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2729151.378915 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.097944e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.160589e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.548080e+05 │ │ │ │ Vprtstp: contraction number = 3.548080e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.149964 │ │ │ │ Vnewton: Attempting damping, relres = 0.557619 │ │ │ │ Vnewton: Damping accepted, relres = 0.149964 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.499638e-01 │ │ │ │ Vprtstp: contraction number = 1.499638e-01 │ │ │ │ Vnewton: Using errtol_s: 409273.850655 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.834354e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.189895e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.220624e+04 │ │ │ │ Vprtstp: contraction number = 6.220624e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.835999e-02 │ │ │ │ Vprtstp: contraction number = 1.891123e-01 │ │ │ │ Vnewton: Using errtol_s: 77398.710345 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.264224e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.752131e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.402989e+04 │ │ │ │ Vprtstp: contraction number = 1.402989e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.278471e-03 │ │ │ │ Vprtstp: contraction number = 2.213848e-01 │ │ │ │ Vnewton: Using errtol_s: 17134.898633 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.694457e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.521132e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.695573e+03 │ │ │ │ Vprtstp: contraction number = 3.695573e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.396538e-03 │ │ │ │ Vprtstp: contraction number = 2.224328e-01 │ │ │ │ Vnewton: Using errtol_s: 3811.362986 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.110113e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030983e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.003191e+03 │ │ │ │ Vprtstp: contraction number = 1.003191e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.340894e-04 │ │ │ │ Vprtstp: contraction number = 2.392269e-01 │ │ │ │ Vnewton: Using errtol_s: 911.780505 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051591e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184609e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.777519e+02 │ │ │ │ Vprtstp: contraction number = 2.777519e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.159963e-05 │ │ │ │ Vprtstp: contraction number = 2.741770e-01 │ │ │ │ Vnewton: Using errtol_s: 249.989261 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193711e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.359687e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.121282e+01 │ │ │ │ Vprtstp: contraction number = 8.121282e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.678181e-05 │ │ │ │ Vprtstp: contraction number = 2.923790e-01 │ │ │ │ Vnewton: Using errtol_s: 73.091601 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.335741e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.530516e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.430204e+01 │ │ │ │ Vprtstp: contraction number = 2.430204e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.014155e-06 │ │ │ │ Vprtstp: contraction number = 2.992388e-01 │ │ │ │ Vnewton: Using errtol_s: 21.871842 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.477963e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.678671e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.369042e+00 │ │ │ │ Vprtstp: contraction number = 7.369042e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.430110e-06 │ │ │ │ Vprtstp: contraction number = 3.032272e-01 │ │ │ │ Vnewton: Using errtol_s: 6.632138 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.620114e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.855441e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.256893e+00 │ │ │ │ Vprtstp: contraction number = 2.256893e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.442621e-07 │ │ │ │ Vprtstp: contraction number = 3.062668e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.498159e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.559760e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.740214e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.807153e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -3382,17 +3382,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.061471335399E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.568309380303E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.283186160859E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.371250e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.387830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.075 │ │ │ │ Vpbe_ctor2: xkappa = 0.0891766 │ │ │ │ @@ -3439,160 +3439,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0651756 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.890997 │ │ │ │ +Vacc_SASA: Time elapsed: 0.857161 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.867876e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.855827e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.408540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.495400e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.321680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.049450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.994715e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.246234e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2820294.276955 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.071771e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.329083e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.376310e+05 │ │ │ │ Vprtstp: contraction number = 4.376310e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.171074 │ │ │ │ Vnewton: Attempting damping, relres = 0.569073 │ │ │ │ Vnewton: Damping accepted, relres = 0.171074 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.710740e-01 │ │ │ │ Vprtstp: contraction number = 1.710740e-01 │ │ │ │ Vnewton: Using errtol_s: 482478.932943 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.245304e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.543210e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.516733e+04 │ │ │ │ Vprtstp: contraction number = 8.516733e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.468956e-02 │ │ │ │ Vprtstp: contraction number = 2.027752e-01 │ │ │ │ Vnewton: Using errtol_s: 97834.754534 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.388079e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.721713e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.072493e+04 │ │ │ │ Vprtstp: contraction number = 2.072493e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.178682e-03 │ │ │ │ Vprtstp: contraction number = 2.357678e-01 │ │ │ │ Vnewton: Using errtol_s: 23066.288642 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.530476e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.900483e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.715545e+03 │ │ │ │ Vprtstp: contraction number = 5.715545e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.982874e-03 │ │ │ │ Vprtstp: contraction number = 2.424442e-01 │ │ │ │ Vnewton: Using errtol_s: 5592.288694 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.673339e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.072247e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.627358e+03 │ │ │ │ Vprtstp: contraction number = 1.627358e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.213861e-04 │ │ │ │ Vprtstp: contraction number = 2.629446e-01 │ │ │ │ Vnewton: Using errtol_s: 1470.462342 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.816058e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.251671e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.759299e+02 │ │ │ │ Vprtstp: contraction number = 4.759299e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.518795e-04 │ │ │ │ Vprtstp: contraction number = 2.912995e-01 │ │ │ │ Vnewton: Using errtol_s: 428.344902 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.960619e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.431793e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.460718e+02 │ │ │ │ Vprtstp: contraction number = 1.460718e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.661385e-05 │ │ │ │ Vprtstp: contraction number = 3.069133e-01 │ │ │ │ Vnewton: Using errtol_s: 131.464764 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.103360e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.610305e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.608450e+01 │ │ │ │ Vprtstp: contraction number = 4.608450e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.470629e-05 │ │ │ │ Vprtstp: contraction number = 3.154918e-01 │ │ │ │ Vnewton: Using errtol_s: 41.476059 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.244709e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.765612e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.483594e+01 │ │ │ │ Vprtstp: contraction number = 1.483594e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.734380e-06 │ │ │ │ Vprtstp: contraction number = 3.219290e-01 │ │ │ │ Vnewton: Using errtol_s: 13.352345 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.386569e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.940195e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.855098e+00 │ │ │ │ Vprtstp: contraction number = 4.855098e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.549338e-06 │ │ │ │ Vprtstp: contraction number = 3.272525e-01 │ │ │ │ Vnewton: Using errtol_s: 4.369588 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.528025e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.099803e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.609852e+00 │ │ │ │ Vprtstp: contraction number = 1.609852e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.137291e-07 │ │ │ │ Vprtstp: contraction number = 3.315798e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.642419e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.704612e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.987970e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.057291e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -3602,17 +3602,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.043656925356E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.952923600964E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475493408028E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.367170e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.392750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -3639,151 +3639,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.316285 │ │ │ │ +Vacc_SASA: Time elapsed: 0.299835 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.138930e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.130360e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.382460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.391230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.310280e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.592880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.069935e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.669140e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 782805.209515 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.147544e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.749287e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.066964e+05 │ │ │ │ Vprtstp: contraction number = 1.066964e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.130466 │ │ │ │ Vnewton: Attempting damping, relres = 0.559276 │ │ │ │ Vnewton: Damping accepted, relres = 0.130466 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.304657e-01 │ │ │ │ Vprtstp: contraction number = 1.304657e-01 │ │ │ │ Vnewton: Using errtol_s: 102129.196068 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.326322e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.939438e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.906966e+04 │ │ │ │ Vprtstp: contraction number = 1.906966e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.228836e-02 │ │ │ │ Vprtstp: contraction number = 1.708370e-01 │ │ │ │ Vnewton: Using errtol_s: 17447.447142 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.467148e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.092551e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.144180e+03 │ │ │ │ Vprtstp: contraction number = 4.144180e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.766221e-03 │ │ │ │ Vprtstp: contraction number = 2.138435e-01 │ │ │ │ Vnewton: Using errtol_s: 3731.022666 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.607497e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.251708e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.018149e+03 │ │ │ │ Vprtstp: contraction number = 1.018149e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.170583e-03 │ │ │ │ Vprtstp: contraction number = 2.455999e-01 │ │ │ │ Vnewton: Using errtol_s: 916.338711 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.746876e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.401967e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.682787e+02 │ │ │ │ Vprtstp: contraction number = 2.682787e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.084434e-04 │ │ │ │ Vprtstp: contraction number = 2.634955e-01 │ │ │ │ Vnewton: Using errtol_s: 241.451081 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.887225e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.554184e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.355327e+01 │ │ │ │ Vprtstp: contraction number = 7.355327e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 8.456504e-05 │ │ │ │ Vprtstp: contraction number = 2.741672e-01 │ │ │ │ Vnewton: Using errtol_s: 66.197957 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.030199e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.706471e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.070399e+01 │ │ │ │ Vprtstp: contraction number = 2.070399e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.380361e-05 │ │ │ │ Vprtstp: contraction number = 2.814829e-01 │ │ │ │ Vnewton: Using errtol_s: 18.633591 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.171750e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.861936e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.943814e+00 │ │ │ │ Vprtstp: contraction number = 5.943814e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 6.833671e-06 │ │ │ │ Vprtstp: contraction number = 2.870855e-01 │ │ │ │ Vnewton: Using errtol_s: 5.349433 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.311880e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.014367e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.733432e+00 │ │ │ │ Vprtstp: contraction number = 1.733432e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.992946e-06 │ │ │ │ Vprtstp: contraction number = 2.916363e-01 │ │ │ │ Vnewton: Using errtol_s: 1.560089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.452097e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.165211e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.119221e-01 │ │ │ │ Vprtstp: contraction number = 5.119221e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 5.885626e-07 │ │ │ │ Vprtstp: contraction number = 2.953228e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.489988e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.551690e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.612514e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.676095e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -3793,17 +3793,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.580382874271E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.835549724492E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.415749841387E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403630e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.392580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.075 │ │ │ │ Vpbe_ctor2: xkappa = 0.0891766 │ │ │ │ @@ -3850,160 +3850,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00827481 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.312028 │ │ │ │ +Vacc_SASA: Time elapsed: 0.295052 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.774090e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.599860e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.381030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.313150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.320060e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.505970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.725870e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.446097e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 817942.139336 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.802219e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.524715e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.333917e+05 │ │ │ │ Vprtstp: contraction number = 1.333917e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153834 │ │ │ │ Vnewton: Attempting damping, relres = 0.571434 │ │ │ │ Vnewton: Damping accepted, relres = 0.153834 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.538338e-01 │ │ │ │ Vprtstp: contraction number = 1.538338e-01 │ │ │ │ Vnewton: Using errtol_s: 125827.150717 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.975151e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.716669e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.649228e+04 │ │ │ │ Vprtstp: contraction number = 2.649228e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.948474e-02 │ │ │ │ Vprtstp: contraction number = 1.916662e-01 │ │ │ │ Vnewton: Using errtol_s: 24116.815003 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.115797e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.869578e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.270875e+03 │ │ │ │ Vprtstp: contraction number = 6.270875e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.901762e-03 │ │ │ │ Vprtstp: contraction number = 2.340791e-01 │ │ │ │ Vnewton: Using errtol_s: 5645.242129 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.258339e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.023772e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.605106e+03 │ │ │ │ Vprtstp: contraction number = 1.605106e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.766147e-03 │ │ │ │ Vprtstp: contraction number = 2.558981e-01 │ │ │ │ Vnewton: Using errtol_s: 1444.606457 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.399276e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.176040e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.329441e+02 │ │ │ │ Vprtstp: contraction number = 4.329441e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.763791e-04 │ │ │ │ Vprtstp: contraction number = 2.697278e-01 │ │ │ │ Vnewton: Using errtol_s: 389.650539 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.540606e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.328141e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.211228e+02 │ │ │ │ Vprtstp: contraction number = 1.211228e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.332742e-04 │ │ │ │ Vprtstp: contraction number = 2.797649e-01 │ │ │ │ Vnewton: Using errtol_s: 109.010550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.683252e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.471661e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.484891e+01 │ │ │ │ Vprtstp: contraction number = 3.484891e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.834504e-05 │ │ │ │ Vprtstp: contraction number = 2.877155e-01 │ │ │ │ Vnewton: Using errtol_s: 31.364026 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.823318e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.622930e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.027201e+01 │ │ │ │ Vprtstp: contraction number = 1.027201e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.130252e-05 │ │ │ │ Vprtstp: contraction number = 2.947583e-01 │ │ │ │ Vnewton: Using errtol_s: 9.244807 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.964328e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.773879e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.098070e+00 │ │ │ │ Vprtstp: contraction number = 3.098070e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.408876e-06 │ │ │ │ Vprtstp: contraction number = 3.016032e-01 │ │ │ │ Vnewton: Using errtol_s: 2.788263 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.104287e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.924676e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.532281e-01 │ │ │ │ Vprtstp: contraction number = 9.532281e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.048858e-06 │ │ │ │ Vprtstp: contraction number = 3.076845e-01 │ │ │ │ Vnewton: Using errtol_s: 0.857905 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.246037e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.074218e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.981595e-01 │ │ │ │ Vprtstp: contraction number = 2.981595e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.280716e-07 │ │ │ │ Vprtstp: contraction number = 3.127892e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.627920e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.689734e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.743970e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.806122e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4013,17 +4013,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.573110826930E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.068060919052E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.032015460715E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.439100e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.354050e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -4050,151 +4050,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.497780 │ │ │ │ +Vacc_SASA: Time elapsed: 0.456324 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.075995e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.046717e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.376390e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.297200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.339120e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.455130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.809092e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.621244e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2117741.361264 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.886221e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.698972e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.981667e+05 │ │ │ │ Vprtstp: contraction number = 2.981667e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.251946 │ │ │ │ Vnewton: Attempting damping, relres = 0.566227 │ │ │ │ Vnewton: Damping accepted, relres = 0.251946 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.519462e-01 │ │ │ │ Vprtstp: contraction number = 2.519462e-01 │ │ │ │ Vnewton: Using errtol_s: 533556.965989 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.057340e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.878291e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.927315e+04 │ │ │ │ Vprtstp: contraction number = 5.927315e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 6.069562e-02 │ │ │ │ Vprtstp: contraction number = 2.409070e-01 │ │ │ │ Vnewton: Using errtol_s: 128537.620946 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.198409e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.036036e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.480174e+04 │ │ │ │ Vprtstp: contraction number = 1.480174e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.600227e-02 │ │ │ │ Vprtstp: contraction number = 2.636478e-01 │ │ │ │ Vnewton: Using errtol_s: 33888.662126 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.342904e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.189589e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.318636e+03 │ │ │ │ Vprtstp: contraction number = 4.318636e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.683613e-03 │ │ │ │ Vprtstp: contraction number = 2.301932e-01 │ │ │ │ Vnewton: Using errtol_s: 7800.938716 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.483515e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.339212e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.240563e+03 │ │ │ │ Vprtstp: contraction number = 1.240563e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 6.541706e-04 │ │ │ │ Vprtstp: contraction number = 1.775894e-01 │ │ │ │ Vnewton: Using errtol_s: 1385.364119 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.624628e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.487017e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.070828e+02 │ │ │ │ Vprtstp: contraction number = 3.070828e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.315622e-04 │ │ │ │ Vprtstp: contraction number = 2.011130e-01 │ │ │ │ Vnewton: Using errtol_s: 278.614703 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.763882e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.634146e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.245841e+01 │ │ │ │ Vprtstp: contraction number = 8.245841e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.504428e-05 │ │ │ │ Vprtstp: contraction number = 2.663704e-01 │ │ │ │ Vnewton: Using errtol_s: 74.214712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.903854e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.780781e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.449789e+01 │ │ │ │ Vprtstp: contraction number = 2.449789e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.041114e-05 │ │ │ │ Vprtstp: contraction number = 2.970854e-01 │ │ │ │ Vnewton: Using errtol_s: 22.048109 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.042159e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.928810e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.450269e+00 │ │ │ │ Vprtstp: contraction number = 7.450269e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.166223e-06 │ │ │ │ Vprtstp: contraction number = 3.041187e-01 │ │ │ │ Vnewton: Using errtol_s: 6.705242 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.182054e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.007713e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.280137e+00 │ │ │ │ Vprtstp: contraction number = 2.280137e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.690153e-07 │ │ │ │ Vprtstp: contraction number = 3.060477e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.479473e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.541509e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.571202e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.632657e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4204,17 +4204,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.019051099333E+01 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.875636108518E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.362891956470E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.387190e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.358280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.075 │ │ │ │ Vpbe_ctor2: xkappa = 0.0891766 │ │ │ │ @@ -4261,160 +4261,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0483679 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.501081 │ │ │ │ +Vacc_SASA: Time elapsed: 0.463999 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.295133e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.269384e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.383150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.305130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.259440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.472360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.495762e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039708e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2182522.884057 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.573034e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047400e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.686053e+05 │ │ │ │ Vprtstp: contraction number = 3.686053e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.272056 │ │ │ │ Vnewton: Attempting damping, relres = 0.578831 │ │ │ │ Vnewton: Damping accepted, relres = 0.272056 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.720560e-01 │ │ │ │ Vprtstp: contraction number = 2.720560e-01 │ │ │ │ Vnewton: Using errtol_s: 593768.373592 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.748650e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065403e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.934239e+04 │ │ │ │ Vprtstp: contraction number = 7.934239e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 6.680635e-02 │ │ │ │ Vprtstp: contraction number = 2.455611e-01 │ │ │ │ Vnewton: Using errtol_s: 145806.393631 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.891010e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081202e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.075932e+04 │ │ │ │ Vprtstp: contraction number = 2.075932e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.784022e-02 │ │ │ │ Vprtstp: contraction number = 2.670438e-01 │ │ │ │ Vnewton: Using errtol_s: 38936.692163 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003277e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.096925e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.202423e+03 │ │ │ │ Vprtstp: contraction number = 6.202423e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 4.287010e-03 │ │ │ │ Vprtstp: contraction number = 2.403003e-01 │ │ │ │ Vnewton: Using errtol_s: 9356.498262 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.017561e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112036e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.844032e+03 │ │ │ │ Vprtstp: contraction number = 1.844032e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 8.713644e-04 │ │ │ │ Vprtstp: contraction number = 2.032569e-01 │ │ │ │ Vnewton: Using errtol_s: 1901.772758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031693e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126955e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.035865e+02 │ │ │ │ Vprtstp: contraction number = 5.035865e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.084187e-04 │ │ │ │ Vprtstp: contraction number = 2.391867e-01 │ │ │ │ Vnewton: Using errtol_s: 454.878668 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045841e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141779e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.482404e+02 │ │ │ │ Vprtstp: contraction number = 1.482404e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.113004e-05 │ │ │ │ Vprtstp: contraction number = 2.933039e-01 │ │ │ │ Vnewton: Using errtol_s: 133.417702 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059993e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156589e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.685160e+01 │ │ │ │ Vprtstp: contraction number = 4.685160e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.932006e-05 │ │ │ │ Vprtstp: contraction number = 3.160485e-01 │ │ │ │ Vnewton: Using errtol_s: 42.166463 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074068e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.171356e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.516259e+01 │ │ │ │ Vprtstp: contraction number = 1.516259e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 6.252549e-06 │ │ │ │ Vprtstp: contraction number = 3.236300e-01 │ │ │ │ Vnewton: Using errtol_s: 13.646331 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088263e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.186175e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.968000e+00 │ │ │ │ Vprtstp: contraction number = 4.968000e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.048639e-06 │ │ │ │ Vprtstp: contraction number = 3.276485e-01 │ │ │ │ Vnewton: Using errtol_s: 4.471200 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102763e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201058e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.642278e+00 │ │ │ │ Vprtstp: contraction number = 1.642278e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.772208e-07 │ │ │ │ Vprtstp: contraction number = 3.305711e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.640070e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.701543e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.728817e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.790509e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4424,29 +4424,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.017305990862E+01 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.137374131733E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.067158704261E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.382290e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.339120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.142500e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.239880e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:43:12 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:31:35 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -4716,151 +4716,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.898724 │ │ │ │ +Vacc_SASA: Time elapsed: 0.847129 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.615373e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.534149e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.377320e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.328800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.241990e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.524910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.309161e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.228539e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2581577.235420 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.081011e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.008878e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.353899e+05 │ │ │ │ Vprtstp: contraction number = 3.353899e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.146634 │ │ │ │ Vnewton: Attempting damping, relres = 0.557407 │ │ │ │ Vnewton: Damping accepted, relres = 0.146634 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.466339e-01 │ │ │ │ Vprtstp: contraction number = 1.466339e-01 │ │ │ │ Vnewton: Using errtol_s: 378546.858038 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.808743e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.891680e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.923639e+04 │ │ │ │ Vprtstp: contraction number = 5.923639e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.740677e-02 │ │ │ │ Vprtstp: contraction number = 1.869061e-01 │ │ │ │ Vnewton: Using errtol_s: 70752.704235 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.230869e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.481846e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.351296e+04 │ │ │ │ Vprtstp: contraction number = 1.351296e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.004523e-03 │ │ │ │ Vprtstp: contraction number = 2.190890e-01 │ │ │ │ Vnewton: Using errtol_s: 15501.138648 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.647362e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.058632e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.562530e+03 │ │ │ │ Vprtstp: contraction number = 3.562530e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.351206e-03 │ │ │ │ Vprtstp: contraction number = 2.250314e-01 │ │ │ │ Vnewton: Using errtol_s: 3488.243698 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.076050e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.618732e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.669348e+02 │ │ │ │ Vprtstp: contraction number = 9.669348e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.383252e-04 │ │ │ │ Vprtstp: contraction number = 2.503875e-01 │ │ │ │ Vnewton: Using errtol_s: 873.412615 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049749e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126110e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.719290e+02 │ │ │ │ Vprtstp: contraction number = 2.719290e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.480245e-05 │ │ │ │ Vprtstp: contraction number = 2.802110e-01 │ │ │ │ Vnewton: Using errtol_s: 244.739841 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.191218e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.281493e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.995844e+01 │ │ │ │ Vprtstp: contraction number = 7.995844e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.787545e-05 │ │ │ │ Vprtstp: contraction number = 2.940373e-01 │ │ │ │ Vnewton: Using errtol_s: 71.962638 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.331941e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.436861e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.395977e+01 │ │ │ │ Vprtstp: contraction number = 2.395977e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.352954e-06 │ │ │ │ Vprtstp: contraction number = 2.996527e-01 │ │ │ │ Vnewton: Using errtol_s: 21.563797 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472413e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.594051e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.269734e+00 │ │ │ │ Vprtstp: contraction number = 7.269734e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.534405e-06 │ │ │ │ Vprtstp: contraction number = 3.034141e-01 │ │ │ │ Vnewton: Using errtol_s: 6.542761 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612740e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.758027e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.227052e+00 │ │ │ │ Vprtstp: contraction number = 2.227052e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.764038e-07 │ │ │ │ Vprtstp: contraction number = 3.063457e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.489297e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.550571e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.662390e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.724600e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -4870,17 +4870,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.906130010441E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.568022982352E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.283111172254E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.370260e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.343840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.1 │ │ │ │ Vpbe_ctor2: xkappa = 0.102972 │ │ │ │ @@ -4927,160 +4927,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.046103 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.882898 │ │ │ │ +Vacc_SASA: Time elapsed: 0.832458 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.855069e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.798176e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.391670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.308380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.280750e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.427310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.983533e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.141857e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2663765.095172 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.060194e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219847e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.151111e+05 │ │ │ │ Vprtstp: contraction number = 4.151111e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.168665 │ │ │ │ Vnewton: Attempting damping, relres = 0.569219 │ │ │ │ Vnewton: Damping accepted, relres = 0.168665 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.686646e-01 │ │ │ │ Vprtstp: contraction number = 1.686646e-01 │ │ │ │ Vnewton: Using errtol_s: 449282.900987 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.228863e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.416871e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.120110e+04 │ │ │ │ Vprtstp: contraction number = 8.120110e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.393027e-02 │ │ │ │ Vprtstp: contraction number = 2.011700e-01 │ │ │ │ Vnewton: Using errtol_s: 90382.255629 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.366675e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.580025e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.991839e+04 │ │ │ │ Vprtstp: contraction number = 1.991839e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.954387e-03 │ │ │ │ Vprtstp: contraction number = 2.344334e-01 │ │ │ │ Vnewton: Using errtol_s: 21188.618171 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.506106e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.747283e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.497898e+03 │ │ │ │ Vprtstp: contraction number = 5.497898e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.952447e-03 │ │ │ │ Vprtstp: contraction number = 2.454554e-01 │ │ │ │ Vnewton: Using errtol_s: 5200.860154 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.644916e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.913842e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.566684e+03 │ │ │ │ Vprtstp: contraction number = 1.566684e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.300165e-04 │ │ │ │ Vprtstp: contraction number = 2.714627e-01 │ │ │ │ Vnewton: Using errtol_s: 1411.839327 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.783439e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.074040e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.634720e+02 │ │ │ │ Vprtstp: contraction number = 4.634720e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.565934e-04 │ │ │ │ Vprtstp: contraction number = 2.954500e-01 │ │ │ │ Vnewton: Using errtol_s: 417.127917 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.923041e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.233889e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.430369e+02 │ │ │ │ Vprtstp: contraction number = 1.430369e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.832756e-05 │ │ │ │ Vprtstp: contraction number = 3.086182e-01 │ │ │ │ Vnewton: Using errtol_s: 128.733272 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.062863e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.393729e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.523062e+01 │ │ │ │ Vprtstp: contraction number = 4.523062e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.528197e-05 │ │ │ │ Vprtstp: contraction number = 3.162164e-01 │ │ │ │ Vnewton: Using errtol_s: 40.707568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.201325e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.551345e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.458043e+01 │ │ │ │ Vprtstp: contraction number = 1.458043e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.926255e-06 │ │ │ │ Vprtstp: contraction number = 3.223574e-01 │ │ │ │ Vnewton: Using errtol_s: 13.122387 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.340842e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.715922e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.774711e+00 │ │ │ │ Vprtstp: contraction number = 4.774711e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.613220e-06 │ │ │ │ Vprtstp: contraction number = 3.274740e-01 │ │ │ │ Vnewton: Using errtol_s: 4.297240 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.480480e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.877220e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.583552e+00 │ │ │ │ Vprtstp: contraction number = 1.583552e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.350309e-07 │ │ │ │ Vprtstp: contraction number = 3.316539e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.603428e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.665199e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.863511e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.924504e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -5090,17 +5090,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.889253587078E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.952637303887E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475418891145E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.362240e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.339190e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -5127,151 +5127,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.309836 │ │ │ │ +Vacc_SASA: Time elapsed: 0.297973 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.043630e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.004400e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.389800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.327850e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.283470e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.470880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.016983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.413947e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 745120.170523 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.094263e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.492591e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.014015e+05 │ │ │ │ Vprtstp: contraction number = 1.014015e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.130811 │ │ │ │ Vnewton: Attempting damping, relres = 0.559104 │ │ │ │ Vnewton: Damping accepted, relres = 0.130811 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.308109e-01 │ │ │ │ Vprtstp: contraction number = 1.308109e-01 │ │ │ │ Vnewton: Using errtol_s: 97469.809951 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.264469e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.676353e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.835986e+04 │ │ │ │ Vprtstp: contraction number = 1.835986e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.256558e-02 │ │ │ │ Vprtstp: contraction number = 1.725054e-01 │ │ │ │ Vnewton: Using errtol_s: 16814.071331 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.403007e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.831504e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.045264e+03 │ │ │ │ Vprtstp: contraction number = 4.045264e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.887910e-03 │ │ │ │ Vprtstp: contraction number = 2.166091e-01 │ │ │ │ Vnewton: Using errtol_s: 3642.080543 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.540646e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.983008e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.003527e+03 │ │ │ │ Vprtstp: contraction number = 1.003527e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.212126e-03 │ │ │ │ Vprtstp: contraction number = 2.479845e-01 │ │ │ │ Vnewton: Using errtol_s: 903.179662 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.678436e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.135117e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660395e+02 │ │ │ │ Vprtstp: contraction number = 2.660395e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.213385e-04 │ │ │ │ Vprtstp: contraction number = 2.651031e-01 │ │ │ │ Vnewton: Using errtol_s: 239.435768 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.815884e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.287423e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.320387e+01 │ │ │ │ Vprtstp: contraction number = 7.320387e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 8.841996e-05 │ │ │ │ Vprtstp: contraction number = 2.751615e-01 │ │ │ │ Vnewton: Using errtol_s: 65.883497 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.952686e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.439062e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.064818e+01 │ │ │ │ Vprtstp: contraction number = 2.064818e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.494009e-05 │ │ │ │ Vprtstp: contraction number = 2.820641e-01 │ │ │ │ Vnewton: Using errtol_s: 18.583367 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.090416e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.591679e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.934502e+00 │ │ │ │ Vprtstp: contraction number = 5.934502e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.168040e-06 │ │ │ │ Vprtstp: contraction number = 2.874103e-01 │ │ │ │ Vnewton: Using errtol_s: 5.341051 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.229228e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.743923e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.731750e+00 │ │ │ │ Vprtstp: contraction number = 1.731750e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.091710e-06 │ │ │ │ Vprtstp: contraction number = 2.918105e-01 │ │ │ │ Vnewton: Using errtol_s: 1.558575 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.365875e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.899001e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.115793e-01 │ │ │ │ Vprtstp: contraction number = 5.115793e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.179156e-07 │ │ │ │ Vprtstp: contraction number = 2.954117e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.453965e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.515828e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.602696e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.664472e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -5281,17 +5281,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.655453691226E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.834706672328E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.415300525959E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.397690e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.391820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.1 │ │ │ │ Vpbe_ctor2: xkappa = 0.102972 │ │ │ │ @@ -5338,160 +5338,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00688905 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.313541 │ │ │ │ +Vacc_SASA: Time elapsed: 0.303412 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.690060e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.731470e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.393760e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.395000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.254770e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.670330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.635646e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.184871e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 777935.905465 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.712944e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.263992e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.267239e+05 │ │ │ │ Vprtstp: contraction number = 1.267239e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.154165 │ │ │ │ Vnewton: Attempting damping, relres = 0.571273 │ │ │ │ Vnewton: Damping accepted, relres = 0.154165 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.541646e-01 │ │ │ │ Vprtstp: contraction number = 1.541646e-01 │ │ │ │ Vnewton: Using errtol_s: 119930.213668 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.886587e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.450351e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.535999e+04 │ │ │ │ Vprtstp: contraction number = 2.535999e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.969700e-02 │ │ │ │ Vprtstp: contraction number = 1.926317e-01 │ │ │ │ Vnewton: Using errtol_s: 23102.366146 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.026318e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.605447e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.051917e+03 │ │ │ │ Vprtstp: contraction number = 6.051917e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.003479e-03 │ │ │ │ Vprtstp: contraction number = 2.358312e-01 │ │ │ │ Vnewton: Using errtol_s: 5448.257890 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.167261e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.764998e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.559687e+03 │ │ │ │ Vprtstp: contraction number = 1.559687e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.804429e-03 │ │ │ │ Vprtstp: contraction number = 2.576475e-01 │ │ │ │ Vnewton: Using errtol_s: 1403.729913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.307522e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.918781e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.232949e+02 │ │ │ │ Vprtstp: contraction number = 4.232949e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.897143e-04 │ │ │ │ Vprtstp: contraction number = 2.713957e-01 │ │ │ │ Vnewton: Using errtol_s: 380.966319 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.447690e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.073227e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.190545e+02 │ │ │ │ Vprtstp: contraction number = 1.190545e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.377351e-04 │ │ │ │ Vprtstp: contraction number = 2.812561e-01 │ │ │ │ Vnewton: Using errtol_s: 107.149093 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.587999e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.227098e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.440341e+01 │ │ │ │ Vprtstp: contraction number = 3.440341e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.980158e-05 │ │ │ │ Vprtstp: contraction number = 2.889719e-01 │ │ │ │ Vnewton: Using errtol_s: 30.963075 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.729300e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.380629e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.017569e+01 │ │ │ │ Vprtstp: contraction number = 1.017569e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.177234e-05 │ │ │ │ Vprtstp: contraction number = 2.957757e-01 │ │ │ │ Vnewton: Using errtol_s: 9.158125 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.870365e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.536279e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.077041e+00 │ │ │ │ Vprtstp: contraction number = 3.077041e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.559852e-06 │ │ │ │ Vprtstp: contraction number = 3.023913e-01 │ │ │ │ Vnewton: Using errtol_s: 2.769337 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.011343e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.691642e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.486014e-01 │ │ │ │ Vprtstp: contraction number = 9.486014e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.097444e-06 │ │ │ │ Vprtstp: contraction number = 3.082837e-01 │ │ │ │ Vnewton: Using errtol_s: 0.853741 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.151610e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.843397e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.971293e-01 │ │ │ │ Vprtstp: contraction number = 2.971293e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.437512e-07 │ │ │ │ Vprtstp: contraction number = 3.132288e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.623356e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.684853e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.782688e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.847249e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -5501,17 +5501,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.647978359783E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.067221403363E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.031568484712E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.391010e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.406450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -5538,162 +5538,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.498651 │ │ │ │ +Vacc_SASA: Time elapsed: 0.466498 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.076478e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.057811e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379720e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.358700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.250740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.497800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.712698e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.402437e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1939359.308692 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.792005e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.480059e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.739516e+05 │ │ │ │ Vprtstp: contraction number = 2.739516e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.235690 │ │ │ │ Vnewton: Attempting damping, relres = 0.566181 │ │ │ │ Vnewton: Damping accepted, relres = 0.235690 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.356901e-01 │ │ │ │ Vprtstp: contraction number = 2.356901e-01 │ │ │ │ Vnewton: Using errtol_s: 457087.767732 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.964971e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.661075e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.385706e+04 │ │ │ │ Vprtstp: contraction number = 5.385706e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.455782e-02 │ │ │ │ Vprtstp: contraction number = 2.314812e-01 │ │ │ │ Vnewton: Using errtol_s: 105807.213748 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.106428e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.819856e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.345524e+04 │ │ │ │ Vprtstp: contraction number = 1.345524e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.370821e-02 │ │ │ │ Vprtstp: contraction number = 2.512602e-01 │ │ │ │ Vnewton: Using errtol_s: 26585.137711 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.247346e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.975196e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.888746e+03 │ │ │ │ Vprtstp: contraction number = 3.888746e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.963355e-03 │ │ │ │ Vprtstp: contraction number = 2.161738e-01 │ │ │ │ Vnewton: Using errtol_s: 5747.009743 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.387632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.125559e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.082322e+03 │ │ │ │ Vprtstp: contraction number = 1.082322e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.510650e-04 │ │ │ │ Vprtstp: contraction number = 1.859598e-01 │ │ │ │ Vnewton: Using errtol_s: 1068.713018 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.528775e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.275457e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.783449e+02 │ │ │ │ Vprtstp: contraction number = 2.783449e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.293604e-04 │ │ │ │ Vprtstp: contraction number = 2.347461e-01 │ │ │ │ Vnewton: Using errtol_s: 250.876218 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.670203e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.425786e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.935007e+01 │ │ │ │ Vprtstp: contraction number = 7.935007e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.682419e-05 │ │ │ │ Vprtstp: contraction number = 2.846636e-01 │ │ │ │ Vnewton: Using errtol_s: 71.415338 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.811287e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.577210e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.391930e+01 │ │ │ │ Vprtstp: contraction number = 2.391930e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.110025e-05 │ │ │ │ Vprtstp: contraction number = 3.014391e-01 │ │ │ │ Vnewton: Using errtol_s: 21.527377 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.951386e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.731145e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.292472e+00 │ │ │ │ Vprtstp: contraction number = 7.292472e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.384223e-06 │ │ │ │ Vprtstp: contraction number = 3.048781e-01 │ │ │ │ Vnewton: Using errtol_s: 6.563225 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.091907e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.881330e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.233482e+00 │ │ │ │ Vprtstp: contraction number = 2.233482e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.036494e-06 │ │ │ │ Vprtstp: contraction number = 3.062723e-01 │ │ │ │ Vnewton: Using errtol_s: 2.010134 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.232198e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003631e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.858053e-01 │ │ │ │ Vprtstp: contraction number = 6.858053e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.182622e-07 │ │ │ │ Vprtstp: contraction number = 3.070566e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.628414e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.689744e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.751058e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.813758e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -5703,17 +5703,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.820035378222E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.875217906563E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.361966912953E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.402970e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.368100e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.1 │ │ │ │ Vpbe_ctor2: xkappa = 0.102972 │ │ │ │ @@ -5760,160 +5760,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0305183 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.492473 │ │ │ │ +Vacc_SASA: Time elapsed: 0.464442 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.296234e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.273458e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.304200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.258000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.392870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.548177e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035771e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1996023.779999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.625362e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.043476e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.403294e+05 │ │ │ │ Vprtstp: contraction number = 3.403294e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.257870 │ │ │ │ Vnewton: Attempting damping, relres = 0.579346 │ │ │ │ Vnewton: Damping accepted, relres = 0.257870 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.578703e-01 │ │ │ │ Vprtstp: contraction number = 2.578703e-01 │ │ │ │ Vnewton: Using errtol_s: 514715.207917 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.796649e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061989e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.253173e+04 │ │ │ │ Vprtstp: contraction number = 7.253173e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 6.121431e-02 │ │ │ │ Vprtstp: contraction number = 2.373841e-01 │ │ │ │ Vnewton: Using errtol_s: 122185.216313 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.938450e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078260e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.904030e+04 │ │ │ │ Vprtstp: contraction number = 1.904030e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.572892e-02 │ │ │ │ Vprtstp: contraction number = 2.569484e-01 │ │ │ │ Vnewton: Using errtol_s: 31395.299569 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008030e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094263e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.659593e+03 │ │ │ │ Vprtstp: contraction number = 5.659593e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.629998e-03 │ │ │ │ Vprtstp: contraction number = 2.307850e-01 │ │ │ │ Vnewton: Using errtol_s: 7245.562904 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022314e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.110003e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.651310e+03 │ │ │ │ Vprtstp: contraction number = 1.651310e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.856291e-04 │ │ │ │ Vprtstp: contraction number = 2.164268e-01 │ │ │ │ Vnewton: Using errtol_s: 1568.134340 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.036450e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.125375e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.661219e+02 │ │ │ │ Vprtstp: contraction number = 4.661219e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.102913e-04 │ │ │ │ Vprtstp: contraction number = 2.676725e-01 │ │ │ │ Vnewton: Using errtol_s: 419.746448 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.050582e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141368e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.425822e+02 │ │ │ │ Vprtstp: contraction number = 1.425822e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.428993e-05 │ │ │ │ Vprtstp: contraction number = 3.057184e-01 │ │ │ │ Vnewton: Using errtol_s: 128.324228 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064744e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156866e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.557507e+01 │ │ │ │ Vprtstp: contraction number = 4.557507e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.054964e-05 │ │ │ │ Vprtstp: contraction number = 3.196401e-01 │ │ │ │ Vnewton: Using errtol_s: 41.017570 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078650e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.171998e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.480670e+01 │ │ │ │ Vprtstp: contraction number = 1.480670e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 6.676290e-06 │ │ │ │ Vprtstp: contraction number = 3.248860e-01 │ │ │ │ Vnewton: Using errtol_s: 13.326033 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.092765e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.187600e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.862220e+00 │ │ │ │ Vprtstp: contraction number = 4.862220e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.192358e-06 │ │ │ │ Vprtstp: contraction number = 3.283797e-01 │ │ │ │ Vnewton: Using errtol_s: 4.375998 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.106840e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.203337e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.609470e+00 │ │ │ │ Vprtstp: contraction number = 1.609470e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.257041e-07 │ │ │ │ Vprtstp: contraction number = 3.310154e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.626542e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.687598e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.799877e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.860695e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -5923,29 +5923,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.804365657787E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.136955879048E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.067066513912E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.377930e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.363430e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.146610e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.243068e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:44:07 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:32:55 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -6215,151 +6215,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.894768 │ │ │ │ +Vacc_SASA: Time elapsed: 0.852487 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.615329e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.545693e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.378540e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.343350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.257790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.425000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.310972e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.233842e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2482316.849131 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.086057e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.999208e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.222887e+05 │ │ │ │ Vprtstp: contraction number = 3.222887e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.143642 │ │ │ │ Vnewton: Attempting damping, relres = 0.557204 │ │ │ │ Vnewton: Damping accepted, relres = 0.143642 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.436423e-01 │ │ │ │ Vprtstp: contraction number = 1.436423e-01 │ │ │ │ Vnewton: Using errtol_s: 356565.753990 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.817381e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.919367e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.719340e+04 │ │ │ │ Vprtstp: contraction number = 5.719340e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.655317e-02 │ │ │ │ Vprtstp: contraction number = 1.848561e-01 │ │ │ │ Vnewton: Using errtol_s: 65913.370564 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.229867e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.597943e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.314754e+04 │ │ │ │ Vprtstp: contraction number = 1.314754e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.777425e-03 │ │ │ │ Vprtstp: contraction number = 2.175795e-01 │ │ │ │ Vnewton: Using errtol_s: 14341.400512 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.651473e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.259645e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.464763e+03 │ │ │ │ Vprtstp: contraction number = 3.464763e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.322569e-03 │ │ │ │ Vprtstp: contraction number = 2.289202e-01 │ │ │ │ Vnewton: Using errtol_s: 3283.035896 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.067536e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.889109e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.430238e+02 │ │ │ │ Vprtstp: contraction number = 9.430238e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.423711e-04 │ │ │ │ Vprtstp: contraction number = 2.588682e-01 │ │ │ │ Vnewton: Using errtol_s: 849.873571 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047147e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.151079e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.680844e+02 │ │ │ │ Vprtstp: contraction number = 2.680844e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.719850e-05 │ │ │ │ Vprtstp: contraction number = 2.838981e-01 │ │ │ │ Vnewton: Using errtol_s: 241.277472 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188288e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.314302e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.904724e+01 │ │ │ │ Vprtstp: contraction number = 7.904724e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.865974e-05 │ │ │ │ Vprtstp: contraction number = 2.948578e-01 │ │ │ │ Vnewton: Using errtol_s: 71.142545 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.329831e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.477563e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.370878e+01 │ │ │ │ Vprtstp: contraction number = 2.370878e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.595964e-06 │ │ │ │ Vprtstp: contraction number = 2.999317e-01 │ │ │ │ Vnewton: Using errtol_s: 21.337905 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.470249e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.641079e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.196546e+00 │ │ │ │ Vprtstp: contraction number = 7.196546e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.609212e-06 │ │ │ │ Vprtstp: contraction number = 3.035392e-01 │ │ │ │ Vnewton: Using errtol_s: 6.476891 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.610765e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.805581e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.205063e+00 │ │ │ │ Vprtstp: contraction number = 2.205063e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.994776e-07 │ │ │ │ Vprtstp: contraction number = 3.064057e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.488154e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.549476e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.709544e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.770981e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -6369,17 +6369,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.741026947407E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567804611788E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.283053686435E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.374430e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.351230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.125 │ │ │ │ Vpbe_ctor2: xkappa = 0.115127 │ │ │ │ @@ -6426,160 +6426,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0353875 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.882757 │ │ │ │ +Vacc_SASA: Time elapsed: 0.828902 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.864867e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.804175e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.382920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.335150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.380630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.428160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.984427e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.190860e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2557475.753383 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.061478e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.268922e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.996924e+05 │ │ │ │ Vprtstp: contraction number = 3.996924e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.166335 │ │ │ │ Vnewton: Attempting damping, relres = 0.569269 │ │ │ │ Vnewton: Damping accepted, relres = 0.166335 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.663353e-01 │ │ │ │ Vprtstp: contraction number = 1.663353e-01 │ │ │ │ Vnewton: Using errtol_s: 425398.550037 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.231868e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.465743e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.844641e+04 │ │ │ │ Vprtstp: contraction number = 7.844641e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.321581e-02 │ │ │ │ Vprtstp: contraction number = 1.996918e-01 │ │ │ │ Vnewton: Using errtol_s: 84948.619306 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.379912e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.632931e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.934802e+04 │ │ │ │ Vprtstp: contraction number = 1.934802e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.763061e-03 │ │ │ │ Vprtstp: contraction number = 2.337159e-01 │ │ │ │ Vnewton: Using errtol_s: 19853.840744 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.521204e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.793821e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.339655e+03 │ │ │ │ Vprtstp: contraction number = 5.339655e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.934926e-03 │ │ │ │ Vprtstp: contraction number = 2.492478e-01 │ │ │ │ Vnewton: Using errtol_s: 4948.526141 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.662812e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.952772e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.525404e+03 │ │ │ │ Vprtstp: contraction number = 1.525404e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.370526e-04 │ │ │ │ Vprtstp: contraction number = 2.775572e-01 │ │ │ │ Vnewton: Using errtol_s: 1373.498967 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.804226e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.108216e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.551328e+02 │ │ │ │ Vprtstp: contraction number = 4.551328e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.601661e-04 │ │ │ │ Vprtstp: contraction number = 2.982316e-01 │ │ │ │ Vnewton: Using errtol_s: 409.620859 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.944627e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.264862e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.409185e+02 │ │ │ │ Vprtstp: contraction number = 1.409185e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.959057e-05 │ │ │ │ Vprtstp: contraction number = 3.096197e-01 │ │ │ │ Vnewton: Using errtol_s: 126.826691 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.087242e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.427247e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.462999e+01 │ │ │ │ Vprtstp: contraction number = 4.462999e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.570572e-05 │ │ │ │ Vprtstp: contraction number = 3.167077e-01 │ │ │ │ Vnewton: Using errtol_s: 40.166995 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.232005e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.594907e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.440051e+01 │ │ │ │ Vprtstp: contraction number = 1.440051e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.067675e-06 │ │ │ │ Vprtstp: contraction number = 3.226643e-01 │ │ │ │ Vnewton: Using errtol_s: 12.960456 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.401178e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.761366e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.718013e+00 │ │ │ │ Vprtstp: contraction number = 4.718013e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.660314e-06 │ │ │ │ Vprtstp: contraction number = 3.276283e-01 │ │ │ │ Vnewton: Using errtol_s: 4.246212 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.578159e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.930726e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.564985e+00 │ │ │ │ Vprtstp: contraction number = 1.564985e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.507330e-07 │ │ │ │ Vprtstp: contraction number = 3.317042e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.705917e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.768510e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.873910e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.935415e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -6589,17 +6589,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.724934425703E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.952419017164E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475361712291E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.367930e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.344670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -6626,151 +6626,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.310514 │ │ │ │ +Vacc_SASA: Time elapsed: 0.295252 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.213980e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.038270e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.471590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.320660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.313730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.409180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.127498e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.482142e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 720364.541598 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.203995e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.559792e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.787737e+04 │ │ │ │ Vprtstp: contraction number = 9.787737e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.130881 │ │ │ │ Vnewton: Attempting damping, relres = 0.558946 │ │ │ │ Vnewton: Damping accepted, relres = 0.130881 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.308815e-01 │ │ │ │ Vprtstp: contraction number = 1.308815e-01 │ │ │ │ Vnewton: Using errtol_s: 94282.387082 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.376707e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.743292e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.788353e+04 │ │ │ │ Vprtstp: contraction number = 1.788353e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.273611e-02 │ │ │ │ Vprtstp: contraction number = 1.737152e-01 │ │ │ │ Vnewton: Using errtol_s: 16378.286782 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.519982e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.893721e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.978150e+03 │ │ │ │ Vprtstp: contraction number = 3.978150e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 4.972005e-03 │ │ │ │ Vprtstp: contraction number = 2.186832e-01 │ │ │ │ Vnewton: Using errtol_s: 3581.655852 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.659386e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.044835e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.935846e+02 │ │ │ │ Vprtstp: contraction number = 9.935846e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.241360e-03 │ │ │ │ Vprtstp: contraction number = 2.496698e-01 │ │ │ │ Vnewton: Using errtol_s: 894.231472 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.800773e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.196142e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.645071e+02 │ │ │ │ Vprtstp: contraction number = 2.645071e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.304670e-04 │ │ │ │ Vprtstp: contraction number = 2.662137e-01 │ │ │ │ Vnewton: Using errtol_s: 238.056677 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.939793e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.347103e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.296267e+01 │ │ │ │ Vprtstp: contraction number = 7.296267e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.115721e-05 │ │ │ │ Vprtstp: contraction number = 2.758437e-01 │ │ │ │ Vnewton: Using errtol_s: 65.666425 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.082036e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.494091e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.060915e+01 │ │ │ │ Vprtstp: contraction number = 2.060915e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.574840e-05 │ │ │ │ Vprtstp: contraction number = 2.824615e-01 │ │ │ │ Vnewton: Using errtol_s: 18.548236 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.222160e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.643651e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.927860e+00 │ │ │ │ Vprtstp: contraction number = 5.927860e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.406076e-06 │ │ │ │ Vprtstp: contraction number = 2.876324e-01 │ │ │ │ Vnewton: Using errtol_s: 5.335074 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.363274e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.788255e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.730517e+00 │ │ │ │ Vprtstp: contraction number = 1.730517e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.162052e-06 │ │ │ │ Vprtstp: contraction number = 2.919295e-01 │ │ │ │ Vnewton: Using errtol_s: 1.557466 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.504093e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.940618e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.113205e-01 │ │ │ │ Vprtstp: contraction number = 5.113205e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.388271e-07 │ │ │ │ Vprtstp: contraction number = 2.954726e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.485931e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.549011e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.572967e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.634026e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -6780,17 +6780,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.705203011942E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.834032014754E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.414947804784E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.416260e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.125 │ │ │ │ Vpbe_ctor2: xkappa = 0.115127 │ │ │ │ @@ -6837,160 +6837,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0059523 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.303880 │ │ │ │ +Vacc_SASA: Time elapsed: 0.294392 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.725700e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.731210e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.361940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.323760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.277590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.447960e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.778340e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.220390e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 751497.765770 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.855863e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.298543e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.222283e+05 │ │ │ │ Vprtstp: contraction number = 1.222283e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.154183 │ │ │ │ Vnewton: Attempting damping, relres = 0.571098 │ │ │ │ Vnewton: Damping accepted, relres = 0.154183 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.541833e-01 │ │ │ │ Vprtstp: contraction number = 1.541833e-01 │ │ │ │ Vnewton: Using errtol_s: 115868.383651 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.028911e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.487018e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.458734e+04 │ │ │ │ Vprtstp: contraction number = 2.458734e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.980652e-02 │ │ │ │ Vprtstp: contraction number = 1.933188e-01 │ │ │ │ Vnewton: Using errtol_s: 22399.536309 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.169971e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.640731e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.900997e+03 │ │ │ │ Vprtstp: contraction number = 5.900997e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.069086e-03 │ │ │ │ Vprtstp: contraction number = 2.371657e-01 │ │ │ │ Vnewton: Using errtol_s: 5312.402554 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.308861e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.792241e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.528364e+03 │ │ │ │ Vprtstp: contraction number = 1.528364e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.830398e-03 │ │ │ │ Vprtstp: contraction number = 2.589300e-01 │ │ │ │ Vnewton: Using errtol_s: 1375.540379 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.449815e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.947087e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.166306e+02 │ │ │ │ Vprtstp: contraction number = 4.166306e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.989616e-04 │ │ │ │ Vprtstp: contraction number = 2.725973e-01 │ │ │ │ Vnewton: Using errtol_s: 374.968546 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.590755e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.100440e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.176231e+02 │ │ │ │ Vprtstp: contraction number = 1.176231e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.408665e-04 │ │ │ │ Vprtstp: contraction number = 2.823194e-01 │ │ │ │ Vnewton: Using errtol_s: 105.860894 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.730473e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.255392e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.409436e+01 │ │ │ │ Vprtstp: contraction number = 3.409436e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.083170e-05 │ │ │ │ Vprtstp: contraction number = 2.898609e-01 │ │ │ │ Vnewton: Using errtol_s: 30.684933 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.871348e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.402762e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.010867e+01 │ │ │ │ Vprtstp: contraction number = 1.010867e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.210623e-05 │ │ │ │ Vprtstp: contraction number = 2.964909e-01 │ │ │ │ Vnewton: Using errtol_s: 9.097804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.012207e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.565584e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.062356e+00 │ │ │ │ Vprtstp: contraction number = 3.062356e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.667504e-06 │ │ │ │ Vprtstp: contraction number = 3.029435e-01 │ │ │ │ Vnewton: Using errtol_s: 2.756121 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.151402e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.732047e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.453520e-01 │ │ │ │ Vprtstp: contraction number = 9.453520e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.132162e-06 │ │ │ │ Vprtstp: contraction number = 3.087009e-01 │ │ │ │ Vnewton: Using errtol_s: 0.850817 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.290513e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.899325e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.964013e-01 │ │ │ │ Vprtstp: contraction number = 2.964013e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.549727e-07 │ │ │ │ Vprtstp: contraction number = 3.135354e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.620747e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.681910e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.817512e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.879087e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -7000,15 +7000,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.697571697895E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.066549555181E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.031217527268E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.455350e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.821230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -7037,162 +7037,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.485843 │ │ │ │ +Vacc_SASA: Time elapsed: 0.469550 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.073417e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.066548e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.373130e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.330050e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.251560e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.476010e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.849438e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.494874e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1823063.193603 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.926012e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.572594e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.580519e+05 │ │ │ │ Vprtstp: contraction number = 2.580519e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.222567 │ │ │ │ Vnewton: Attempting damping, relres = 0.565989 │ │ │ │ Vnewton: Damping accepted, relres = 0.222567 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.225671e-01 │ │ │ │ Vprtstp: contraction number = 2.225671e-01 │ │ │ │ Vnewton: Using errtol_s: 405753.919509 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.099023e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.754664e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.022631e+04 │ │ │ │ Vprtstp: contraction number = 5.022631e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.970113e-02 │ │ │ │ Vprtstp: contraction number = 2.233085e-01 │ │ │ │ Vnewton: Using errtol_s: 90608.292404 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.237828e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.920305e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.257885e+04 │ │ │ │ Vprtstp: contraction number = 1.257885e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.198700e-02 │ │ │ │ Vprtstp: contraction number = 2.411816e-01 │ │ │ │ Vnewton: Using errtol_s: 21853.051255 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.375570e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.073408e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.600602e+03 │ │ │ │ Vprtstp: contraction number = 3.600602e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.500944e-03 │ │ │ │ Vprtstp: contraction number = 2.086381e-01 │ │ │ │ Vnewton: Using errtol_s: 4559.378536 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.514890e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.230382e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.867332e+02 │ │ │ │ Vprtstp: contraction number = 9.867332e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.056164e-04 │ │ │ │ Vprtstp: contraction number = 2.021702e-01 │ │ │ │ Vnewton: Using errtol_s: 921.770690 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.655421e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.385261e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.646218e+02 │ │ │ │ Vprtstp: contraction number = 2.646218e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.306754e-04 │ │ │ │ Vprtstp: contraction number = 2.584478e-01 │ │ │ │ Vnewton: Using errtol_s: 238.229561 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.795506e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.536790e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.765679e+01 │ │ │ │ Vprtstp: contraction number = 7.765679e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.833723e-05 │ │ │ │ Vprtstp: contraction number = 2.933775e-01 │ │ │ │ Vnewton: Using errtol_s: 69.891187 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.933791e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.691735e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.351839e+01 │ │ │ │ Vprtstp: contraction number = 2.351839e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.161043e-05 │ │ │ │ Vprtstp: contraction number = 3.028501e-01 │ │ │ │ Vnewton: Using errtol_s: 21.166555 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.073038e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.848114e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.178418e+00 │ │ │ │ Vprtstp: contraction number = 7.178418e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.543803e-06 │ │ │ │ Vprtstp: contraction number = 3.052257e-01 │ │ │ │ Vnewton: Using errtol_s: 6.460576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.212948e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.998480e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.199458e+00 │ │ │ │ Vprtstp: contraction number = 2.199458e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.085817e-06 │ │ │ │ Vprtstp: contraction number = 3.063988e-01 │ │ │ │ Vnewton: Using errtol_s: 1.979513 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.352589e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014875e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.755609e-01 │ │ │ │ Vprtstp: contraction number = 6.755609e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.335073e-07 │ │ │ │ Vprtstp: contraction number = 3.071488e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.610417e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.671598e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.770998e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.832941e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -7202,17 +7202,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.498944659129E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.874900883074E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.361242882871E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390940e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.387240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.125 │ │ │ │ Vpbe_ctor2: xkappa = 0.115127 │ │ │ │ @@ -7259,160 +7259,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0207746 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.486968 │ │ │ │ +Vacc_SASA: Time elapsed: 0.470108 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.291074e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.280450e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.390600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.340980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.274550e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.512880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.666693e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047262e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1873431.596335 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.743997e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.055063e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.215071e+05 │ │ │ │ Vprtstp: contraction number = 3.215071e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.246235 │ │ │ │ Vnewton: Attempting damping, relres = 0.579562 │ │ │ │ Vnewton: Damping accepted, relres = 0.246235 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.462348e-01 │ │ │ │ Vprtstp: contraction number = 2.462348e-01 │ │ │ │ Vnewton: Using errtol_s: 461304.132219 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.917973e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073403e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.793925e+04 │ │ │ │ Vprtstp: contraction number = 6.793925e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.674078e-02 │ │ │ │ Vprtstp: contraction number = 2.304336e-01 │ │ │ │ Vnewton: Using errtol_s: 106299.974305 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005980e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089344e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.790128e+04 │ │ │ │ Vprtstp: contraction number = 1.790128e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.413343e-02 │ │ │ │ Vprtstp: contraction number = 2.490877e-01 │ │ │ │ Vnewton: Using errtol_s: 26478.015957 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020137e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.105780e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.289572e+03 │ │ │ │ Vprtstp: contraction number = 5.289572e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 3.207748e-03 │ │ │ │ Vprtstp: contraction number = 2.269618e-01 │ │ │ │ Vnewton: Using errtol_s: 6009.496862 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034189e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120723e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.531645e+03 │ │ │ │ Vprtstp: contraction number = 1.531645e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.505521e-04 │ │ │ │ Vprtstp: contraction number = 2.339810e-01 │ │ │ │ Vnewton: Using errtol_s: 1406.107935 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048075e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.135791e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.459814e+02 │ │ │ │ Vprtstp: contraction number = 4.459814e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.142740e-04 │ │ │ │ Vprtstp: contraction number = 2.854885e-01 │ │ │ │ Vnewton: Using errtol_s: 401.427706 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062166e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.151630e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.392761e+02 │ │ │ │ Vprtstp: contraction number = 1.392761e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.690856e-05 │ │ │ │ Vprtstp: contraction number = 3.122570e-01 │ │ │ │ Vnewton: Using errtol_s: 125.348607 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.075863e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.166820e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.474617e+01 │ │ │ │ Vprtstp: contraction number = 4.474617e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.149615e-05 │ │ │ │ Vprtstp: contraction number = 3.212765e-01 │ │ │ │ Vnewton: Using errtol_s: 40.271562 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089768e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.182581e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.457086e+01 │ │ │ │ Vprtstp: contraction number = 1.457086e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 6.999869e-06 │ │ │ │ Vprtstp: contraction number = 3.256337e-01 │ │ │ │ Vnewton: Using errtol_s: 13.113776 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103644e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.198486e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.791596e+00 │ │ │ │ Vprtstp: contraction number = 4.791596e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.301892e-06 │ │ │ │ Vprtstp: contraction number = 3.288478e-01 │ │ │ │ Vnewton: Using errtol_s: 4.312437 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.117747e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.213855e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.587543e+00 │ │ │ │ Vprtstp: contraction number = 1.587543e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.626585e-07 │ │ │ │ Vprtstp: contraction number = 3.313182e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.618063e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.679544e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.788916e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.851250e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -7422,29 +7422,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.484583962909E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.136638905481E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066994369938E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.372990e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.420970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.157500e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.255242e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:45:03 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:34:24 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -7714,151 +7714,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.904032 │ │ │ │ +Vacc_SASA: Time elapsed: 0.847927 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.665589e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.542997e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.407410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.338450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.308620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.584380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.365769e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.245942e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2410732.356899 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.146760e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.037177e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.128143e+05 │ │ │ │ Vprtstp: contraction number = 3.128143e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.141068 │ │ │ │ Vnewton: Attempting damping, relres = 0.557017 │ │ │ │ Vnewton: Damping accepted, relres = 0.141068 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.410683e-01 │ │ │ │ Vprtstp: contraction number = 1.410683e-01 │ │ │ │ Vnewton: Using errtol_s: 340078.014247 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.897164e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.012930e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.570013e+04 │ │ │ │ Vprtstp: contraction number = 5.570013e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.582927e-02 │ │ │ │ Vprtstp: contraction number = 1.830975e-01 │ │ │ │ Vnewton: Using errtol_s: 62267.446259 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.358235e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648381e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.287475e+04 │ │ │ │ Vprtstp: contraction number = 1.287475e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.599207e-03 │ │ │ │ Vprtstp: contraction number = 2.167776e-01 │ │ │ │ Vnewton: Using errtol_s: 13498.190114 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.764094e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.324024e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.390785e+03 │ │ │ │ Vprtstp: contraction number = 3.390785e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.306467e-03 │ │ │ │ Vprtstp: contraction number = 2.333308e-01 │ │ │ │ Vnewton: Using errtol_s: 3149.543372 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.159059e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.879806e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.269338e+02 │ │ │ │ Vprtstp: contraction number = 9.269338e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.462424e-04 │ │ │ │ Vprtstp: contraction number = 2.650218e-01 │ │ │ │ Vnewton: Using errtol_s: 834.697770 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068959e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143495e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.654672e+02 │ │ │ │ Vprtstp: contraction number = 2.654672e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.910734e-05 │ │ │ │ Vprtstp: contraction number = 2.862369e-01 │ │ │ │ Vnewton: Using errtol_s: 238.921266 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229250e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.300086e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.840492e+01 │ │ │ │ Vprtstp: contraction number = 7.840492e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.927096e-05 │ │ │ │ Vprtstp: contraction number = 2.953460e-01 │ │ │ │ Vnewton: Using errtol_s: 70.564451 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.379780e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.456687e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.353183e+01 │ │ │ │ Vprtstp: contraction number = 2.353183e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.785152e-06 │ │ │ │ Vprtstp: contraction number = 3.001320e-01 │ │ │ │ Vnewton: Using errtol_s: 21.178651 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.521250e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.612743e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.144902e+00 │ │ │ │ Vprtstp: contraction number = 7.144902e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.667410e-06 │ │ │ │ Vprtstp: contraction number = 3.036271e-01 │ │ │ │ Vnewton: Using errtol_s: 6.430412 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.663070e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.768728e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.189586e+00 │ │ │ │ Vprtstp: contraction number = 2.189586e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.174393e-07 │ │ │ │ Vprtstp: contraction number = 3.064543e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.534724e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.596955e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.666740e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.729717e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -7868,15 +7868,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.581693957245E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567629004923E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.283007133277E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.358980e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.354820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ @@ -7925,160 +7925,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0289035 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.870967 │ │ │ │ +Vacc_SASA: Time elapsed: 0.849711 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.847989e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.837179e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.364260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.324020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.254210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.487910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.033109e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.153010e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2480363.897694 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.110303e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.229525e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.884147e+05 │ │ │ │ Vprtstp: contraction number = 3.884147e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.164249 │ │ │ │ Vnewton: Attempting damping, relres = 0.569268 │ │ │ │ Vnewton: Damping accepted, relres = 0.164249 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.642495e-01 │ │ │ │ Vprtstp: contraction number = 1.642495e-01 │ │ │ │ Vnewton: Using errtol_s: 407398.416424 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.284236e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.415871e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.641742e+04 │ │ │ │ Vprtstp: contraction number = 7.641742e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.259356e-02 │ │ │ │ Vprtstp: contraction number = 1.984394e-01 │ │ │ │ Vnewton: Using errtol_s: 80843.885291 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.426329e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.572251e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.892121e+04 │ │ │ │ Vprtstp: contraction number = 1.892121e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.611596e-03 │ │ │ │ Vprtstp: contraction number = 2.335307e-01 │ │ │ │ Vnewton: Using errtol_s: 18879.528241 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.571099e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.734528e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.219825e+03 │ │ │ │ Vprtstp: contraction number = 5.219825e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.927310e-03 │ │ │ │ Vprtstp: contraction number = 2.532071e-01 │ │ │ │ Vnewton: Using errtol_s: 4780.429766 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.714733e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.891870e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.496544e+03 │ │ │ │ Vprtstp: contraction number = 1.496544e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.431250e-04 │ │ │ │ Vprtstp: contraction number = 2.818047e-01 │ │ │ │ Vnewton: Using errtol_s: 1347.147545 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.856809e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.049689e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.492633e+02 │ │ │ │ Vprtstp: contraction number = 4.492633e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.630155e-04 │ │ │ │ Vprtstp: contraction number = 3.001437e-01 │ │ │ │ Vnewton: Using errtol_s: 404.337796 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.998414e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.207532e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.394005e+02 │ │ │ │ Vprtstp: contraction number = 1.394005e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.058149e-05 │ │ │ │ Vprtstp: contraction number = 3.102863e-01 │ │ │ │ Vnewton: Using errtol_s: 125.460496 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.140627e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.370643e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.420063e+01 │ │ │ │ Vprtstp: contraction number = 4.420063e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.603820e-05 │ │ │ │ Vprtstp: contraction number = 3.170765e-01 │ │ │ │ Vnewton: Using errtol_s: 39.780577 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.281202e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.527699e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.427219e+01 │ │ │ │ Vprtstp: contraction number = 1.427219e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.178663e-06 │ │ │ │ Vprtstp: contraction number = 3.228955e-01 │ │ │ │ Vnewton: Using errtol_s: 12.844969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.422513e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.689755e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.677701e+00 │ │ │ │ Vprtstp: contraction number = 4.677701e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.697304e-06 │ │ │ │ Vprtstp: contraction number = 3.277495e-01 │ │ │ │ Vnewton: Using errtol_s: 4.209931 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.565009e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.847709e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.551790e+00 │ │ │ │ Vprtstp: contraction number = 1.551790e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.630670e-07 │ │ │ │ Vprtstp: contraction number = 3.317420e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.641093e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.702173e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.825703e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.887557e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8088,17 +8088,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.566249593084E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.952243483734E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475315373786E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.359670e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.342360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -8125,151 +8125,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.310101 │ │ │ │ +Vacc_SASA: Time elapsed: 0.295064 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.520980e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.036360e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.345910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.329000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.227030e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.454220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.107368e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.396433e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 702833.844391 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.184705e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.474557e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.535199e+04 │ │ │ │ Vprtstp: contraction number = 9.535199e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.130807 │ │ │ │ Vnewton: Attempting damping, relres = 0.558803 │ │ │ │ Vnewton: Damping accepted, relres = 0.130807 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.308068e-01 │ │ │ │ Vprtstp: contraction number = 1.308068e-01 │ │ │ │ Vnewton: Using errtol_s: 91935.456218 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.357226e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.656395e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.754021e+04 │ │ │ │ Vprtstp: contraction number = 1.754021e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.284568e-02 │ │ │ │ Vprtstp: contraction number = 1.746521e-01 │ │ │ │ Vnewton: Using errtol_s: 16056.717423 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.497824e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.804929e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.929316e+03 │ │ │ │ Vprtstp: contraction number = 3.929316e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.033389e-03 │ │ │ │ Vprtstp: contraction number = 2.203212e-01 │ │ │ │ Vnewton: Using errtol_s: 3537.635824 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.638327e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.955236e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.863417e+02 │ │ │ │ Vprtstp: contraction number = 9.863417e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.263048e-03 │ │ │ │ Vprtstp: contraction number = 2.509340e-01 │ │ │ │ Vnewton: Using errtol_s: 887.712932 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.779222e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.103421e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.633855e+02 │ │ │ │ Vprtstp: contraction number = 2.633855e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.372735e-04 │ │ │ │ Vprtstp: contraction number = 2.670314e-01 │ │ │ │ Vnewton: Using errtol_s: 237.047224 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.917537e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.252663e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.278494e+01 │ │ │ │ Vprtstp: contraction number = 7.278494e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.320334e-05 │ │ │ │ Vprtstp: contraction number = 2.763435e-01 │ │ │ │ Vnewton: Using errtol_s: 65.506461 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.055434e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.400936e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.058009e+01 │ │ │ │ Vprtstp: contraction number = 2.058009e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.635343e-05 │ │ │ │ Vprtstp: contraction number = 2.827520e-01 │ │ │ │ Vnewton: Using errtol_s: 18.522083 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.195541e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.553551e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.922842e+00 │ │ │ │ Vprtstp: contraction number = 5.922842e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.584378e-06 │ │ │ │ Vprtstp: contraction number = 2.877947e-01 │ │ │ │ Vnewton: Using errtol_s: 5.330558 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.334777e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.706643e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.729569e+00 │ │ │ │ Vprtstp: contraction number = 1.729569e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.214765e-06 │ │ │ │ Vprtstp: contraction number = 2.920167e-01 │ │ │ │ Vnewton: Using errtol_s: 1.556612 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.475982e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.854339e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.111172e-01 │ │ │ │ Vprtstp: contraction number = 5.111172e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.545011e-07 │ │ │ │ Vprtstp: contraction number = 2.955171e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.477526e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.538269e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.575066e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.636788e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8279,17 +8279,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.740193498696E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.833468589698E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.414657798024E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.425650e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.419050e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.126115 │ │ │ │ @@ -8336,160 +8336,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00524143 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.314600 │ │ │ │ +Vacc_SASA: Time elapsed: 0.295296 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.810180e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.783420e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.375450e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.374460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.255680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.531900e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.750897e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.139200e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 732702.640135 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.827372e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.217933e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.189776e+05 │ │ │ │ Vprtstp: contraction number = 1.189776e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.154045 │ │ │ │ Vnewton: Attempting damping, relres = 0.570927 │ │ │ │ Vnewton: Damping accepted, relres = 0.154045 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.540451e-01 │ │ │ │ Vprtstp: contraction number = 1.540451e-01 │ │ │ │ Vnewton: Using errtol_s: 112869.287383 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.999200e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.399210e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.402351e+04 │ │ │ │ Vprtstp: contraction number = 2.402351e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.986126e-02 │ │ │ │ Vprtstp: contraction number = 1.938474e-01 │ │ │ │ Vnewton: Using errtol_s: 21879.422460 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.139582e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.553923e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.789967e+03 │ │ │ │ Vprtstp: contraction number = 5.789967e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.113936e-03 │ │ │ │ Vprtstp: contraction number = 2.382330e-01 │ │ │ │ Vnewton: Using errtol_s: 5212.399665 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.281973e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.707557e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.505316e+03 │ │ │ │ Vprtstp: contraction number = 1.505316e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.849041e-03 │ │ │ │ Vprtstp: contraction number = 2.599182e-01 │ │ │ │ Vnewton: Using errtol_s: 1354.797457 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.421363e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.860625e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.117226e+02 │ │ │ │ Vprtstp: contraction number = 4.117226e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.057322e-04 │ │ │ │ Vprtstp: contraction number = 2.735105e-01 │ │ │ │ Vnewton: Using errtol_s: 370.551343 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.560620e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.009369e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.165670e+02 │ │ │ │ Vprtstp: contraction number = 1.165670e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.431828e-04 │ │ │ │ Vprtstp: contraction number = 2.831198e-01 │ │ │ │ Vnewton: Using errtol_s: 104.910419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.700251e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.163801e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.386584e+01 │ │ │ │ Vprtstp: contraction number = 3.386584e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.159841e-05 │ │ │ │ Vprtstp: contraction number = 2.905266e-01 │ │ │ │ Vnewton: Using errtol_s: 30.479265 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.838531e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.316250e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.005899e+01 │ │ │ │ Vprtstp: contraction number = 1.005899e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.235575e-05 │ │ │ │ Vprtstp: contraction number = 2.970246e-01 │ │ │ │ Vnewton: Using errtol_s: 9.053091 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.977471e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.468760e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.051439e+00 │ │ │ │ Vprtstp: contraction number = 3.051439e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.748171e-06 │ │ │ │ Vprtstp: contraction number = 3.033544e-01 │ │ │ │ Vnewton: Using errtol_s: 2.746295 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.118083e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.616546e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.429257e-01 │ │ │ │ Vprtstp: contraction number = 9.429257e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.158223e-06 │ │ │ │ Vprtstp: contraction number = 3.090102e-01 │ │ │ │ Vnewton: Using errtol_s: 0.848633 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.257150e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.770493e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.958550e-01 │ │ │ │ Vprtstp: contraction number = 2.958550e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.634073e-07 │ │ │ │ Vprtstp: contraction number = 3.137628e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.612954e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.674240e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.753072e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.816202e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8499,17 +8499,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.732432041867E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.065988471810E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.030928944477E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.402530e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.392740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -8536,162 +8536,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.490550 │ │ │ │ +Vacc_SASA: Time elapsed: 0.468725 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.081470e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.061154e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.371640e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.347470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.272680e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.579510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.820286e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.339349e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1741500.081736 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.897218e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.418302e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.468341e+05 │ │ │ │ Vprtstp: contraction number = 2.468341e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.211968 │ │ │ │ Vnewton: Attempting damping, relres = 0.565739 │ │ │ │ Vnewton: Damping accepted, relres = 0.211968 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.119682e-01 │ │ │ │ Vprtstp: contraction number = 2.119682e-01 │ │ │ │ Vnewton: Using errtol_s: 369142.647388 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.069119e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.603346e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.765545e+04 │ │ │ │ Vprtstp: contraction number = 4.765545e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.585316e-02 │ │ │ │ Vprtstp: contraction number = 2.163209e-01 │ │ │ │ Vnewton: Using errtol_s: 79853.288161 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.210715e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.772022e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.196657e+04 │ │ │ │ Vprtstp: contraction number = 1.196657e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.069307e-02 │ │ │ │ Vprtstp: contraction number = 2.332024e-01 │ │ │ │ Vnewton: Using errtol_s: 18621.978068 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.350843e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.927072e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.396204e+03 │ │ │ │ Vprtstp: contraction number = 3.396204e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.206422e-03 │ │ │ │ Vprtstp: contraction number = 2.063414e-01 │ │ │ │ Vnewton: Using errtol_s: 3842.484890 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.490892e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.080135e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.262198e+02 │ │ │ │ Vprtstp: contraction number = 9.262198e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.857523e-04 │ │ │ │ Vprtstp: contraction number = 2.201538e-01 │ │ │ │ Vnewton: Using errtol_s: 845.937714 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.631768e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.237220e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.568315e+02 │ │ │ │ Vprtstp: contraction number = 2.568315e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.327389e-04 │ │ │ │ Vprtstp: contraction number = 2.732646e-01 │ │ │ │ Vnewton: Using errtol_s: 231.164809 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.773255e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.392731e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.648381e+01 │ │ │ │ Vprtstp: contraction number = 7.648381e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.952654e-05 │ │ │ │ Vprtstp: contraction number = 2.977766e-01 │ │ │ │ Vnewton: Using errtol_s: 68.835472 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.912499e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.545937e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.321302e+01 │ │ │ │ Vprtstp: contraction number = 2.321302e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.199639e-05 │ │ │ │ Vprtstp: contraction number = 3.035022e-01 │ │ │ │ Vnewton: Using errtol_s: 20.891720 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.051239e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.698135e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.089761e+00 │ │ │ │ Vprtstp: contraction number = 7.089761e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.663959e-06 │ │ │ │ Vprtstp: contraction number = 3.054217e-01 │ │ │ │ Vnewton: Using errtol_s: 6.380785 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.191637e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.853838e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.172932e+00 │ │ │ │ Vprtstp: contraction number = 2.172932e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.122962e-06 │ │ │ │ Vprtstp: contraction number = 3.064887e-01 │ │ │ │ Vnewton: Using errtol_s: 1.955639 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.330847e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000863e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.675659e-01 │ │ │ │ Vprtstp: contraction number = 6.675659e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.449953e-07 │ │ │ │ Vprtstp: contraction number = 3.072190e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.618400e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.679719e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.790132e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.853218e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8701,17 +8701,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.219214525491E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.874647090507E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.360649736533E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.406810e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.385170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.15 │ │ │ │ Vpbe_ctor2: xkappa = 0.126115 │ │ │ │ @@ -8758,160 +8758,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0149776 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.500920 │ │ │ │ +Vacc_SASA: Time elapsed: 0.467218 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.309770e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.282031e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.369580e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.320590e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.252530e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.400150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.647329e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033493e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1787000.080841 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.725164e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.041202e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.080871e+05 │ │ │ │ Vprtstp: contraction number = 3.080871e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.236727 │ │ │ │ Vnewton: Attempting damping, relres = 0.579616 │ │ │ │ Vnewton: Damping accepted, relres = 0.236727 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.367272e-01 │ │ │ │ Vprtstp: contraction number = 2.367272e-01 │ │ │ │ Vnewton: Using errtol_s: 423031.456074 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.897799e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059003e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.466075e+04 │ │ │ │ Vprtstp: contraction number = 6.466075e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.316615e-02 │ │ │ │ Vprtstp: contraction number = 2.245883e-01 │ │ │ │ Vnewton: Using errtol_s: 95007.918174 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003993e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.075341e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.709590e+04 │ │ │ │ Vprtstp: contraction number = 1.709590e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.292750e-02 │ │ │ │ Vprtstp: contraction number = 2.431528e-01 │ │ │ │ Vnewton: Using errtol_s: 23101.438026 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018097e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090582e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.023315e+03 │ │ │ │ Vprtstp: contraction number = 5.023315e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.939979e-03 │ │ │ │ Vprtstp: contraction number = 2.274206e-01 │ │ │ │ Vnewton: Using errtol_s: 5253.742566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032190e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.105999e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.453031e+03 │ │ │ │ Vprtstp: contraction number = 1.453031e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.371716e-04 │ │ │ │ Vprtstp: contraction number = 2.507404e-01 │ │ │ │ Vnewton: Using errtol_s: 1317.325709 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.046219e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.121331e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.332970e+02 │ │ │ │ Vprtstp: contraction number = 4.332970e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.182303e-04 │ │ │ │ Vprtstp: contraction number = 2.960373e-01 │ │ │ │ Vnewton: Using errtol_s: 389.977573 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060098e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.136098e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.367395e+02 │ │ │ │ Vprtstp: contraction number = 1.367395e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 6.886719e-05 │ │ │ │ Vprtstp: contraction number = 3.155711e-01 │ │ │ │ Vnewton: Using errtol_s: 123.065671 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073833e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.150788e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.406045e+01 │ │ │ │ Vprtstp: contraction number = 4.406045e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.219049e-05 │ │ │ │ Vprtstp: contraction number = 3.222216e-01 │ │ │ │ Vnewton: Using errtol_s: 39.654416 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.087905e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.165621e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.437042e+01 │ │ │ │ Vprtstp: contraction number = 1.437042e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.237482e-06 │ │ │ │ Vprtstp: contraction number = 3.261524e-01 │ │ │ │ Vnewton: Using errtol_s: 12.933382 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101891e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180622e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.730536e+00 │ │ │ │ Vprtstp: contraction number = 4.730536e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.382475e-06 │ │ │ │ Vprtstp: contraction number = 3.291856e-01 │ │ │ │ Vnewton: Using errtol_s: 4.257482 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.115847e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.195239e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.568402e+00 │ │ │ │ Vprtstp: contraction number = 1.568402e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 7.899057e-07 │ │ │ │ Vprtstp: contraction number = 3.315484e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.618420e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.679664e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.733525e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.794428e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -8921,29 +8921,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 9.205829898099E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.136385155975E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066935223116E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.408760e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.155800e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.235145e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:45:59 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:35:54 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -9213,151 +9213,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.903220 │ │ │ │ +Vacc_SASA: Time elapsed: 0.845950 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.611525e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.538689e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.320950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.268300e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.479340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306295e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.227965e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2356583.284651 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.085745e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.003953e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.056288e+05 │ │ │ │ Vprtstp: contraction number = 3.056288e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.138875 │ │ │ │ Vnewton: Attempting damping, relres = 0.556850 │ │ │ │ Vnewton: Damping accepted, relres = 0.138875 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.388745e-01 │ │ │ │ Vprtstp: contraction number = 1.388745e-01 │ │ │ │ Vnewton: Using errtol_s: 327269.333015 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.831922e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.905273e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.456208e+04 │ │ │ │ Vprtstp: contraction number = 5.456208e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.522390e-02 │ │ │ │ Vprtstp: contraction number = 1.816309e-01 │ │ │ │ Vnewton: Using errtol_s: 59442.210907 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.250041e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.498073e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.266310e+04 │ │ │ │ Vprtstp: contraction number = 1.266310e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.461794e-03 │ │ │ │ Vprtstp: contraction number = 2.165325e-01 │ │ │ │ Vnewton: Using errtol_s: 12871.173067 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.657051e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.069052e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.333848e+03 │ │ │ │ Vprtstp: contraction number = 3.333848e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.298357e-03 │ │ │ │ Vprtstp: contraction number = 2.377162e-01 │ │ │ │ Vnewton: Using errtol_s: 3059.685767 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.072306e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.603737e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.158069e+02 │ │ │ │ Vprtstp: contraction number = 9.158069e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.498387e-04 │ │ │ │ Vprtstp: contraction number = 2.694473e-01 │ │ │ │ Vnewton: Using errtol_s: 824.424114 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.049040e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.120180e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.635874e+02 │ │ │ │ Vprtstp: contraction number = 2.635874e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.006665e-04 │ │ │ │ Vprtstp: contraction number = 2.877513e-01 │ │ │ │ Vnewton: Using errtol_s: 237.229108 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.191093e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.276295e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.793651e+01 │ │ │ │ Vprtstp: contraction number = 7.793651e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.976465e-05 │ │ │ │ Vprtstp: contraction number = 2.956757e-01 │ │ │ │ Vnewton: Using errtol_s: 70.142875 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.332707e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.434710e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.340231e+01 │ │ │ │ Vprtstp: contraction number = 2.340231e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.937548e-06 │ │ │ │ Vprtstp: contraction number = 3.002739e-01 │ │ │ │ Vnewton: Using errtol_s: 21.062077 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.475232e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.592966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.107171e+00 │ │ │ │ Vprtstp: contraction number = 7.107171e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.714292e-06 │ │ │ │ Vprtstp: contraction number = 3.036953e-01 │ │ │ │ Vnewton: Using errtol_s: 6.396454 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.617205e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.747514e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.178301e+00 │ │ │ │ Vprtstp: contraction number = 2.178301e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.319126e-07 │ │ │ │ Vprtstp: contraction number = 3.064934e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.496127e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.557405e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.647550e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.709242e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -9367,17 +9367,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.432923079367E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567482695315E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282968021669E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.378280e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.369050e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.175 │ │ │ │ Vpbe_ctor2: xkappa = 0.13622 │ │ │ │ @@ -9424,160 +9424,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.024752 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.896371 │ │ │ │ +Vacc_SASA: Time elapsed: 0.842287 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.883253e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.827099e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.328330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.383640e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.515330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.993654e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.131430e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2421825.168549 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.070378e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.209234e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.797843e+05 │ │ │ │ Vprtstp: contraction number = 3.797843e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.162423 │ │ │ │ Vnewton: Attempting damping, relres = 0.569239 │ │ │ │ Vnewton: Damping accepted, relres = 0.162423 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.624227e-01 │ │ │ │ Vprtstp: contraction number = 1.624227e-01 │ │ │ │ Vnewton: Using errtol_s: 393359.388162 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.244970e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.395585e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.485976e+04 │ │ │ │ Vprtstp: contraction number = 7.485976e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.206345e-02 │ │ │ │ Vprtstp: contraction number = 1.974075e-01 │ │ │ │ Vnewton: Using errtol_s: 77652.078067 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.386456e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.552071e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.858810e+04 │ │ │ │ Vprtstp: contraction number = 1.858810e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.494162e-03 │ │ │ │ Vprtstp: contraction number = 2.337291e-01 │ │ │ │ Vnewton: Using errtol_s: 18149.549466 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.528507e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.708832e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.126907e+03 │ │ │ │ Vprtstp: contraction number = 5.126907e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.925418e-03 │ │ │ │ Vprtstp: contraction number = 2.569223e-01 │ │ │ │ Vnewton: Using errtol_s: 4663.024844 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.669999e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.863310e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.475836e+03 │ │ │ │ Vprtstp: contraction number = 1.475836e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.485012e-04 │ │ │ │ Vprtstp: contraction number = 2.848739e-01 │ │ │ │ Vnewton: Using errtol_s: 1328.373956 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.810573e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.022517e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.449115e+02 │ │ │ │ Vprtstp: contraction number = 4.449115e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.653385e-04 │ │ │ │ Vprtstp: contraction number = 3.014369e-01 │ │ │ │ Vnewton: Using errtol_s: 400.420960 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.953033e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.181782e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.382677e+02 │ │ │ │ Vprtstp: contraction number = 1.382677e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.138313e-05 │ │ │ │ Vprtstp: contraction number = 3.107753e-01 │ │ │ │ Vnewton: Using errtol_s: 124.440953 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.094655e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.346475e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.388153e+01 │ │ │ │ Vprtstp: contraction number = 4.388153e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.630728e-05 │ │ │ │ Vprtstp: contraction number = 3.173665e-01 │ │ │ │ Vnewton: Using errtol_s: 39.493386 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.236016e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.503166e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.417721e+01 │ │ │ │ Vprtstp: contraction number = 1.417721e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.268543e-06 │ │ │ │ Vprtstp: contraction number = 3.230792e-01 │ │ │ │ Vnewton: Using errtol_s: 12.759491 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.378804e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.667441e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.647969e+00 │ │ │ │ Vprtstp: contraction number = 4.647969e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.727281e-06 │ │ │ │ Vprtstp: contraction number = 3.278479e-01 │ │ │ │ Vnewton: Using errtol_s: 4.183172 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.522544e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.825238e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.542077e+00 │ │ │ │ Vprtstp: contraction number = 1.542077e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.730676e-07 │ │ │ │ Vprtstp: contraction number = 3.317744e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.638386e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.700807e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.825546e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.887700e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -9587,17 +9587,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.418015826462E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.952097240352E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475276420502E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.384970e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.373230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -9624,151 +9624,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.310170 │ │ │ │ +Vacc_SASA: Time elapsed: 0.300236 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.029890e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.101620e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.376310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.328610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.245280e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.540300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.062667e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.378714e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 689766.139707 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.139257e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.457543e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.344903e+04 │ │ │ │ Vprtstp: contraction number = 9.344903e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.130653 │ │ │ │ Vnewton: Attempting damping, relres = 0.558674 │ │ │ │ Vnewton: Damping accepted, relres = 0.130653 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.306530e-01 │ │ │ │ Vprtstp: contraction number = 1.306530e-01 │ │ │ │ Vnewton: Using errtol_s: 90120.018484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.311285e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.640846e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.728022e+04 │ │ │ │ Vprtstp: contraction number = 1.728022e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.291797e-02 │ │ │ │ Vprtstp: contraction number = 1.754110e-01 │ │ │ │ Vnewton: Using errtol_s: 15808.042794 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.454929e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.794238e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.892059e+03 │ │ │ │ Vprtstp: contraction number = 3.892059e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.080008e-03 │ │ │ │ Vprtstp: contraction number = 2.216604e-01 │ │ │ │ Vnewton: Using errtol_s: 3504.017199 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.595034e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.945090e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.808109e+02 │ │ │ │ Vprtstp: contraction number = 9.808109e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.279760e-03 │ │ │ │ Vprtstp: contraction number = 2.519209e-01 │ │ │ │ Vnewton: Using errtol_s: 882.735296 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.737148e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.097677e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.625258e+02 │ │ │ │ Vprtstp: contraction number = 2.625258e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.425414e-04 │ │ │ │ Vprtstp: contraction number = 2.676606e-01 │ │ │ │ Vnewton: Using errtol_s: 236.273473 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.879824e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.247222e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.264793e+01 │ │ │ │ Vprtstp: contraction number = 7.264793e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.479032e-05 │ │ │ │ Vprtstp: contraction number = 2.767266e-01 │ │ │ │ Vnewton: Using errtol_s: 65.383155 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.020116e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.395903e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.055752e+01 │ │ │ │ Vprtstp: contraction number = 2.055752e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.682325e-05 │ │ │ │ Vprtstp: contraction number = 2.829746e-01 │ │ │ │ Vnewton: Using errtol_s: 18.501770 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.162912e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.550093e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.918897e+00 │ │ │ │ Vprtstp: contraction number = 5.918897e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.722918e-06 │ │ │ │ Vprtstp: contraction number = 2.879188e-01 │ │ │ │ Vnewton: Using errtol_s: 5.327008 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.301619e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.702515e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.728813e+00 │ │ │ │ Vprtstp: contraction number = 1.728813e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.255738e-06 │ │ │ │ Vprtstp: contraction number = 2.920837e-01 │ │ │ │ Vnewton: Using errtol_s: 1.555932 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.441014e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.857945e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.109531e-01 │ │ │ │ Vprtstp: contraction number = 5.109531e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.666866e-07 │ │ │ │ Vprtstp: contraction number = 2.955514e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.484149e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.545123e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.601893e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.664361e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -9778,17 +9778,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.765725415923E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.832984433292E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.414411854652E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.428640e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.425160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.175 │ │ │ │ Vpbe_ctor2: xkappa = 0.13622 │ │ │ │ @@ -9835,160 +9835,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00466833 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.307615 │ │ │ │ +Vacc_SASA: Time elapsed: 0.293656 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.705900e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.792290e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.348190e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.349530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.319170e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.624120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.712008e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.148815e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 718654.980128 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.789519e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.227864e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.165117e+05 │ │ │ │ Vprtstp: contraction number = 1.165117e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153827 │ │ │ │ Vnewton: Attempting damping, relres = 0.570766 │ │ │ │ Vnewton: Damping accepted, relres = 0.153827 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.538266e-01 │ │ │ │ Vprtstp: contraction number = 1.538266e-01 │ │ │ │ Vnewton: Using errtol_s: 110548.228061 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.965446e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.414772e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.359273e+04 │ │ │ │ Vprtstp: contraction number = 2.359273e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.988514e-02 │ │ │ │ Vprtstp: contraction number = 1.942782e-01 │ │ │ │ Vnewton: Using errtol_s: 21477.106835 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.107560e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.573554e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.704562e+03 │ │ │ │ Vprtstp: contraction number = 5.704562e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.145907e-03 │ │ │ │ Vprtstp: contraction number = 2.391124e-01 │ │ │ │ Vnewton: Using errtol_s: 5135.441496 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.255375e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.730202e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.487585e+03 │ │ │ │ Vprtstp: contraction number = 1.487585e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.862980e-03 │ │ │ │ Vprtstp: contraction number = 2.607059e-01 │ │ │ │ Vnewton: Using errtol_s: 1338.839679 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.399507e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.889569e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.079440e+02 │ │ │ │ Vprtstp: contraction number = 4.079440e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.108858e-04 │ │ │ │ Vprtstp: contraction number = 2.742305e-01 │ │ │ │ Vnewton: Using errtol_s: 367.150629 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.540850e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.046938e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.157528e+02 │ │ │ │ Vprtstp: contraction number = 1.157528e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.449619e-04 │ │ │ │ Vprtstp: contraction number = 2.837461e-01 │ │ │ │ Vnewton: Using errtol_s: 104.177567 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.688937e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.203335e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.368933e+01 │ │ │ │ Vprtstp: contraction number = 3.368933e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.219048e-05 │ │ │ │ Vprtstp: contraction number = 2.910454e-01 │ │ │ │ Vnewton: Using errtol_s: 30.320401 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.838449e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.360792e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.002053e+01 │ │ │ │ Vprtstp: contraction number = 1.002053e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.254910e-05 │ │ │ │ Vprtstp: contraction number = 2.974392e-01 │ │ │ │ Vnewton: Using errtol_s: 9.018476 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.981570e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.519568e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.042966e+00 │ │ │ │ Vprtstp: contraction number = 3.042966e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.810826e-06 │ │ │ │ Vprtstp: contraction number = 3.036732e-01 │ │ │ │ Vnewton: Using errtol_s: 2.738669 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.127802e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.676422e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.410367e-01 │ │ │ │ Vprtstp: contraction number = 9.410367e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.178497e-06 │ │ │ │ Vprtstp: contraction number = 3.092499e-01 │ │ │ │ Vnewton: Using errtol_s: 0.846933 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.274518e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.835590e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.954277e-01 │ │ │ │ Vprtstp: contraction number = 2.954277e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.699758e-07 │ │ │ │ Vprtstp: contraction number = 3.139386e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.673616e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.735129e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.809214e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.872723e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -9998,17 +9998,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.757851015992E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.065506328732E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.030684199537E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.389050e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.404720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -10035,162 +10035,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.504677 │ │ │ │ +Vacc_SASA: Time elapsed: 0.479595 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.081178e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.080104e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.394400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.389070e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.526740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.552930e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.844706e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.408637e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1681345.800904 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.923152e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.486914e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.385175e+05 │ │ │ │ Vprtstp: contraction number = 2.385175e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.203314 │ │ │ │ Vnewton: Attempting damping, relres = 0.565471 │ │ │ │ Vnewton: Damping accepted, relres = 0.203314 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.033139e-01 │ │ │ │ Vprtstp: contraction number = 2.033139e-01 │ │ │ │ Vnewton: Using errtol_s: 341841.011255 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.095498e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.671243e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.575913e+04 │ │ │ │ Vprtstp: contraction number = 4.575913e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.277261e-02 │ │ │ │ Vprtstp: contraction number = 2.103772e-01 │ │ │ │ Vnewton: Using errtol_s: 71915.546235 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.235626e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.833629e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.151626e+04 │ │ │ │ Vprtstp: contraction number = 1.151626e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.711565e-03 │ │ │ │ Vprtstp: contraction number = 2.270510e-01 │ │ │ │ Vnewton: Using errtol_s: 16328.498943 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.376812e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.991645e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.244716e+03 │ │ │ │ Vprtstp: contraction number = 3.244716e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.018619e-03 │ │ │ │ Vprtstp: contraction number = 2.078572e-01 │ │ │ │ Vnewton: Using errtol_s: 3393.995992 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.518030e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.150535e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.861858e+02 │ │ │ │ Vprtstp: contraction number = 8.861858e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.771677e-04 │ │ │ │ Vprtstp: contraction number = 2.363833e-01 │ │ │ │ Vnewton: Using errtol_s: 802.283944 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.659246e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.304510e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.516488e+02 │ │ │ │ Vprtstp: contraction number = 2.516488e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.347069e-04 │ │ │ │ Vprtstp: contraction number = 2.823051e-01 │ │ │ │ Vnewton: Using errtol_s: 226.488825 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.800432e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.461623e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.546930e+01 │ │ │ │ Vprtstp: contraction number = 7.546930e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.039764e-05 │ │ │ │ Vprtstp: contraction number = 2.998929e-01 │ │ │ │ Vnewton: Using errtol_s: 67.922396 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.940860e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.615502e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.293241e+01 │ │ │ │ Vprtstp: contraction number = 2.293241e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.227539e-05 │ │ │ │ Vprtstp: contraction number = 3.038640e-01 │ │ │ │ Vnewton: Using errtol_s: 20.639168 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.080939e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.773160e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.006994e+00 │ │ │ │ Vprtstp: contraction number = 7.006994e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.750742e-06 │ │ │ │ Vprtstp: contraction number = 3.055499e-01 │ │ │ │ Vnewton: Using errtol_s: 6.306295 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.220259e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.930371e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.148054e+00 │ │ │ │ Vprtstp: contraction number = 2.148054e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.149822e-06 │ │ │ │ Vprtstp: contraction number = 3.065586e-01 │ │ │ │ Vnewton: Using errtol_s: 1.933249 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.361061e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008724e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.600422e-01 │ │ │ │ Vprtstp: contraction number = 6.600422e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.533110e-07 │ │ │ │ Vprtstp: contraction number = 3.072745e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624006e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.688153e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.801556e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.865181e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -10200,15 +10200,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.973061479643E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.874436395142E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.360148310218E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.378700e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ @@ -10257,160 +10257,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.011302 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.496809 │ │ │ │ +Vacc_SASA: Time elapsed: 0.481344 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.289793e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.305384e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.381110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.394740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.235570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.771530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.674826e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042309e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1723046.376364 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.752353e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.050311e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.980547e+05 │ │ │ │ Vprtstp: contraction number = 2.980547e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.228891 │ │ │ │ Vnewton: Attempting damping, relres = 0.579579 │ │ │ │ Vnewton: Damping accepted, relres = 0.228891 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.288909e-01 │ │ │ │ Vprtstp: contraction number = 2.288909e-01 │ │ │ │ Vnewton: Using errtol_s: 394389.718028 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.924658e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.069380e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.222537e+04 │ │ │ │ Vprtstp: contraction number = 6.222537e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 5.028364e-02 │ │ │ │ Vprtstp: contraction number = 2.196838e-01 │ │ │ │ Vnewton: Using errtol_s: 86641.047132 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.006485e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086717e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.649630e+04 │ │ │ │ Vprtstp: contraction number = 1.649630e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.200939e-02 │ │ │ │ Vprtstp: contraction number = 2.388330e-01 │ │ │ │ Vnewton: Using errtol_s: 20692.741964 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020454e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103222e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.824465e+03 │ │ │ │ Vprtstp: contraction number = 4.824465e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.771121e-03 │ │ │ │ Vprtstp: contraction number = 2.307461e-01 │ │ │ │ Vnewton: Using errtol_s: 4774.769213 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034415e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119436e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.399802e+03 │ │ │ │ Vprtstp: contraction number = 1.399802e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.332377e-04 │ │ │ │ Vprtstp: contraction number = 2.645997e-01 │ │ │ │ Vnewton: Using errtol_s: 1263.402543 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048247e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.135439e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.245121e+02 │ │ │ │ Vprtstp: contraction number = 4.245121e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.217376e-04 │ │ │ │ Vprtstp: contraction number = 3.024089e-01 │ │ │ │ Vnewton: Using errtol_s: 382.064121 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.062090e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.151262e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.346888e+02 │ │ │ │ Vprtstp: contraction number = 1.346888e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.035216e-05 │ │ │ │ Vprtstp: contraction number = 3.172767e-01 │ │ │ │ Vnewton: Using errtol_s: 121.220033 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.075986e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.167260e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.348380e+01 │ │ │ │ Vprtstp: contraction number = 4.348380e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.271293e-05 │ │ │ │ Vprtstp: contraction number = 3.228462e-01 │ │ │ │ Vnewton: Using errtol_s: 39.135424 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090118e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183160e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.419901e+01 │ │ │ │ Vprtstp: contraction number = 1.419901e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.416577e-06 │ │ │ │ Vprtstp: contraction number = 3.265355e-01 │ │ │ │ Vnewton: Using errtol_s: 12.779106 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103940e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.199542e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.677787e+00 │ │ │ │ Vprtstp: contraction number = 4.677787e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.443352e-06 │ │ │ │ Vprtstp: contraction number = 3.294447e-01 │ │ │ │ Vnewton: Using errtol_s: 4.210009 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.117938e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.215672e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.551755e+00 │ │ │ │ Vprtstp: contraction number = 1.551755e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.105291e-07 │ │ │ │ Vprtstp: contraction number = 3.317283e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.610495e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.671514e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.858270e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.924040e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -10420,29 +10420,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.960413626041E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.136174499148E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066885194167E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.372760e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.396160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.157871e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.256849e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:46:54 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:38:01 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -10712,151 +10712,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.892965 │ │ │ │ +Vacc_SASA: Time elapsed: 0.870387 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.620447e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.572269e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.383970e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.406850e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.275990e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.675540e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.315993e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.297493e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2314164.846818 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.092150e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.087546e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.999858e+05 │ │ │ │ Vprtstp: contraction number = 2.999858e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.137001 │ │ │ │ Vnewton: Attempting damping, relres = 0.556699 │ │ │ │ Vnewton: Damping accepted, relres = 0.137001 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.370010e-01 │ │ │ │ Vprtstp: contraction number = 1.370010e-01 │ │ │ │ Vnewton: Using errtol_s: 317042.938668 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.812966e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.064829e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.366653e+04 │ │ │ │ Vprtstp: contraction number = 5.366653e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.471777e-02 │ │ │ │ Vprtstp: contraction number = 1.804203e-01 │ │ │ │ Vnewton: Using errtol_s: 57200.987288 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.210062e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.753587e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.249422e+04 │ │ │ │ Vprtstp: contraction number = 1.249422e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.356401e-03 │ │ │ │ Vprtstp: contraction number = 2.167025e-01 │ │ │ │ Vnewton: Using errtol_s: 12395.595920 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.613129e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.442594e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.289496e+03 │ │ │ │ Vprtstp: contraction number = 3.289496e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.295127e-03 │ │ │ │ Vprtstp: contraction number = 2.417905e-01 │ │ │ │ Vnewton: Using errtol_s: 2997.137107 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.029518e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010468e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.079428e+02 │ │ │ │ Vprtstp: contraction number = 9.079428e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.531481e-04 │ │ │ │ Vprtstp: contraction number = 2.726745e-01 │ │ │ │ Vnewton: Using errtol_s: 817.243005 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042023e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.178456e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.621817e+02 │ │ │ │ Vprtstp: contraction number = 2.621817e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.019650e-04 │ │ │ │ Vprtstp: contraction number = 2.887315e-01 │ │ │ │ Vnewton: Using errtol_s: 235.963838 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.182678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.348294e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.758363e+01 │ │ │ │ Vprtstp: contraction number = 7.758363e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.017299e-05 │ │ │ │ Vprtstp: contraction number = 2.959152e-01 │ │ │ │ Vnewton: Using errtol_s: 69.825280 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321534e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.514476e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.330457e+01 │ │ │ │ Vprtstp: contraction number = 2.330457e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.063361e-06 │ │ │ │ Vprtstp: contraction number = 3.003799e-01 │ │ │ │ Vnewton: Using errtol_s: 20.974111 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.461843e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.679982e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.078759e+00 │ │ │ │ Vprtstp: contraction number = 7.078759e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.752995e-06 │ │ │ │ Vprtstp: contraction number = 3.037499e-01 │ │ │ │ Vnewton: Using errtol_s: 6.370884 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.600924e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.849491e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.169820e+00 │ │ │ │ Vprtstp: contraction number = 2.169820e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.438628e-07 │ │ │ │ Vprtstp: contraction number = 3.065254e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.475481e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.537035e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.753871e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.818902e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -10866,17 +10866,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.295748470746E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567357663948E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282934286498E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.378420e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.365850e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.2 │ │ │ │ Vpbe_ctor2: xkappa = 0.145625 │ │ │ │ @@ -10923,160 +10923,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0219675 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.881766 │ │ │ │ +Vacc_SASA: Time elapsed: 0.859340 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.870532e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.856400e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367400e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.417710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.339780e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.758840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.972109e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.251563e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2375881.010490 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.049538e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.331574e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.729565e+05 │ │ │ │ Vprtstp: contraction number = 3.729565e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.160831 │ │ │ │ Vnewton: Attempting damping, relres = 0.569195 │ │ │ │ Vnewton: Damping accepted, relres = 0.160831 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.608306e-01 │ │ │ │ Vprtstp: contraction number = 1.608306e-01 │ │ │ │ Vnewton: Using errtol_s: 382114.425441 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.221928e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.533900e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.362534e+04 │ │ │ │ Vprtstp: contraction number = 7.362534e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.161380e-02 │ │ │ │ Vprtstp: contraction number = 1.965658e-01 │ │ │ │ Vnewton: Using errtol_s: 75110.631839 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.363027e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.706009e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.832017e+04 │ │ │ │ Vprtstp: contraction number = 1.832017e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.403849e-03 │ │ │ │ Vprtstp: contraction number = 2.341967e-01 │ │ │ │ Vnewton: Using errtol_s: 17590.663892 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.502838e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.875748e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.053669e+03 │ │ │ │ Vprtstp: contraction number = 5.053669e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.926673e-03 │ │ │ │ Vprtstp: contraction number = 2.602258e-01 │ │ │ │ Vnewton: Using errtol_s: 4577.545268 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.644771e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.042173e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.460468e+03 │ │ │ │ Vprtstp: contraction number = 1.460468e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.532624e-04 │ │ │ │ Vprtstp: contraction number = 2.871595e-01 │ │ │ │ Vnewton: Using errtol_s: 1314.485731 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.785797e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.212614e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.415879e+02 │ │ │ │ Vprtstp: contraction number = 4.415879e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.672767e-04 │ │ │ │ Vprtstp: contraction number = 3.023461e-01 │ │ │ │ Vnewton: Using errtol_s: 397.429641 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.926516e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.382686e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.374012e+02 │ │ │ │ Vprtstp: contraction number = 1.374012e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.204853e-05 │ │ │ │ Vprtstp: contraction number = 3.111522e-01 │ │ │ │ Vnewton: Using errtol_s: 123.661104 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.067782e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.556093e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.363894e+01 │ │ │ │ Vprtstp: contraction number = 4.363894e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.653073e-05 │ │ │ │ Vprtstp: contraction number = 3.176023e-01 │ │ │ │ Vnewton: Using errtol_s: 39.275049 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.207509e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.725841e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.410540e+01 │ │ │ │ Vprtstp: contraction number = 1.410540e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.343223e-06 │ │ │ │ Vprtstp: contraction number = 3.232297e-01 │ │ │ │ Vnewton: Using errtol_s: 12.694863 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.348313e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.899256e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.625592e+00 │ │ │ │ Vprtstp: contraction number = 4.625592e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.752206e-06 │ │ │ │ Vprtstp: contraction number = 3.279305e-01 │ │ │ │ Vnewton: Using errtol_s: 4.163033 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.488327e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.071759e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.534788e+00 │ │ │ │ Vprtstp: contraction number = 1.534788e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.813881e-07 │ │ │ │ Vprtstp: contraction number = 3.318035e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624726e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.686561e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.959190e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.025316e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11086,17 +11086,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.281289332707E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951972269789E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475242807069E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.353020e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.374990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -11123,151 +11123,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.310577 │ │ │ │ +Vacc_SASA: Time elapsed: 0.302852 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.133970e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.195350e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.398660e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.288300e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.669510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.025047e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.642657e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 679651.374556 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.103369e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.721921e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.196081e+04 │ │ │ │ Vprtstp: contraction number = 9.196081e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.130456 │ │ │ │ Vnewton: Attempting damping, relres = 0.558557 │ │ │ │ Vnewton: Damping accepted, relres = 0.130456 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.304558e-01 │ │ │ │ Vprtstp: contraction number = 1.304558e-01 │ │ │ │ Vnewton: Using errtol_s: 88664.431621 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.274392e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.903700e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.707604e+04 │ │ │ │ Vprtstp: contraction number = 1.707604e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.296641e-02 │ │ │ │ Vprtstp: contraction number = 1.760475e-01 │ │ │ │ Vnewton: Using errtol_s: 15609.155466 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.414180e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.055756e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.862634e+03 │ │ │ │ Vprtstp: contraction number = 3.862634e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.116511e-03 │ │ │ │ Vprtstp: contraction number = 2.227823e-01 │ │ │ │ Vnewton: Using errtol_s: 3477.443419 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.554102e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.206853e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.764405e+02 │ │ │ │ Vprtstp: contraction number = 9.764405e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.293019e-03 │ │ │ │ Vprtstp: contraction number = 2.527150e-01 │ │ │ │ Vnewton: Using errtol_s: 878.801976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.694718e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.358235e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.618442e+02 │ │ │ │ Vprtstp: contraction number = 2.618442e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.467366e-04 │ │ │ │ Vprtstp: contraction number = 2.681606e-01 │ │ │ │ Vnewton: Using errtol_s: 235.660041 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.833594e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.508296e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.253883e+01 │ │ │ │ Vprtstp: contraction number = 7.253883e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.605654e-05 │ │ │ │ Vprtstp: contraction number = 2.770303e-01 │ │ │ │ Vnewton: Using errtol_s: 65.284962 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.971811e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.657805e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.053942e+01 │ │ │ │ Vprtstp: contraction number = 2.053942e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.719848e-05 │ │ │ │ Vprtstp: contraction number = 2.831507e-01 │ │ │ │ Vnewton: Using errtol_s: 18.485484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.110903e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.807489e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.915703e+00 │ │ │ │ Vprtstp: contraction number = 5.915703e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.833623e-06 │ │ │ │ Vprtstp: contraction number = 2.880170e-01 │ │ │ │ Vnewton: Using errtol_s: 5.324133 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.250001e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.957109e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.728194e+00 │ │ │ │ Vprtstp: contraction number = 1.728194e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.288489e-06 │ │ │ │ Vprtstp: contraction number = 2.921367e-01 │ │ │ │ Vnewton: Using errtol_s: 1.555375 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.388936e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.106176e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.108177e-01 │ │ │ │ Vprtstp: contraction number = 5.108177e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.764290e-07 │ │ │ │ Vprtstp: contraction number = 2.955789e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.470840e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.532417e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.577463e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.642263e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11277,17 +11277,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.784786682149E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.832559781230E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.414198595280E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.419360e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.2 │ │ │ │ Vpbe_ctor2: xkappa = 0.145625 │ │ │ │ @@ -11334,160 +11334,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00419075 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.311666 │ │ │ │ +Vacc_SASA: Time elapsed: 0.295618 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.695540e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.772120e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.385740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.383770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.364150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.668590e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.661802e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.389236e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 707760.874892 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.739005e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.468231e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.145732e+05 │ │ │ │ Vprtstp: contraction number = 1.145732e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153567 │ │ │ │ Vnewton: Attempting damping, relres = 0.570617 │ │ │ │ Vnewton: Damping accepted, relres = 0.153567 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.535669e-01 │ │ │ │ Vprtstp: contraction number = 1.535669e-01 │ │ │ │ Vnewton: Using errtol_s: 108688.631756 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.915141e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.657853e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.325223e+04 │ │ │ │ Vprtstp: contraction number = 2.325223e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.989096e-02 │ │ │ │ Vprtstp: contraction number = 1.946446e-01 │ │ │ │ Vnewton: Using errtol_s: 21155.653880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.057672e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.812400e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.636674e+03 │ │ │ │ Vprtstp: contraction number = 5.636674e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.169438e-03 │ │ │ │ Vprtstp: contraction number = 2.398530e-01 │ │ │ │ Vnewton: Using errtol_s: 5074.248008 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.201533e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.967830e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.473491e+03 │ │ │ │ Vprtstp: contraction number = 1.473491e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.873734e-03 │ │ │ │ Vprtstp: contraction number = 2.613502e-01 │ │ │ │ Vnewton: Using errtol_s: 1326.155494 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.344131e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.127051e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.049387e+02 │ │ │ │ Vprtstp: contraction number = 4.049387e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.149280e-04 │ │ │ │ Vprtstp: contraction number = 2.748139e-01 │ │ │ │ Vnewton: Using errtol_s: 364.445920 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.486853e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.284148e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.151043e+02 │ │ │ │ Vprtstp: contraction number = 1.151043e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.463685e-04 │ │ │ │ Vprtstp: contraction number = 2.842504e-01 │ │ │ │ Vnewton: Using errtol_s: 103.593915 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.630848e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.441274e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.354853e+01 │ │ │ │ Vprtstp: contraction number = 3.354853e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.266085e-05 │ │ │ │ Vprtstp: contraction number = 2.914619e-01 │ │ │ │ Vnewton: Using errtol_s: 30.193683 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.772948e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.602410e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.989786e+00 │ │ │ │ Vprtstp: contraction number = 9.989786e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.270317e-05 │ │ │ │ Vprtstp: contraction number = 2.977712e-01 │ │ │ │ Vnewton: Using errtol_s: 8.990808 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.916197e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.761456e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.036177e+00 │ │ │ │ Vprtstp: contraction number = 3.036177e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.860851e-06 │ │ │ │ Vprtstp: contraction number = 3.039281e-01 │ │ │ │ Vnewton: Using errtol_s: 2.732559 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.058719e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.917121e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.395196e-01 │ │ │ │ Vprtstp: contraction number = 9.395196e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.194708e-06 │ │ │ │ Vprtstp: contraction number = 3.094416e-01 │ │ │ │ Vnewton: Using errtol_s: 0.845568 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.203944e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.074055e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.950830e-01 │ │ │ │ Vprtstp: contraction number = 2.950830e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.752323e-07 │ │ │ │ Vprtstp: contraction number = 3.140786e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.651669e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.714086e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.808962e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.873801e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11497,17 +11497,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.776812399064E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.065083445518E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.030471976313E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.385980e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.385880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -11534,162 +11534,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.490873 │ │ │ │ +Vacc_SASA: Time elapsed: 0.474322 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.076350e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.075833e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.377180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.388110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.235050e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.607720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.766595e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.649809e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1635307.042590 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.843906e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.728444e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.321219e+05 │ │ │ │ Vprtstp: contraction number = 2.321219e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.196154 │ │ │ │ Vnewton: Attempting damping, relres = 0.565205 │ │ │ │ Vnewton: Damping accepted, relres = 0.196154 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.961538e-01 │ │ │ │ Vprtstp: contraction number = 1.961538e-01 │ │ │ │ Vnewton: Using errtol_s: 320771.668801 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.016521e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.915019e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.431372e+04 │ │ │ │ Vprtstp: contraction number = 4.431372e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.027511e-02 │ │ │ │ Vprtstp: contraction number = 2.053242e-01 │ │ │ │ Vnewton: Using errtol_s: 65862.177446 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.157909e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.077838e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117167e+04 │ │ │ │ Vprtstp: contraction number = 1.117167e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.959711e-03 │ │ │ │ Vprtstp: contraction number = 2.224627e-01 │ │ │ │ Vnewton: Using errtol_s: 14651.878140 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.297773e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.234572e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.129072e+03 │ │ │ │ Vprtstp: contraction number = 3.129072e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.898262e-03 │ │ │ │ Vprtstp: contraction number = 2.118664e-01 │ │ │ │ Vnewton: Using errtol_s: 3104.240662 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.438761e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.392117e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.589092e+02 │ │ │ │ Vprtstp: contraction number = 8.589092e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.739068e-04 │ │ │ │ Vprtstp: contraction number = 2.496530e-01 │ │ │ │ Vnewton: Using errtol_s: 774.983094 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.580903e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.544365e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.479971e+02 │ │ │ │ Vprtstp: contraction number = 2.479971e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.364875e-04 │ │ │ │ Vprtstp: contraction number = 2.880050e-01 │ │ │ │ Vnewton: Using errtol_s: 223.198993 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.720946e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.697900e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.463517e+01 │ │ │ │ Vprtstp: contraction number = 7.463517e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.107588e-05 │ │ │ │ Vprtstp: contraction number = 3.009497e-01 │ │ │ │ Vnewton: Using errtol_s: 67.171671 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.861955e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.855849e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.269594e+01 │ │ │ │ Vprtstp: contraction number = 2.269594e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.249083e-05 │ │ │ │ Vprtstp: contraction number = 3.040916e-01 │ │ │ │ Vnewton: Using errtol_s: 20.426343 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.003113e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001323e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.936769e+00 │ │ │ │ Vprtstp: contraction number = 6.936769e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.817688e-06 │ │ │ │ Vprtstp: contraction number = 3.056392e-01 │ │ │ │ Vnewton: Using errtol_s: 6.243092 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.142820e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016965e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.126909e+00 │ │ │ │ Vprtstp: contraction number = 2.126909e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.170556e-06 │ │ │ │ Vprtstp: contraction number = 3.066138e-01 │ │ │ │ Vnewton: Using errtol_s: 1.914218 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.283640e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032622e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.536389e-01 │ │ │ │ Vprtstp: contraction number = 6.536389e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.597337e-07 │ │ │ │ Vprtstp: contraction number = 3.073187e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624627e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.685721e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.799446e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.863581e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11699,17 +11699,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.754232717219E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.874256879798E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.359714713535E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.421370e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.384680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.2 │ │ │ │ Vpbe_ctor2: xkappa = 0.145625 │ │ │ │ @@ -11756,160 +11756,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00885234 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.498383 │ │ │ │ +Vacc_SASA: Time elapsed: 0.480297 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.300143e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.305596e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367630e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.270000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.721880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.599212e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066093e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1674007.100681 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.676366e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074050e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.902880e+05 │ │ │ │ Vprtstp: contraction number = 2.902880e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.222356 │ │ │ │ Vnewton: Attempting damping, relres = 0.579491 │ │ │ │ Vnewton: Damping accepted, relres = 0.222356 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.223561e-01 │ │ │ │ Vprtstp: contraction number = 2.223561e-01 │ │ │ │ Vnewton: Using errtol_s: 372225.695633 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.851306e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.093086e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.035839e+04 │ │ │ │ Vprtstp: contraction number = 6.035839e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.793121e-02 │ │ │ │ Vprtstp: contraction number = 2.155606e-01 │ │ │ │ Vnewton: Using errtol_s: 80237.189117 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.993623e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.110314e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.603151e+04 │ │ │ │ Vprtstp: contraction number = 1.603151e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.130393e-02 │ │ │ │ Vprtstp: contraction number = 2.358364e-01 │ │ │ │ Vnewton: Using errtol_s: 18922.853010 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.013419e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126686e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.671524e+03 │ │ │ │ Vprtstp: contraction number = 4.671524e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.665747e-03 │ │ │ │ Vprtstp: contraction number = 2.358248e-01 │ │ │ │ Vnewton: Using errtol_s: 4462.478601 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.027403e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.142950e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.362565e+03 │ │ │ │ Vprtstp: contraction number = 1.362565e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.334180e-04 │ │ │ │ Vprtstp: contraction number = 2.751267e-01 │ │ │ │ Vnewton: Using errtol_s: 1227.746995 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.041315e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158941e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.182590e+02 │ │ │ │ Vprtstp: contraction number = 4.182590e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.248702e-04 │ │ │ │ Vprtstp: contraction number = 3.066058e-01 │ │ │ │ Vnewton: Using errtol_s: 376.434346 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.055629e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174963e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.331321e+02 │ │ │ │ Vprtstp: contraction number = 1.331321e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.157615e-05 │ │ │ │ Vprtstp: contraction number = 3.182998e-01 │ │ │ │ Vnewton: Using errtol_s: 119.818985 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.069922e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190924e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.304104e+01 │ │ │ │ Vprtstp: contraction number = 4.304104e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.314025e-05 │ │ │ │ Vprtstp: contraction number = 3.232955e-01 │ │ │ │ Vnewton: Using errtol_s: 38.736937 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.084223e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206899e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.406731e+01 │ │ │ │ Vprtstp: contraction number = 1.406731e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.563038e-06 │ │ │ │ Vprtstp: contraction number = 3.268348e-01 │ │ │ │ Vnewton: Using errtol_s: 12.660580 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098454e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.223059e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.637253e+00 │ │ │ │ Vprtstp: contraction number = 4.637253e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.493136e-06 │ │ │ │ Vprtstp: contraction number = 3.296474e-01 │ │ │ │ Vnewton: Using errtol_s: 4.173527 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112664e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.239316e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.538961e+00 │ │ │ │ Vprtstp: contraction number = 1.538961e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.273947e-07 │ │ │ │ Vprtstp: contraction number = 3.318691e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.636586e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.698004e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.858241e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.922937e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -11919,29 +11919,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.742146487539E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135995019180E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066841914089E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.389330e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.397960e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.152883e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.281247e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:47:49 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:40:45 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -12211,151 +12211,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.898914 │ │ │ │ +Vacc_SASA: Time elapsed: 0.852596 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.614266e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.556911e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.374210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.394690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.336610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.651470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.313916e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.278484e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2280031.151733 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.090523e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.070088e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.954329e+05 │ │ │ │ Vprtstp: contraction number = 2.954329e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.135391 │ │ │ │ Vnewton: Attempting damping, relres = 0.556564 │ │ │ │ Vnewton: Damping accepted, relres = 0.135391 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.353914e-01 │ │ │ │ Vprtstp: contraction number = 1.353914e-01 │ │ │ │ Vnewton: Using errtol_s: 308696.705205 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.831359e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.029304e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.294410e+04 │ │ │ │ Vprtstp: contraction number = 5.294410e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.429290e-02 │ │ │ │ Vprtstp: contraction number = 1.794272e-01 │ │ │ │ Vnewton: Using errtol_s: 55388.580044 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.256024e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.718276e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.235644e+04 │ │ │ │ Vprtstp: contraction number = 1.235644e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.275732e-03 │ │ │ │ Vprtstp: contraction number = 2.171717e-01 │ │ │ │ Vnewton: Using errtol_s: 12028.832542 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.658255e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.386980e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.254639e+03 │ │ │ │ Vprtstp: contraction number = 3.254639e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.294905e-03 │ │ │ │ Vprtstp: contraction number = 2.454457e-01 │ │ │ │ Vnewton: Using errtol_s: 2952.424699 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.070932e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.001031e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.022338e+02 │ │ │ │ Vprtstp: contraction number = 9.022338e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.561621e-04 │ │ │ │ Vprtstp: contraction number = 2.750487e-01 │ │ │ │ Vnewton: Using errtol_s: 812.060580 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047279e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.164957e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.611146e+02 │ │ │ │ Vprtstp: contraction number = 2.611146e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.030702e-04 │ │ │ │ Vprtstp: contraction number = 2.893914e-01 │ │ │ │ Vnewton: Using errtol_s: 235.003369 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188512e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330765e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.731468e+01 │ │ │ │ Vprtstp: contraction number = 7.731468e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.051854e-05 │ │ │ │ Vprtstp: contraction number = 2.960946e-01 │ │ │ │ Vnewton: Using errtol_s: 69.583224 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330445e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.496100e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.323028e+01 │ │ │ │ Vprtstp: contraction number = 2.323028e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.169724e-06 │ │ │ │ Vprtstp: contraction number = 3.004640e-01 │ │ │ │ Vnewton: Using errtol_s: 20.907256 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472353e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.663119e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.057246e+00 │ │ │ │ Vprtstp: contraction number = 7.057246e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.785717e-06 │ │ │ │ Vprtstp: contraction number = 3.037951e-01 │ │ │ │ Vnewton: Using errtol_s: 6.351522 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.615940e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.828293e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.163411e+00 │ │ │ │ Vprtstp: contraction number = 2.163411e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.539662e-07 │ │ │ │ Vprtstp: contraction number = 3.065517e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.494749e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.556537e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.731949e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.796633e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12365,17 +12365,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.169811385763E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567248755988E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282904610946E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.375890e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.383540e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.225 │ │ │ │ Vpbe_ctor2: xkappa = 0.154458 │ │ │ │ @@ -12422,160 +12422,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0200222 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.889251 │ │ │ │ +Vacc_SASA: Time elapsed: 0.868442 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.869146e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.872743e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.422820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.230120e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.786880e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.989941e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.229451e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2338884.582029 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.066860e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.309195e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.674153e+05 │ │ │ │ Vprtstp: contraction number = 3.674153e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.159441 │ │ │ │ Vnewton: Attempting damping, relres = 0.569142 │ │ │ │ Vnewton: Damping accepted, relres = 0.159441 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.594406e-01 │ │ │ │ Vprtstp: contraction number = 1.594406e-01 │ │ │ │ Vnewton: Using errtol_s: 372913.066228 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.241443e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.511068e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.262273e+04 │ │ │ │ Vprtstp: contraction number = 7.262273e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.123186e-02 │ │ │ │ Vprtstp: contraction number = 1.958841e-01 │ │ │ │ Vnewton: Using errtol_s: 73047.725996 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.379776e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.686940e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.810013e+04 │ │ │ │ Vprtstp: contraction number = 1.810013e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.334559e-03 │ │ │ │ Vprtstp: contraction number = 2.348422e-01 │ │ │ │ Vnewton: Using errtol_s: 17154.687500 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.517903e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.861431e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.995290e+03 │ │ │ │ Vprtstp: contraction number = 4.995290e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.929832e-03 │ │ │ │ Vprtstp: contraction number = 2.631149e-01 │ │ │ │ Vnewton: Using errtol_s: 4513.654553 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.656680e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.033435e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.448761e+03 │ │ │ │ Vprtstp: contraction number = 1.448761e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.574979e-04 │ │ │ │ Vprtstp: contraction number = 2.888841e-01 │ │ │ │ Vnewton: Using errtol_s: 1303.923175 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.796781e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.205384e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.389996e+02 │ │ │ │ Vprtstp: contraction number = 4.389996e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.689267e-04 │ │ │ │ Vprtstp: contraction number = 3.030087e-01 │ │ │ │ Vnewton: Using errtol_s: 395.100089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.935164e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.376353e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.367279e+02 │ │ │ │ Vprtstp: contraction number = 1.367279e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.261275e-05 │ │ │ │ Vprtstp: contraction number = 3.114531e-01 │ │ │ │ Vnewton: Using errtol_s: 123.055159 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.074391e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.547993e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.345198e+01 │ │ │ │ Vprtstp: contraction number = 4.345198e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.672027e-05 │ │ │ │ Vprtstp: contraction number = 3.177988e-01 │ │ │ │ Vnewton: Using errtol_s: 39.106785 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.213319e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.717312e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.405050e+01 │ │ │ │ Vprtstp: contraction number = 1.405050e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.406615e-06 │ │ │ │ Vprtstp: contraction number = 3.233569e-01 │ │ │ │ Vnewton: Using errtol_s: 12.645449 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.352652e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.887143e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.608577e+00 │ │ │ │ Vprtstp: contraction number = 4.608577e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.773375e-06 │ │ │ │ Vprtstp: contraction number = 3.280010e-01 │ │ │ │ Vnewton: Using errtol_s: 4.147720 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.492076e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.060698e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.529264e+00 │ │ │ │ Vprtstp: contraction number = 1.529264e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.884589e-07 │ │ │ │ Vprtstp: contraction number = 3.318299e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.608398e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.669159e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.969545e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.035544e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12585,15 +12585,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.155729316700E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951863418321E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475213228301E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.339990e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.353360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -12622,151 +12622,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.303311 │ │ │ │ +Vacc_SASA: Time elapsed: 0.302490 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.989290e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.187060e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.355660e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.389250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.245820e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.497570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.025621e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.626096e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 671593.797102 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.103316e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.704209e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.076362e+04 │ │ │ │ Vprtstp: contraction number = 9.076362e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.130235 │ │ │ │ Vnewton: Attempting damping, relres = 0.558450 │ │ │ │ Vnewton: Damping accepted, relres = 0.130235 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.302353e-01 │ │ │ │ Vprtstp: contraction number = 1.302353e-01 │ │ │ │ Vnewton: Using errtol_s: 87465.248573 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.274487e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.887495e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.691112e+04 │ │ │ │ Vprtstp: contraction number = 1.691112e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.299894e-02 │ │ │ │ Vprtstp: contraction number = 1.765952e-01 │ │ │ │ Vnewton: Using errtol_s: 15445.947049 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.416061e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.042238e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.838772e+03 │ │ │ │ Vprtstp: contraction number = 3.838772e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.145781e-03 │ │ │ │ Vprtstp: contraction number = 2.237399e-01 │ │ │ │ Vnewton: Using errtol_s: 3455.874833 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.556238e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.199657e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.728949e+02 │ │ │ │ Vprtstp: contraction number = 9.728949e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.303780e-03 │ │ │ │ Vprtstp: contraction number = 2.533688e-01 │ │ │ │ Vnewton: Using errtol_s: 875.610893 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.696207e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.357547e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.612895e+02 │ │ │ │ Vprtstp: contraction number = 2.612895e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.501534e-04 │ │ │ │ Vprtstp: contraction number = 2.685677e-01 │ │ │ │ Vnewton: Using errtol_s: 235.160844 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.836869e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.510161e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.244969e+01 │ │ │ │ Vprtstp: contraction number = 7.244969e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.708955e-05 │ │ │ │ Vprtstp: contraction number = 2.772772e-01 │ │ │ │ Vnewton: Using errtol_s: 65.204742 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.985639e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.666264e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.052456e+01 │ │ │ │ Vprtstp: contraction number = 2.052456e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.750488e-05 │ │ │ │ Vprtstp: contraction number = 2.832939e-01 │ │ │ │ Vnewton: Using errtol_s: 18.472107 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.125890e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.822159e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.913055e+00 │ │ │ │ Vprtstp: contraction number = 5.913055e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.924060e-06 │ │ │ │ Vprtstp: contraction number = 2.880965e-01 │ │ │ │ Vnewton: Using errtol_s: 5.321750 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.265281e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.976461e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.727677e+00 │ │ │ │ Vprtstp: contraction number = 1.727677e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.315252e-06 │ │ │ │ Vprtstp: contraction number = 2.921800e-01 │ │ │ │ Vnewton: Using errtol_s: 1.554909 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.404430e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.131369e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.107037e-01 │ │ │ │ Vprtstp: contraction number = 5.107037e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.843918e-07 │ │ │ │ Vprtstp: contraction number = 2.956014e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.486282e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.547352e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.622442e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.685376e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12776,17 +12776,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.799206762061E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.832181524092E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.414010557344E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.401000e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.387570e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.225 │ │ │ │ Vpbe_ctor2: xkappa = 0.154458 │ │ │ │ @@ -12833,160 +12833,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00378487 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.307575 │ │ │ │ +Vacc_SASA: Time elapsed: 0.297605 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.706280e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.847520e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.365560e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.449220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.239840e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.696180e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.676389e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.419712e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 699069.872719 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.752840e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.499555e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.130075e+05 │ │ │ │ Vprtstp: contraction number = 1.130075e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153289 │ │ │ │ Vnewton: Attempting damping, relres = 0.570479 │ │ │ │ Vnewton: Damping accepted, relres = 0.153289 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.532887e-01 │ │ │ │ Vprtstp: contraction number = 1.532887e-01 │ │ │ │ Vnewton: Using errtol_s: 107159.480370 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.924629e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.692418e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.297596e+04 │ │ │ │ Vprtstp: contraction number = 2.297596e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.988594e-02 │ │ │ │ Vprtstp: contraction number = 1.949651e-01 │ │ │ │ Vnewton: Using errtol_s: 20892.361484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.065075e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.852279e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.581341e+03 │ │ │ │ Vprtstp: contraction number = 5.581341e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.187204e-03 │ │ │ │ Vprtstp: contraction number = 2.404878e-01 │ │ │ │ Vnewton: Using errtol_s: 5024.357995 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.204357e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.012950e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.462004e+03 │ │ │ │ Vprtstp: contraction number = 1.462004e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.882240e-03 │ │ │ │ Vprtstp: contraction number = 2.618876e-01 │ │ │ │ Vnewton: Using errtol_s: 1315.817196 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.344558e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.171727e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.024878e+02 │ │ │ │ Vprtstp: contraction number = 4.024878e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.181744e-04 │ │ │ │ Vprtstp: contraction number = 2.752967e-01 │ │ │ │ Vnewton: Using errtol_s: 362.240101 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.483878e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.330972e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.145747e+02 │ │ │ │ Vprtstp: contraction number = 1.145747e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.475065e-04 │ │ │ │ Vprtstp: contraction number = 2.846658e-01 │ │ │ │ Vnewton: Using errtol_s: 103.117357 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.624007e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.490172e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.343339e+01 │ │ │ │ Vprtstp: contraction number = 3.343339e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.304299e-05 │ │ │ │ Vprtstp: contraction number = 2.918040e-01 │ │ │ │ Vnewton: Using errtol_s: 30.090059 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.764441e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.650114e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.964601e+00 │ │ │ │ Vprtstp: contraction number = 9.964601e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.282868e-05 │ │ │ │ Vprtstp: contraction number = 2.980433e-01 │ │ │ │ Vnewton: Using errtol_s: 8.968142 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.903024e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.811534e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.030606e+00 │ │ │ │ Vprtstp: contraction number = 3.030606e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.901677e-06 │ │ │ │ Vprtstp: contraction number = 3.041372e-01 │ │ │ │ Vnewton: Using errtol_s: 2.727545 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.042159e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.971899e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.382714e-01 │ │ │ │ Vprtstp: contraction number = 9.382714e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.207954e-06 │ │ │ │ Vprtstp: contraction number = 3.095986e-01 │ │ │ │ Vnewton: Using errtol_s: 0.844444 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.183881e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.132375e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.947982e-01 │ │ │ │ Vprtstp: contraction number = 2.947982e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.795306e-07 │ │ │ │ Vprtstp: contraction number = 3.141929e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.615304e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.676377e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.835471e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.901754e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -12996,17 +12996,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.791143336195E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.064706767372E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.030284850929E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.407560e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.397220e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -13033,162 +13033,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.496532 │ │ │ │ +Vacc_SASA: Time elapsed: 0.475218 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.084757e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.074018e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.402970e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.402260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.425520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.651270e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.749922e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.705531e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1599051.147684 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.826606e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.784996e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.270628e+05 │ │ │ │ Vprtstp: contraction number = 2.270628e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.190153 │ │ │ │ Vnewton: Attempting damping, relres = 0.564950 │ │ │ │ Vnewton: Damping accepted, relres = 0.190153 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.901527e-01 │ │ │ │ Vprtstp: contraction number = 1.901527e-01 │ │ │ │ Vnewton: Using errtol_s: 304063.886192 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.999926e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.975916e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.318204e+04 │ │ │ │ Vprtstp: contraction number = 4.318204e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.822370e-02 │ │ │ │ Vprtstp: contraction number = 2.010158e-01 │ │ │ │ Vnewton: Using errtol_s: 61121.655411 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.143216e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.140644e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.090069e+04 │ │ │ │ Vprtstp: contraction number = 1.090069e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.378283e-03 │ │ │ │ Vprtstp: contraction number = 2.191908e-01 │ │ │ │ Vnewton: Using errtol_s: 13397.302580 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.287496e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.305270e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.039014e+03 │ │ │ │ Vprtstp: contraction number = 3.039014e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.821126e-03 │ │ │ │ Vprtstp: contraction number = 2.173626e-01 │ │ │ │ Vnewton: Using errtol_s: 2912.073157 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.431065e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.464075e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.399695e+02 │ │ │ │ Vprtstp: contraction number = 8.399695e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.733052e-04 │ │ │ │ Vprtstp: contraction number = 2.598970e-01 │ │ │ │ Vnewton: Using errtol_s: 756.839199 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.571538e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.623303e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.453869e+02 │ │ │ │ Vprtstp: contraction number = 2.453869e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.381125e-04 │ │ │ │ Vprtstp: contraction number = 2.918043e-01 │ │ │ │ Vnewton: Using errtol_s: 220.848913 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.712372e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.782973e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.399321e+01 │ │ │ │ Vprtstp: contraction number = 7.399321e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.164589e-05 │ │ │ │ Vprtstp: contraction number = 3.015360e-01 │ │ │ │ Vnewton: Using errtol_s: 66.593908 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.854125e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.939933e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.251212e+01 │ │ │ │ Vprtstp: contraction number = 2.251212e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.267058e-05 │ │ │ │ Vprtstp: contraction number = 3.042457e-01 │ │ │ │ Vnewton: Using errtol_s: 20.260912 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.993998e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.009836e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.882100e+00 │ │ │ │ Vprtstp: contraction number = 6.882100e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.873479e-06 │ │ │ │ Vprtstp: contraction number = 3.057064e-01 │ │ │ │ Vnewton: Using errtol_s: 6.193891 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.133605e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.025546e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.110443e+00 │ │ │ │ Vprtstp: contraction number = 2.110443e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.187828e-06 │ │ │ │ Vprtstp: contraction number = 3.066568e-01 │ │ │ │ Vnewton: Using errtol_s: 1.899398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.278441e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.041438e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.486511e-01 │ │ │ │ Vprtstp: contraction number = 6.486511e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.650828e-07 │ │ │ │ Vprtstp: contraction number = 3.073531e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.635547e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.698859e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.831749e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.896520e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -13198,17 +13198,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.557875288957E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.874100920803E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.359333289528E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.384310e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.371820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.225 │ │ │ │ Vpbe_ctor2: xkappa = 0.154458 │ │ │ │ @@ -13255,160 +13255,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00715191 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.486493 │ │ │ │ +Vacc_SASA: Time elapsed: 0.478889 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.284252e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.306307e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.370360e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.382330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.268070e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.577110e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.591395e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074787e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1635353.597903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.668969e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082523e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.841111e+05 │ │ │ │ Vprtstp: contraction number = 2.841111e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.216841 │ │ │ │ Vnewton: Attempting damping, relres = 0.579374 │ │ │ │ Vnewton: Damping accepted, relres = 0.216841 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.168415e-01 │ │ │ │ Vprtstp: contraction number = 2.168415e-01 │ │ │ │ Vnewton: Using errtol_s: 354612.472828 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.839742e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.101166e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.888895e+04 │ │ │ │ Vprtstp: contraction number = 5.888895e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.598888e-02 │ │ │ │ Vprtstp: contraction number = 2.120853e-01 │ │ │ │ Vnewton: Using errtol_s: 75208.075023 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.979488e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.117939e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.566082e+04 │ │ │ │ Vprtstp: contraction number = 1.566082e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.075687e-02 │ │ │ │ Vprtstp: contraction number = 2.339015e-01 │ │ │ │ Vnewton: Using errtol_s: 17591.280350 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.011841e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.133746e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.551176e+03 │ │ │ │ Vprtstp: contraction number = 4.551176e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.599859e-03 │ │ │ │ Vprtstp: contraction number = 2.416930e-01 │ │ │ │ Vnewton: Using errtol_s: 4251.688603 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.025752e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.149395e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.335913e+03 │ │ │ │ Vprtstp: contraction number = 1.335913e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.355871e-04 │ │ │ │ Vprtstp: contraction number = 2.829335e-01 │ │ │ │ Vnewton: Using errtol_s: 1202.945014 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039753e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.165092e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.136155e+02 │ │ │ │ Vprtstp: contraction number = 4.136155e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.276295e-04 │ │ │ │ Vprtstp: contraction number = 3.094528e-01 │ │ │ │ Vnewton: Using errtol_s: 372.254692 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053762e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180904e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.319427e+02 │ │ │ │ Vprtstp: contraction number = 1.319427e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.261334e-05 │ │ │ │ Vprtstp: contraction number = 3.189980e-01 │ │ │ │ Vnewton: Using errtol_s: 118.748486 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067711e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.197753e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.270247e+01 │ │ │ │ Vprtstp: contraction number = 4.270247e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.350087e-05 │ │ │ │ Vprtstp: contraction number = 3.236440e-01 │ │ │ │ Vnewton: Using errtol_s: 38.432230 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081604e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.214173e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.396688e+01 │ │ │ │ Vprtstp: contraction number = 1.396688e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.686528e-06 │ │ │ │ Vprtstp: contraction number = 3.270742e-01 │ │ │ │ Vnewton: Using errtol_s: 12.570191 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095460e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.230364e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.606421e+00 │ │ │ │ Vprtstp: contraction number = 4.606421e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.535096e-06 │ │ │ │ Vprtstp: contraction number = 3.298104e-01 │ │ │ │ Vnewton: Using errtol_s: 4.145779 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109345e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.246149e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.529247e+00 │ │ │ │ Vprtstp: contraction number = 1.529247e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.416053e-07 │ │ │ │ Vprtstp: contraction number = 3.319816e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.608055e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.669364e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.836123e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.899820e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -13418,29 +13418,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.546220466896E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135839093340E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066803828890E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.380520e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.373710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.149058e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.287511e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:48:44 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:43:41 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -13710,151 +13710,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.907362 │ │ │ │ +Vacc_SASA: Time elapsed: 0.915310 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.624074e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.639329e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.372620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.390390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.271880e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.850470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.320728e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.376790e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2251971.697064 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.089869e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.282903e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.916802e+05 │ │ │ │ Vprtstp: contraction number = 2.916802e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.133998 │ │ │ │ Vnewton: Attempting damping, relres = 0.556443 │ │ │ │ Vnewton: Damping accepted, relres = 0.133998 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.339981e-01 │ │ │ │ Vprtstp: contraction number = 1.339981e-01 │ │ │ │ Vnewton: Using errtol_s: 301759.930673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.817357e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.343746e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.235007e+04 │ │ │ │ Vprtstp: contraction number = 5.235007e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.393476e-02 │ │ │ │ Vprtstp: contraction number = 1.786201e-01 │ │ │ │ Vnewton: Using errtol_s: 53900.402880 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.204873e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.107368e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.224190e+04 │ │ │ │ Vprtstp: contraction number = 1.224190e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.213784e-03 │ │ │ │ Vprtstp: contraction number = 2.178331e-01 │ │ │ │ Vnewton: Using errtol_s: 11741.294295 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.600477e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.858609e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.226956e+03 │ │ │ │ Vprtstp: contraction number = 3.226956e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.296373e-03 │ │ │ │ Vprtstp: contraction number = 2.486433e-01 │ │ │ │ Vnewton: Using errtol_s: 2919.394410 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.987467e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057176e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.979745e+02 │ │ │ │ Vprtstp: contraction number = 8.979745e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.588880e-04 │ │ │ │ Vprtstp: contraction number = 2.768402e-01 │ │ │ │ Vnewton: Using errtol_s: 808.205614 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038173e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.232406e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.602996e+02 │ │ │ │ Vprtstp: contraction number = 2.602996e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.040288e-04 │ │ │ │ Vprtstp: contraction number = 2.898642e-01 │ │ │ │ Vnewton: Using errtol_s: 234.269873 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.176657e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.404196e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.710898e+01 │ │ │ │ Vprtstp: contraction number = 7.710898e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.081659e-05 │ │ │ │ Vprtstp: contraction number = 2.962314e-01 │ │ │ │ Vnewton: Using errtol_s: 69.398097 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.317219e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.571328e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.317379e+01 │ │ │ │ Vprtstp: contraction number = 2.317379e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.261402e-06 │ │ │ │ Vprtstp: contraction number = 3.005329e-01 │ │ │ │ Vnewton: Using errtol_s: 20.856415 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.457998e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.739761e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.040959e+00 │ │ │ │ Vprtstp: contraction number = 7.040959e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.813918e-06 │ │ │ │ Vprtstp: contraction number = 3.038328e-01 │ │ │ │ Vnewton: Using errtol_s: 6.336864 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.598734e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.912959e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.158573e+00 │ │ │ │ Vprtstp: contraction number = 2.158573e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.626731e-07 │ │ │ │ Vprtstp: contraction number = 3.065736e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.472658e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.534109e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.826451e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.892647e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -13864,17 +13864,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.054258370854E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567152466024E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282878106932E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.365260e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.052300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.25 │ │ │ │ Vpbe_ctor2: xkappa = 0.162813 │ │ │ │ @@ -13921,160 +13921,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0186115 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.871831 │ │ │ │ +Vacc_SASA: Time elapsed: 0.865818 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.852952e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.869593e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.373560e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.395590e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.260500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.709620e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.967287e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.340611e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2308477.613734 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.045983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.420395e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.628256e+05 │ │ │ │ Vprtstp: contraction number = 3.628256e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.158221 │ │ │ │ Vnewton: Attempting damping, relres = 0.569085 │ │ │ │ Vnewton: Damping accepted, relres = 0.158221 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.582211e-01 │ │ │ │ Vprtstp: contraction number = 1.582211e-01 │ │ │ │ Vnewton: Using errtol_s: 365249.935342 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219266e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.619031e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.179371e+04 │ │ │ │ Vprtstp: contraction number = 7.179371e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.090684e-02 │ │ │ │ Vprtstp: contraction number = 1.953395e-01 │ │ │ │ Vnewton: Using errtol_s: 71347.745828 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.361843e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.792251e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.791601e+04 │ │ │ │ Vprtstp: contraction number = 1.791601e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.281434e-03 │ │ │ │ Vprtstp: contraction number = 2.355930e-01 │ │ │ │ Vnewton: Using errtol_s: 16809.026903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.503157e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.947630e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.947991e+03 │ │ │ │ Vprtstp: contraction number = 4.947991e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.933961e-03 │ │ │ │ Vprtstp: contraction number = 2.656017e-01 │ │ │ │ Vnewton: Using errtol_s: 4464.506758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.649135e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.120914e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.439628e+03 │ │ │ │ Vprtstp: contraction number = 1.439628e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.612744e-04 │ │ │ │ Vprtstp: contraction number = 2.902201e-01 │ │ │ │ Vnewton: Using errtol_s: 1295.689464 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.790596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.293953e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.369472e+02 │ │ │ │ Vprtstp: contraction number = 4.369472e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.703516e-04 │ │ │ │ Vprtstp: contraction number = 3.035087e-01 │ │ │ │ Vnewton: Using errtol_s: 393.252962 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.929897e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.465462e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.361967e+02 │ │ │ │ Vprtstp: contraction number = 1.361967e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.309866e-05 │ │ │ │ Vprtstp: contraction number = 3.117003e-01 │ │ │ │ Vnewton: Using errtol_s: 122.577063 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.074235e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.636427e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.330599e+01 │ │ │ │ Vprtstp: contraction number = 4.330599e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.688359e-05 │ │ │ │ Vprtstp: contraction number = 3.179665e-01 │ │ │ │ Vnewton: Using errtol_s: 38.975398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.214321e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.806880e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.400799e+01 │ │ │ │ Vprtstp: contraction number = 1.400799e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.461259e-06 │ │ │ │ Vprtstp: contraction number = 3.234655e-01 │ │ │ │ Vnewton: Using errtol_s: 12.607195 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.355602e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.978837e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.595493e+00 │ │ │ │ Vprtstp: contraction number = 4.595493e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.791632e-06 │ │ │ │ Vprtstp: contraction number = 3.280621e-01 │ │ │ │ Vnewton: Using errtol_s: 4.135943 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.500696e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.150471e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.525032e+00 │ │ │ │ Vprtstp: contraction number = 1.525032e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.945603e-07 │ │ │ │ Vprtstp: contraction number = 3.318539e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.640467e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.701735e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.948819e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.014096e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -14084,15 +14084,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.040496519362E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951767181280E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475186803356E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.347020e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.766200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -14121,151 +14121,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.311259 │ │ │ │ +Vacc_SASA: Time elapsed: 0.301289 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.082970e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.164000e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.353350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.424470e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.230830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.652130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.038831e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.726245e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 665026.668065 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.115084e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.806197e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.977874e+04 │ │ │ │ Vprtstp: contraction number = 8.977874e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.130004 │ │ │ │ Vnewton: Attempting damping, relres = 0.558352 │ │ │ │ Vnewton: Damping accepted, relres = 0.130004 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.300040e-01 │ │ │ │ Vprtstp: contraction number = 1.300040e-01 │ │ │ │ Vnewton: Using errtol_s: 86456.120106 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.287863e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.997048e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.677494e+04 │ │ │ │ Vprtstp: contraction number = 1.677494e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.302058e-02 │ │ │ │ Vprtstp: contraction number = 1.770760e-01 │ │ │ │ Vnewton: Using errtol_s: 15309.299757 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.429895e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.155165e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.819009e+03 │ │ │ │ Vprtstp: contraction number = 3.819009e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.169720e-03 │ │ │ │ Vprtstp: contraction number = 2.245695e-01 │ │ │ │ Vnewton: Using errtol_s: 3438.001701 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.573208e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.310265e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.699577e+02 │ │ │ │ Vprtstp: contraction number = 9.699577e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.312680e-03 │ │ │ │ Vprtstp: contraction number = 2.539171e-01 │ │ │ │ Vnewton: Using errtol_s: 872.967407 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.711619e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.468500e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.608286e+02 │ │ │ │ Vprtstp: contraction number = 2.608286e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.529874e-04 │ │ │ │ Vprtstp: contraction number = 2.689059e-01 │ │ │ │ Vnewton: Using errtol_s: 234.746058 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.851930e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.625981e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.237536e+01 │ │ │ │ Vprtstp: contraction number = 7.237536e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.794772e-05 │ │ │ │ Vprtstp: contraction number = 2.774822e-01 │ │ │ │ Vnewton: Using errtol_s: 65.137847 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.993091e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.784680e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.051211e+01 │ │ │ │ Vprtstp: contraction number = 2.051211e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.775964e-05 │ │ │ │ Vprtstp: contraction number = 2.834128e-01 │ │ │ │ Vnewton: Using errtol_s: 18.460901 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.133230e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.943355e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.910817e+00 │ │ │ │ Vprtstp: contraction number = 5.910817e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 7.999282e-06 │ │ │ │ Vprtstp: contraction number = 2.881623e-01 │ │ │ │ Vnewton: Using errtol_s: 5.319736 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.273482e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.102026e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.727236e+00 │ │ │ │ Vprtstp: contraction number = 1.727236e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.337519e-06 │ │ │ │ Vprtstp: contraction number = 2.922161e-01 │ │ │ │ Vnewton: Using errtol_s: 1.554512 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.414805e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.261472e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.106059e-01 │ │ │ │ Vprtstp: contraction number = 5.106059e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.910179e-07 │ │ │ │ Vprtstp: contraction number = 2.956203e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.482182e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.542934e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.658605e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.723506e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -14275,15 +14275,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.810176987891E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.831840502654E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.413842577574E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.392910e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.923760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ @@ -14332,160 +14332,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00343543 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.309811 │ │ │ │ +Vacc_SASA: Time elapsed: 0.304443 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.711200e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.962280e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.359390e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.446350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.236500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.822430e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.685177e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.562866e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 691979.805773 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.763464e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.643264e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.117154e+05 │ │ │ │ Vprtstp: contraction number = 1.117154e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153004 │ │ │ │ Vnewton: Attempting damping, relres = 0.570353 │ │ │ │ Vnewton: Damping accepted, relres = 0.153004 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.530041e-01 │ │ │ │ Vprtstp: contraction number = 1.530041e-01 │ │ │ │ Vnewton: Using errtol_s: 105875.763511 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.936872e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.838741e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.274708e+04 │ │ │ │ Vprtstp: contraction number = 2.274708e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.987439e-02 │ │ │ │ Vprtstp: contraction number = 1.952522e-01 │ │ │ │ Vnewton: Using errtol_s: 20672.472417 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.079429e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.001519e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.535330e+03 │ │ │ │ Vprtstp: contraction number = 5.535330e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.200880e-03 │ │ │ │ Vprtstp: contraction number = 2.410386e-01 │ │ │ │ Vnewton: Using errtol_s: 4982.863785 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.221049e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.162178e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.452451e+03 │ │ │ │ Vprtstp: contraction number = 1.452451e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.889102e-03 │ │ │ │ Vprtstp: contraction number = 2.623432e-01 │ │ │ │ Vnewton: Using errtol_s: 1307.220185 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.363817e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.323404e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.004485e+02 │ │ │ │ Vprtstp: contraction number = 4.004485e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.208313e-04 │ │ │ │ Vprtstp: contraction number = 2.757032e-01 │ │ │ │ Vnewton: Using errtol_s: 360.404730 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.505632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.484104e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.141337e+02 │ │ │ │ Vprtstp: contraction number = 1.141337e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.484443e-04 │ │ │ │ Vprtstp: contraction number = 2.850142e-01 │ │ │ │ Vnewton: Using errtol_s: 102.720463 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648330e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.645800e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.333734e+01 │ │ │ │ Vprtstp: contraction number = 3.333734e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.335909e-05 │ │ │ │ Vprtstp: contraction number = 2.920899e-01 │ │ │ │ Vnewton: Using errtol_s: 30.003614 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.789137e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.807105e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.943557e+00 │ │ │ │ Vprtstp: contraction number = 9.943557e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.293275e-05 │ │ │ │ Vprtstp: contraction number = 2.982708e-01 │ │ │ │ Vnewton: Using errtol_s: 8.949202 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.930183e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.968529e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.025944e+00 │ │ │ │ Vprtstp: contraction number = 3.025944e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.935591e-06 │ │ │ │ Vprtstp: contraction number = 3.043120e-01 │ │ │ │ Vnewton: Using errtol_s: 2.723350 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.071562e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.128485e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.372238e-01 │ │ │ │ Vprtstp: contraction number = 9.372238e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.218968e-06 │ │ │ │ Vprtstp: contraction number = 3.097294e-01 │ │ │ │ Vnewton: Using errtol_s: 0.843501 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.210682e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.288429e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.945582e-01 │ │ │ │ Vprtstp: contraction number = 2.945582e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.831071e-07 │ │ │ │ Vprtstp: contraction number = 3.142880e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.632445e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.693238e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.851429e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.918071e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -14495,17 +14495,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.802033666464E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.064367172760E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.030117685645E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.404710e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.869920e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -14532,162 +14532,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.487767 │ │ │ │ +Vacc_SASA: Time elapsed: 0.473740 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.077096e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.077100e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.370630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.376800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.235240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.736710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.771938e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.877057e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1569842.241791 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.849729e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.957401e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.229696e+05 │ │ │ │ Vprtstp: contraction number = 2.229696e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.185061 │ │ │ │ Vnewton: Attempting damping, relres = 0.564709 │ │ │ │ Vnewton: Damping accepted, relres = 0.185061 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.850613e-01 │ │ │ │ Vprtstp: contraction number = 1.850613e-01 │ │ │ │ Vnewton: Using errtol_s: 290517.094461 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.022178e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.149447e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.227646e+04 │ │ │ │ Vprtstp: contraction number = 4.227646e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.651895e-02 │ │ │ │ Vprtstp: contraction number = 1.973343e-01 │ │ │ │ Vnewton: Using errtol_s: 57328.986523 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.164853e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.317829e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.068153e+04 │ │ │ │ Vprtstp: contraction number = 1.068153e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.924548e-03 │ │ │ │ Vprtstp: contraction number = 2.169982e-01 │ │ │ │ Vnewton: Using errtol_s: 12440.289572 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.307138e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.480900e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.967582e+03 │ │ │ │ Vprtstp: contraction number = 2.967582e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.771235e-03 │ │ │ │ Vprtstp: contraction number = 2.235125e-01 │ │ │ │ Vnewton: Using errtol_s: 2780.560196 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.452121e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.636151e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.265098e+02 │ │ │ │ Vprtstp: contraction number = 8.265098e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.740960e-04 │ │ │ │ Vprtstp: contraction number = 2.676640e-01 │ │ │ │ Vnewton: Using errtol_s: 744.255948 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.593683e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.799259e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.434115e+02 │ │ │ │ Vprtstp: contraction number = 2.434115e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.395496e-04 │ │ │ │ Vprtstp: contraction number = 2.943487e-01 │ │ │ │ Vnewton: Using errtol_s: 219.070780 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.736545e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.960609e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.348771e+01 │ │ │ │ Vprtstp: contraction number = 7.348771e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.213095e-05 │ │ │ │ Vprtstp: contraction number = 3.019068e-01 │ │ │ │ Vnewton: Using errtol_s: 66.138952 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.880448e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.012388e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.236672e+01 │ │ │ │ Vprtstp: contraction number = 2.236672e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.282298e-05 │ │ │ │ Vprtstp: contraction number = 3.043600e-01 │ │ │ │ Vnewton: Using errtol_s: 20.130053 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.041255e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028501e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.838847e+00 │ │ │ │ Vprtstp: contraction number = 6.838847e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.920752e-06 │ │ │ │ Vprtstp: contraction number = 3.057599e-01 │ │ │ │ Vnewton: Using errtol_s: 6.154962 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.183373e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.044509e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.097413e+00 │ │ │ │ Vprtstp: contraction number = 2.097413e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.202459e-06 │ │ │ │ Vprtstp: contraction number = 3.066910e-01 │ │ │ │ Vnewton: Using errtol_s: 1.887672 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.326189e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060564e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.447028e-01 │ │ │ │ Vprtstp: contraction number = 6.447028e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.696120e-07 │ │ │ │ Vprtstp: contraction number = 3.073800e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.663970e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.724959e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.852673e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.918086e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -14697,17 +14697,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.380223605804E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.873963354108E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.358993220617E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.433830e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.842690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.25 │ │ │ │ Vpbe_ctor2: xkappa = 0.162813 │ │ │ │ @@ -14754,160 +14754,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00593059 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.492708 │ │ │ │ +Vacc_SASA: Time elapsed: 0.482761 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.298532e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.314573e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.352160e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.413720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.261080e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.721340e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.643542e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094779e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1604207.937715 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.720934e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102792e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.790911e+05 │ │ │ │ Vprtstp: contraction number = 2.790911e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.212135 │ │ │ │ Vnewton: Attempting damping, relres = 0.579242 │ │ │ │ Vnewton: Damping accepted, relres = 0.212135 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.121354e-01 │ │ │ │ Vprtstp: contraction number = 2.121354e-01 │ │ │ │ Vnewton: Using errtol_s: 340309.311873 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.893198e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.122537e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.770596e+04 │ │ │ │ Vprtstp: contraction number = 5.770596e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.436697e-02 │ │ │ │ Vprtstp: contraction number = 2.091445e-01 │ │ │ │ Vnewton: Using errtol_s: 71173.837804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003415e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.139704e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.535772e+04 │ │ │ │ Vprtstp: contraction number = 1.535772e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 1.032915e-02 │ │ │ │ Vprtstp: contraction number = 2.328117e-01 │ │ │ │ Vnewton: Using errtol_s: 16570.101449 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.017421e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.156421e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.454547e+03 │ │ │ │ Vprtstp: contraction number = 4.454547e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.558458e-03 │ │ │ │ Vprtstp: contraction number = 2.476930e-01 │ │ │ │ Vnewton: Using errtol_s: 4104.298326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031244e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.172845e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.316329e+03 │ │ │ │ Vprtstp: contraction number = 1.316329e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.386763e-04 │ │ │ │ Vprtstp: contraction number = 2.887193e-01 │ │ │ │ Vnewton: Using errtol_s: 1184.990339 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045244e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.189200e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.099732e+02 │ │ │ │ Vprtstp: contraction number = 4.099732e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.300054e-04 │ │ │ │ Vprtstp: contraction number = 3.113751e-01 │ │ │ │ Vnewton: Using errtol_s: 368.976439 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.059116e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.205599e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.309902e+02 │ │ │ │ Vprtstp: contraction number = 1.309902e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.348872e-05 │ │ │ │ Vprtstp: contraction number = 3.195087e-01 │ │ │ │ Vnewton: Using errtol_s: 117.891195 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.073128e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.221974e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.243118e+01 │ │ │ │ Vprtstp: contraction number = 4.243118e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.380494e-05 │ │ │ │ Vprtstp: contraction number = 3.239264e-01 │ │ │ │ Vnewton: Using errtol_s: 38.188070 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.086903e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238363e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.388647e+01 │ │ │ │ Vprtstp: contraction number = 1.388647e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.790652e-06 │ │ │ │ Vprtstp: contraction number = 3.272704e-01 │ │ │ │ Vnewton: Using errtol_s: 12.497826 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.100824e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.254853e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.581763e+00 │ │ │ │ Vprtstp: contraction number = 4.581763e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.570482e-06 │ │ │ │ Vprtstp: contraction number = 3.299443e-01 │ │ │ │ Vnewton: Using errtol_s: 4.123587 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.114630e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.271352e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.521483e+00 │ │ │ │ Vprtstp: contraction number = 1.521483e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.535894e-07 │ │ │ │ Vprtstp: contraction number = 3.320737e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.608974e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.670057e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.894619e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.960277e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -14917,29 +14917,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.368902130517E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135701558187E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066769863960E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.409830e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.802000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 2.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.154652e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.314246e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:49:39 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:46:49 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -15209,151 +15209,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.890995 │ │ │ │ +Vacc_SASA: Time elapsed: 0.870796 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.614188e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.572076e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.372410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.349210e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.286620e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.701390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.310309e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.296450e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2228500.711111 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.076146e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.090342e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.885324e+05 │ │ │ │ Vprtstp: contraction number = 2.885324e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.132783 │ │ │ │ Vnewton: Attempting damping, relres = 0.556333 │ │ │ │ Vnewton: Damping accepted, relres = 0.132783 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.327828e-01 │ │ │ │ Vprtstp: contraction number = 1.327828e-01 │ │ │ │ Vnewton: Using errtol_s: 295906.495800 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.789446e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.105624e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.185298e+04 │ │ │ │ Vprtstp: contraction number = 5.185298e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.363031e-02 │ │ │ │ Vprtstp: contraction number = 1.779622e-01 │ │ │ │ Vnewton: Using errtol_s: 52660.160944 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.190784e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.835528e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.214543e+04 │ │ │ │ Vprtstp: contraction number = 1.214543e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.166063e-03 │ │ │ │ Vprtstp: contraction number = 2.186202e-01 │ │ │ │ Vnewton: Using errtol_s: 11512.574293 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.602377e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.520061e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.204841e+03 │ │ │ │ Vprtstp: contraction number = 3.204841e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.298834e-03 │ │ │ │ Vprtstp: contraction number = 2.514166e-01 │ │ │ │ Vnewton: Using errtol_s: 2894.452376 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.994896e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.022048e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.947420e+02 │ │ │ │ Vprtstp: contraction number = 8.947420e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.613575e-04 │ │ │ │ Vprtstp: contraction number = 2.782168e-01 │ │ │ │ Vnewton: Using errtol_s: 805.285400 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040981e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190734e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.596666e+02 │ │ │ │ Vprtstp: contraction number = 2.596666e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.048688e-04 │ │ │ │ Vprtstp: contraction number = 2.902078e-01 │ │ │ │ Vnewton: Using errtol_s: 233.700117 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180674e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.361162e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.695052e+01 │ │ │ │ Vprtstp: contraction number = 7.695052e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.107716e-05 │ │ │ │ Vprtstp: contraction number = 2.963434e-01 │ │ │ │ Vnewton: Using errtol_s: 69.255484 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321020e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.530988e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.313064e+01 │ │ │ │ Vprtstp: contraction number = 2.313064e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.341518e-06 │ │ │ │ Vprtstp: contraction number = 3.005911e-01 │ │ │ │ Vnewton: Using errtol_s: 20.817580 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.462375e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.700804e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.028571e+00 │ │ │ │ Vprtstp: contraction number = 7.028571e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.838551e-06 │ │ │ │ Vprtstp: contraction number = 3.038640e-01 │ │ │ │ Vnewton: Using errtol_s: 6.325714 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.603371e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.868832e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.154905e+00 │ │ │ │ Vprtstp: contraction number = 2.154905e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.702776e-07 │ │ │ │ Vprtstp: contraction number = 3.065922e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.480667e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.542195e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.774810e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.839352e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15363,17 +15363,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.948103828558E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.567066305004E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282854148760E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.381150e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.381390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.275 │ │ │ │ Vpbe_ctor2: xkappa = 0.17076 │ │ │ │ @@ -15420,160 +15420,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0175518 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.881571 │ │ │ │ +Vacc_SASA: Time elapsed: 0.874183 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.868338e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.882149e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.387600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.382350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.273830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.698140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.976133e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.273607e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2283064.573073 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.052926e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.353830e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.589605e+05 │ │ │ │ Vprtstp: contraction number = 3.589605e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.157146 │ │ │ │ Vnewton: Attempting damping, relres = 0.569027 │ │ │ │ Vnewton: Damping accepted, relres = 0.157146 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.571455e-01 │ │ │ │ Vprtstp: contraction number = 1.571455e-01 │ │ │ │ Vnewton: Using errtol_s: 358773.390898 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.227410e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.559550e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.109555e+04 │ │ │ │ Vprtstp: contraction number = 7.109555e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.062803e-02 │ │ │ │ Vprtstp: contraction number = 1.949023e-01 │ │ │ │ Vnewton: Using errtol_s: 69925.774403 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.369360e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.732506e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.775956e+04 │ │ │ │ Vprtstp: contraction number = 1.775956e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.240527e-03 │ │ │ │ Vprtstp: contraction number = 2.364020e-01 │ │ │ │ Vnewton: Using errtol_s: 16530.590965 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.511312e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.904603e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.909187e+03 │ │ │ │ Vprtstp: contraction number = 4.909187e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.938451e-03 │ │ │ │ Vprtstp: contraction number = 2.677224e-01 │ │ │ │ Vnewton: Using errtol_s: 4425.608962 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.654073e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.075198e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.432328e+03 │ │ │ │ Vprtstp: contraction number = 1.432328e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.646405e-04 │ │ │ │ Vprtstp: contraction number = 2.912844e-01 │ │ │ │ Vnewton: Using errtol_s: 1289.110788 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.796597e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.249178e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.352860e+02 │ │ │ │ Vprtstp: contraction number = 4.352860e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.715930e-04 │ │ │ │ Vprtstp: contraction number = 3.038977e-01 │ │ │ │ Vnewton: Using errtol_s: 391.757810 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.943637e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.419745e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.357704e+02 │ │ │ │ Vprtstp: contraction number = 1.357704e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.352166e-05 │ │ │ │ Vprtstp: contraction number = 3.119106e-01 │ │ │ │ Vnewton: Using errtol_s: 122.193412 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.086468e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.591923e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.319013e+01 │ │ │ │ Vprtstp: contraction number = 4.319013e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.702585e-05 │ │ │ │ Vprtstp: contraction number = 3.181115e-01 │ │ │ │ Vnewton: Using errtol_s: 38.871124 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.228163e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.765272e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.397456e+01 │ │ │ │ Vprtstp: contraction number = 1.397456e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.508868e-06 │ │ │ │ Vprtstp: contraction number = 3.235590e-01 │ │ │ │ Vnewton: Using errtol_s: 12.577101 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.368632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.938816e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.585274e+00 │ │ │ │ Vprtstp: contraction number = 4.585274e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.807547e-06 │ │ │ │ Vprtstp: contraction number = 3.281159e-01 │ │ │ │ Vnewton: Using errtol_s: 4.126746 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.509368e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.112532e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.521742e+00 │ │ │ │ Vprtstp: contraction number = 1.521742e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 5.998813e-07 │ │ │ │ Vprtstp: contraction number = 3.318759e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.640255e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.701675e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.978915e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.043515e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15583,17 +15583,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.934616474565E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951681070136E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475162911234E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.338810e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.361260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -15620,151 +15620,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.318263 │ │ │ │ +Vacc_SASA: Time elapsed: 0.296998 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.135940e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.092170e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.375360e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.274290e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.679250e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.046616e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.682112e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 659573.848020 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.124137e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.761437e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.895379e+04 │ │ │ │ Vprtstp: contraction number = 8.895379e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.129769 │ │ │ │ Vnewton: Attempting damping, relres = 0.558262 │ │ │ │ Vnewton: Damping accepted, relres = 0.129769 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.297694e-01 │ │ │ │ Vprtstp: contraction number = 1.297694e-01 │ │ │ │ Vnewton: Using errtol_s: 85592.483355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.298317e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.951534e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.666045e+04 │ │ │ │ Vprtstp: contraction number = 1.666045e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.303462e-02 │ │ │ │ Vprtstp: contraction number = 1.775043e-01 │ │ │ │ Vnewton: Using errtol_s: 15193.035895 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.439903e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.109150e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.802357e+03 │ │ │ │ Vprtstp: contraction number = 3.802357e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.189623e-03 │ │ │ │ Vprtstp: contraction number = 2.252966e-01 │ │ │ │ Vnewton: Using errtol_s: 3422.939434 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.582002e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.266056e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.674822e+02 │ │ │ │ Vprtstp: contraction number = 9.674822e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.320155e-03 │ │ │ │ Vprtstp: contraction number = 2.543835e-01 │ │ │ │ Vnewton: Using errtol_s: 870.739405 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.725128e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.423071e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.604392e+02 │ │ │ │ Vprtstp: contraction number = 2.604392e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.553742e-04 │ │ │ │ Vprtstp: contraction number = 2.691914e-01 │ │ │ │ Vnewton: Using errtol_s: 234.395549 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.865951e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.581947e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.231232e+01 │ │ │ │ Vprtstp: contraction number = 7.231232e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.867144e-05 │ │ │ │ Vprtstp: contraction number = 2.776550e-01 │ │ │ │ Vnewton: Using errtol_s: 65.081104 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.006858e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.740717e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.050149e+01 │ │ │ │ Vprtstp: contraction number = 2.050149e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.797465e-05 │ │ │ │ Vprtstp: contraction number = 2.835131e-01 │ │ │ │ Vnewton: Using errtol_s: 18.451347 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.149431e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.899159e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.908895e+00 │ │ │ │ Vprtstp: contraction number = 5.908895e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.062791e-06 │ │ │ │ Vprtstp: contraction number = 2.882178e-01 │ │ │ │ Vnewton: Using errtol_s: 5.318006 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.291473e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.058624e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.726854e+00 │ │ │ │ Vprtstp: contraction number = 1.726854e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.356322e-06 │ │ │ │ Vprtstp: contraction number = 2.922465e-01 │ │ │ │ Vnewton: Using errtol_s: 1.554169 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.435566e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.215636e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.105208e-01 │ │ │ │ Vprtstp: contraction number = 5.105208e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.966145e-07 │ │ │ │ Vprtstp: contraction number = 2.956364e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.497355e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.558717e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.656114e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.720443e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15774,17 +15774,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.818510917310E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.831530055588E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.413690932719E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.412720e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.402890e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.275 │ │ │ │ Vpbe_ctor2: xkappa = 0.17076 │ │ │ │ @@ -15831,160 +15831,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00313173 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.311040 │ │ │ │ +Vacc_SASA: Time elapsed: 0.304978 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.005130e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.911440e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.389000e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.376840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.367790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.779770e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.712893e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.509257e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 686089.077180 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.789993e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.588931e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.106303e+05 │ │ │ │ Vprtstp: contraction number = 1.106303e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.152721 │ │ │ │ Vnewton: Attempting damping, relres = 0.570236 │ │ │ │ Vnewton: Damping accepted, relres = 0.152721 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.527207e-01 │ │ │ │ Vprtstp: contraction number = 1.527207e-01 │ │ │ │ Vnewton: Using errtol_s: 104780.035977 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.964678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.781663e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.255423e+04 │ │ │ │ Vprtstp: contraction number = 2.255423e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.985893e-02 │ │ │ │ Vprtstp: contraction number = 1.955132e-01 │ │ │ │ Vnewton: Using errtol_s: 20485.884926 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.107917e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.940722e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.496448e+03 │ │ │ │ Vprtstp: contraction number = 5.496448e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.211588e-03 │ │ │ │ Vprtstp: contraction number = 2.415220e-01 │ │ │ │ Vnewton: Using errtol_s: 4947.791442 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.250704e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.101223e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.444377e+03 │ │ │ │ Vprtstp: contraction number = 1.444377e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.894730e-03 │ │ │ │ Vprtstp: contraction number = 2.627341e-01 │ │ │ │ Vnewton: Using errtol_s: 1299.953373 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.392331e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.257595e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.987236e+02 │ │ │ │ Vprtstp: contraction number = 3.987236e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.230404e-04 │ │ │ │ Vprtstp: contraction number = 2.760502e-01 │ │ │ │ Vnewton: Using errtol_s: 358.852327 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.533757e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.415205e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.137605e+02 │ │ │ │ Vprtstp: contraction number = 1.137605e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.492292e-04 │ │ │ │ Vprtstp: contraction number = 2.853110e-01 │ │ │ │ Vnewton: Using errtol_s: 102.384499 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.673515e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.575914e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.325592e+01 │ │ │ │ Vprtstp: contraction number = 3.325592e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.362456e-05 │ │ │ │ Vprtstp: contraction number = 2.923327e-01 │ │ │ │ Vnewton: Using errtol_s: 29.930336 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.813452e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.736506e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.925690e+00 │ │ │ │ Vprtstp: contraction number = 9.925690e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.302035e-05 │ │ │ │ Vprtstp: contraction number = 2.984638e-01 │ │ │ │ Vnewton: Using errtol_s: 8.933121 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.955048e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.898266e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.021979e+00 │ │ │ │ Vprtstp: contraction number = 3.021979e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.964181e-06 │ │ │ │ Vprtstp: contraction number = 3.044603e-01 │ │ │ │ Vnewton: Using errtol_s: 2.719781 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.099056e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.059803e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.363300e-01 │ │ │ │ Vprtstp: contraction number = 9.363300e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.228262e-06 │ │ │ │ Vprtstp: contraction number = 3.098400e-01 │ │ │ │ Vnewton: Using errtol_s: 0.842697 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.240401e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.219130e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.943527e-01 │ │ │ │ Vprtstp: contraction number = 2.943527e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.861268e-07 │ │ │ │ Vprtstp: contraction number = 3.143685e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.634541e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.696925e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.835459e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.900824e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -15994,17 +15994,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.810295872225E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.064058027536E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.029966775084E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403680e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.406420e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -16031,162 +16031,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.488322 │ │ │ │ +Vacc_SASA: Time elapsed: 0.478989 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.081415e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.082303e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.374280e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.352900e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.744500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.807334e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.801927e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1545868.713233 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.886088e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.882775e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.195959e+05 │ │ │ │ Vprtstp: contraction number = 2.195959e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.180695 │ │ │ │ Vnewton: Attempting damping, relres = 0.564482 │ │ │ │ Vnewton: Damping accepted, relres = 0.180695 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.806948e-01 │ │ │ │ Vprtstp: contraction number = 1.806948e-01 │ │ │ │ Vnewton: Using errtol_s: 279330.491277 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.062919e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.071268e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.153850e+04 │ │ │ │ Vprtstp: contraction number = 4.153850e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.508737e-02 │ │ │ │ Vprtstp: contraction number = 1.941803e-01 │ │ │ │ Vnewton: Using errtol_s: 54240.471315 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.207593e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.233612e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.050009e+04 │ │ │ │ Vprtstp: contraction number = 1.050009e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.567269e-03 │ │ │ │ Vprtstp: contraction number = 2.156693e-01 │ │ │ │ Vnewton: Using errtol_s: 11698.005091 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.353353e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.395312e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.909851e+03 │ │ │ │ Vprtstp: contraction number = 2.909851e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.738825e-03 │ │ │ │ Vprtstp: contraction number = 2.297824e-01 │ │ │ │ Vnewton: Using errtol_s: 2687.995161 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.494341e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.549919e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.166574e+02 │ │ │ │ Vprtstp: contraction number = 8.166574e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.755829e-04 │ │ │ │ Vprtstp: contraction number = 2.735082e-01 │ │ │ │ Vnewton: Using errtol_s: 735.188760 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.635598e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.710041e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.418263e+02 │ │ │ │ Vprtstp: contraction number = 2.418263e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.407907e-04 │ │ │ │ Vprtstp: contraction number = 2.960382e-01 │ │ │ │ Vnewton: Using errtol_s: 217.643927 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.776071e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.868133e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.307074e+01 │ │ │ │ Vprtstp: contraction number = 7.307074e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.254157e-05 │ │ │ │ Vprtstp: contraction number = 3.021618e-01 │ │ │ │ Vnewton: Using errtol_s: 65.763679 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.917600e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002573e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.224627e+01 │ │ │ │ Vprtstp: contraction number = 2.224627e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.295171e-05 │ │ │ │ Vprtstp: contraction number = 3.044484e-01 │ │ │ │ Vnewton: Using errtol_s: 20.021644 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.057209e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.018410e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.802985e+00 │ │ │ │ Vprtstp: contraction number = 6.802985e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.960677e-06 │ │ │ │ Vprtstp: contraction number = 3.058034e-01 │ │ │ │ Vnewton: Using errtol_s: 6.122687 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.200258e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034370e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.086607e+00 │ │ │ │ Vprtstp: contraction number = 2.086607e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.214816e-06 │ │ │ │ Vprtstp: contraction number = 3.067192e-01 │ │ │ │ Vnewton: Using errtol_s: 1.877946 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.342500e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.050050e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.414261e-01 │ │ │ │ Vprtstp: contraction number = 6.414261e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.734363e-07 │ │ │ │ Vprtstp: contraction number = 3.074016e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.643254e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.705528e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.823304e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.888267e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -16196,15 +16196,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.218327471785E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.873840524527E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.358686721845E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403030e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ @@ -16253,160 +16253,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00502725 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.496020 │ │ │ │ +Vacc_SASA: Time elapsed: 0.477537 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.309861e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.301752e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.390140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.407330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.277500e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.698580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.659464e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.083667e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1578654.561343 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.736971e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091679e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.749391e+05 │ │ │ │ Vprtstp: contraction number = 2.749391e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.208079 │ │ │ │ Vnewton: Attempting damping, relres = 0.579104 │ │ │ │ Vnewton: Damping accepted, relres = 0.208079 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.080792e-01 │ │ │ │ Vprtstp: contraction number = 2.080792e-01 │ │ │ │ Vnewton: Using errtol_s: 328485.121608 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.909741e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111120e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.673641e+04 │ │ │ │ Vprtstp: contraction number = 5.673641e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.299902e-02 │ │ │ │ Vprtstp: contraction number = 2.066474e-01 │ │ │ │ Vnewton: Using errtol_s: 67880.597256 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005119e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.128246e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.510541e+04 │ │ │ │ Vprtstp: contraction number = 1.510541e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.991987e-03 │ │ │ │ Vprtstp: contraction number = 2.323771e-01 │ │ │ │ Vnewton: Using errtol_s: 15773.896333 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019146e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.144811e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.375823e+03 │ │ │ │ Vprtstp: contraction number = 4.375823e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.532644e-03 │ │ │ │ Vprtstp: contraction number = 2.534675e-01 │ │ │ │ Vnewton: Using errtol_s: 3998.170369 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.033189e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.160859e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.301537e+03 │ │ │ │ Vprtstp: contraction number = 1.301537e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.421078e-04 │ │ │ │ Vprtstp: contraction number = 2.930170e-01 │ │ │ │ Vnewton: Using errtol_s: 1171.531808 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047492e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.177160e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.070189e+02 │ │ │ │ Vprtstp: contraction number = 4.070189e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.320441e-04 │ │ │ │ Vprtstp: contraction number = 3.126824e-01 │ │ │ │ Vnewton: Using errtol_s: 366.317427 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.061716e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193181e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.302066e+02 │ │ │ │ Vprtstp: contraction number = 1.302066e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.423158e-05 │ │ │ │ Vprtstp: contraction number = 3.199029e-01 │ │ │ │ Vnewton: Using errtol_s: 117.186019 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.076086e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.209301e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.220788e+01 │ │ │ │ Vprtstp: contraction number = 4.220788e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.406296e-05 │ │ │ │ Vprtstp: contraction number = 3.241606e-01 │ │ │ │ Vnewton: Using errtol_s: 37.987094 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090086e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.225393e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.382030e+01 │ │ │ │ Vprtstp: contraction number = 1.382030e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.879032e-06 │ │ │ │ Vprtstp: contraction number = 3.274341e-01 │ │ │ │ Vnewton: Using errtol_s: 12.438270 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104206e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.241477e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.561479e+00 │ │ │ │ Vprtstp: contraction number = 4.561479e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.600526e-06 │ │ │ │ Vprtstp: contraction number = 3.300565e-01 │ │ │ │ Vnewton: Using errtol_s: 4.105331 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118485e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.257710e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.515099e+00 │ │ │ │ Vprtstp: contraction number = 1.515099e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.637667e-07 │ │ │ │ Vprtstp: contraction number = 3.321508e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.633215e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.694827e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.868181e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.933028e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -16416,29 +16416,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.207264728497E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135578758917E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066739245337E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.397540e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.380730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.158822e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.299557e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:50:35 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:49:46 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -16708,151 +16708,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.908903 │ │ │ │ +Vacc_SASA: Time elapsed: 0.867521 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.620597e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.567507e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.397220e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.391680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.229940e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.666950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.316833e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.289862e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2208581.508242 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.087758e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.073566e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.858538e+05 │ │ │ │ Vprtstp: contraction number = 2.858538e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.131715 │ │ │ │ Vnewton: Attempting damping, relres = 0.556234 │ │ │ │ Vnewton: Damping accepted, relres = 0.131715 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.317149e-01 │ │ │ │ Vprtstp: contraction number = 1.317149e-01 │ │ │ │ Vnewton: Using errtol_s: 290903.178824 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.791932e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.020505e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.143090e+04 │ │ │ │ Vprtstp: contraction number = 5.143090e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.336960e-02 │ │ │ │ Vprtstp: contraction number = 1.774256e-01 │ │ │ │ Vnewton: Using errtol_s: 51613.668608 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.197994e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.682469e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.206326e+04 │ │ │ │ Vprtstp: contraction number = 1.206326e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.129225e-03 │ │ │ │ Vprtstp: contraction number = 2.194828e-01 │ │ │ │ Vnewton: Using errtol_s: 11328.310511 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.584215e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.322485e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.187128e+03 │ │ │ │ Vprtstp: contraction number = 3.187128e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.301872e-03 │ │ │ │ Vprtstp: contraction number = 2.538146e-01 │ │ │ │ Vnewton: Using errtol_s: 2875.290058 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.992533e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.945010e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.922285e+02 │ │ │ │ Vprtstp: contraction number = 8.922285e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.635897e-04 │ │ │ │ Vprtstp: contraction number = 2.792822e-01 │ │ │ │ Vnewton: Using errtol_s: 803.017471 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.038493e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.158620e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.591681e+02 │ │ │ │ Vprtstp: contraction number = 2.591681e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.056114e-04 │ │ │ │ Vprtstp: contraction number = 2.904687e-01 │ │ │ │ Vnewton: Using errtol_s: 233.251428 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.177276e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.321968e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.682702e+01 │ │ │ │ Vprtstp: contraction number = 7.682702e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.130712e-05 │ │ │ │ Vprtstp: contraction number = 2.964369e-01 │ │ │ │ Vnewton: Using errtol_s: 69.144331 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.317012e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.485419e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.309726e+01 │ │ │ │ Vprtstp: contraction number = 2.309726e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.412165e-06 │ │ │ │ Vprtstp: contraction number = 3.006398e-01 │ │ │ │ Vnewton: Using errtol_s: 20.787535 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.455621e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.654278e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.019037e+00 │ │ │ │ Vprtstp: contraction number = 7.019037e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.860267e-06 │ │ │ │ Vprtstp: contraction number = 3.038904e-01 │ │ │ │ Vnewton: Using errtol_s: 6.317133 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.596028e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.821680e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.152093e+00 │ │ │ │ Vprtstp: contraction number = 2.152093e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.769810e-07 │ │ │ │ Vprtstp: contraction number = 3.066081e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.471881e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.533229e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.725048e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.789843e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -16862,17 +16862,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.850378362352E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566988443868E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282832279800E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.365030e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.365320e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.3 │ │ │ │ Vpbe_ctor2: xkappa = 0.178353 │ │ │ │ @@ -16919,160 +16919,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0167285 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.887646 │ │ │ │ +Vacc_SASA: Time elapsed: 0.863526 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.861572e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.862545e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.362860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.418670e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.321920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.645590e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.967218e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.221564e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2261526.211377 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.044547e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.300899e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.556600e+05 │ │ │ │ Vprtstp: contraction number = 3.556600e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.156191 │ │ │ │ Vnewton: Attempting damping, relres = 0.568968 │ │ │ │ Vnewton: Damping accepted, relres = 0.156191 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.561910e-01 │ │ │ │ Vprtstp: contraction number = 1.561910e-01 │ │ │ │ Vnewton: Using errtol_s: 353229.985787 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.215690e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.496510e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.049885e+04 │ │ │ │ Vprtstp: contraction number = 7.049885e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.038701e-02 │ │ │ │ Vprtstp: contraction number = 1.945503e-01 │ │ │ │ Vnewton: Using errtol_s: 68721.012670 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.355477e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.667770e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.762526e+04 │ │ │ │ Vprtstp: contraction number = 1.762526e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.209079e-03 │ │ │ │ Vprtstp: contraction number = 2.372422e-01 │ │ │ │ Vnewton: Using errtol_s: 16303.521422 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.495763e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.838051e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.877060e+03 │ │ │ │ Vprtstp: contraction number = 4.877060e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.943013e-03 │ │ │ │ Vprtstp: contraction number = 2.695230e-01 │ │ │ │ Vnewton: Using errtol_s: 4394.173812 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.635409e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.002602e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.426343e+03 │ │ │ │ Vprtstp: contraction number = 1.426343e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.676342e-04 │ │ │ │ Vprtstp: contraction number = 2.921413e-01 │ │ │ │ Vnewton: Using errtol_s: 1283.719712 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.773518e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.169145e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.339166e+02 │ │ │ │ Vprtstp: contraction number = 4.339166e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.726822e-04 │ │ │ │ Vprtstp: contraction number = 3.042139e-01 │ │ │ │ Vnewton: Using errtol_s: 390.525321 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.913632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.341519e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.354221e+02 │ │ │ │ Vprtstp: contraction number = 1.354221e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.389279e-05 │ │ │ │ Vprtstp: contraction number = 3.120924e-01 │ │ │ │ Vnewton: Using errtol_s: 121.879967 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.052599e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.512747e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.309648e+01 │ │ │ │ Vprtstp: contraction number = 4.309648e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.715074e-05 │ │ │ │ Vprtstp: contraction number = 3.182380e-01 │ │ │ │ Vnewton: Using errtol_s: 38.786838 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.192726e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.685685e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.394777e+01 │ │ │ │ Vprtstp: contraction number = 1.394777e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.550675e-06 │ │ │ │ Vprtstp: contraction number = 3.236406e-01 │ │ │ │ Vnewton: Using errtol_s: 12.552997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.331623e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.854860e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.577150e+00 │ │ │ │ Vprtstp: contraction number = 4.577150e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.821529e-06 │ │ │ │ Vprtstp: contraction number = 3.281635e-01 │ │ │ │ Vnewton: Using errtol_s: 4.119435 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.470596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.027001e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.519139e+00 │ │ │ │ Vprtstp: contraction number = 1.519139e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.045585e-07 │ │ │ │ Vprtstp: contraction number = 3.318962e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.610756e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.672258e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.941376e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.006460e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -17082,17 +17082,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.837128515027E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951603256216E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475141098473E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.359830e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.356810e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -17119,151 +17119,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.312404 │ │ │ │ +Vacc_SASA: Time elapsed: 0.300771 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.108110e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.179100e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.364230e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.406590e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.254970e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.742140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.006184e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.595539e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 654975.595106 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.085431e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.675100e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.825232e+04 │ │ │ │ Vprtstp: contraction number = 8.825232e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.129536 │ │ │ │ Vnewton: Attempting damping, relres = 0.558179 │ │ │ │ Vnewton: Damping accepted, relres = 0.129536 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.295360e-01 │ │ │ │ Vprtstp: contraction number = 1.295360e-01 │ │ │ │ Vnewton: Using errtol_s: 84842.899807 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.258289e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.863965e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.656273e+04 │ │ │ │ Vprtstp: contraction number = 1.656273e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.304324e-02 │ │ │ │ Vprtstp: contraction number = 1.778907e-01 │ │ │ │ Vnewton: Using errtol_s: 15092.761763 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.401977e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.020228e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.788125e+03 │ │ │ │ Vprtstp: contraction number = 3.788125e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.206395e-03 │ │ │ │ Vprtstp: contraction number = 2.259402e-01 │ │ │ │ Vnewton: Using errtol_s: 3410.061436 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.585284e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.176655e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.653659e+02 │ │ │ │ Vprtstp: contraction number = 9.653659e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.326515e-03 │ │ │ │ Vprtstp: contraction number = 2.547856e-01 │ │ │ │ Vnewton: Using errtol_s: 868.834666 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.766158e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.332096e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.601053e+02 │ │ │ │ Vprtstp: contraction number = 2.601053e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.574104e-04 │ │ │ │ Vprtstp: contraction number = 2.694357e-01 │ │ │ │ Vnewton: Using errtol_s: 234.095066 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.976693e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.487107e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.225806e+01 │ │ │ │ Vprtstp: contraction number = 7.225806e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.928962e-05 │ │ │ │ Vprtstp: contraction number = 2.778029e-01 │ │ │ │ Vnewton: Using errtol_s: 65.032277 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.189426e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.641635e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.049231e+01 │ │ │ │ Vprtstp: contraction number = 2.049231e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.815843e-05 │ │ │ │ Vprtstp: contraction number = 2.835989e-01 │ │ │ │ Vnewton: Using errtol_s: 18.443082 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.394965e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.796807e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.907221e+00 │ │ │ │ Vprtstp: contraction number = 5.907221e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.117095e-06 │ │ │ │ Vprtstp: contraction number = 2.882652e-01 │ │ │ │ Vnewton: Using errtol_s: 5.316499 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.559666e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.953395e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.726518e+00 │ │ │ │ Vprtstp: contraction number = 1.726518e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.372403e-06 │ │ │ │ Vprtstp: contraction number = 2.922725e-01 │ │ │ │ Vnewton: Using errtol_s: 1.553866 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.700671e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.107780e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.104456e-01 │ │ │ │ Vprtstp: contraction number = 5.104456e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.014018e-07 │ │ │ │ Vprtstp: contraction number = 2.956503e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.801008e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.862175e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.631895e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.697196e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -17273,17 +17273,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.824785455447E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.831245180939E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.413552848131E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.415130e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.407310e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.3 │ │ │ │ Vpbe_ctor2: xkappa = 0.178353 │ │ │ │ @@ -17330,160 +17330,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00286585 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.304760 │ │ │ │ +Vacc_SASA: Time elapsed: 0.301079 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.672690e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.879250e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.360840e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.406830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.394010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.816810e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.972809e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.398871e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 681119.647673 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.049985e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.478771e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.097058e+05 │ │ │ │ Vprtstp: contraction number = 1.097058e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.152443 │ │ │ │ Vnewton: Attempting damping, relres = 0.570128 │ │ │ │ Vnewton: Damping accepted, relres = 0.152443 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.524432e-01 │ │ │ │ Vprtstp: contraction number = 1.524432e-01 │ │ │ │ Vnewton: Using errtol_s: 103832.028377 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.222777e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.669691e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.238938e+04 │ │ │ │ Vprtstp: contraction number = 2.238938e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.984124e-02 │ │ │ │ Vprtstp: contraction number = 1.957533e-01 │ │ │ │ Vnewton: Using errtol_s: 20325.457528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.363533e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.829828e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.463136e+03 │ │ │ │ Vprtstp: contraction number = 5.463136e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.220083e-03 │ │ │ │ Vprtstp: contraction number = 2.419498e-01 │ │ │ │ Vnewton: Using errtol_s: 4917.740487 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.504001e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.986230e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.437458e+03 │ │ │ │ Vprtstp: contraction number = 1.437458e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.899412e-03 │ │ │ │ Vprtstp: contraction number = 2.630734e-01 │ │ │ │ Vnewton: Using errtol_s: 1293.726521 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.644608e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.145167e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.972446e+02 │ │ │ │ Vprtstp: contraction number = 3.972446e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.249023e-04 │ │ │ │ Vprtstp: contraction number = 2.763499e-01 │ │ │ │ Vnewton: Using errtol_s: 357.521241 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.786160e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.303382e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.134401e+02 │ │ │ │ Vprtstp: contraction number = 1.134401e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.498946e-04 │ │ │ │ Vprtstp: contraction number = 2.855667e-01 │ │ │ │ Vnewton: Using errtol_s: 102.096166 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.927022e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.463061e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.318595e+01 │ │ │ │ Vprtstp: contraction number = 3.318595e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.385040e-05 │ │ │ │ Vprtstp: contraction number = 2.925415e-01 │ │ │ │ Vnewton: Using errtol_s: 29.867366 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.068712e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.619407e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.910309e+00 │ │ │ │ Vprtstp: contraction number = 9.910309e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.309503e-05 │ │ │ │ Vprtstp: contraction number = 2.986296e-01 │ │ │ │ Vnewton: Using errtol_s: 8.919279 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.209487e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.778383e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.018558e+00 │ │ │ │ Vprtstp: contraction number = 3.018558e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.988583e-06 │ │ │ │ Vprtstp: contraction number = 3.045877e-01 │ │ │ │ Vnewton: Using errtol_s: 2.716702 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.350892e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.938736e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.355568e-01 │ │ │ │ Vprtstp: contraction number = 9.355568e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.236201e-06 │ │ │ │ Vprtstp: contraction number = 3.099350e-01 │ │ │ │ Vnewton: Using errtol_s: 0.842001 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.493797e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.096288e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.941742e-01 │ │ │ │ Vprtstp: contraction number = 2.941742e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.887082e-07 │ │ │ │ Vprtstp: contraction number = 3.144376e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.627541e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.689935e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.821582e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.887635e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -17493,17 +17493,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.816506018339E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.063774350048E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.029829357702E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.416700e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.388490e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -17530,162 +17530,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.493939 │ │ │ │ +Vacc_SASA: Time elapsed: 0.481805 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.082866e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.082386e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.375010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.387830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.355640e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.686160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.055642e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.678076e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1525884.348969 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.133716e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.757187e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.167719e+05 │ │ │ │ Vprtstp: contraction number = 2.167719e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.176913 │ │ │ │ Vnewton: Attempting damping, relres = 0.564272 │ │ │ │ Vnewton: Damping accepted, relres = 0.176913 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.769126e-01 │ │ │ │ Vprtstp: contraction number = 1.769126e-01 │ │ │ │ Vnewton: Using errtol_s: 269948.173272 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.307563e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.944642e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.092694e+04 │ │ │ │ Vprtstp: contraction number = 4.092694e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.387341e-02 │ │ │ │ Vprtstp: contraction number = 1.914697e-01 │ │ │ │ Vnewton: Using errtol_s: 51686.903490 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.450302e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.109445e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.034780e+04 │ │ │ │ Vprtstp: contraction number = 1.034780e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.283807e-03 │ │ │ │ Vprtstp: contraction number = 2.150302e-01 │ │ │ │ Vnewton: Using errtol_s: 11114.247135 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.593424e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.269334e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.862719e+03 │ │ │ │ Vprtstp: contraction number = 2.862719e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.717625e-03 │ │ │ │ Vprtstp: contraction number = 2.358142e-01 │ │ │ │ Vnewton: Using errtol_s: 2620.897639 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.736392e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.425550e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.092476e+02 │ │ │ │ Vprtstp: contraction number = 8.092476e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.773796e-04 │ │ │ │ Vprtstp: contraction number = 2.779300e-01 │ │ │ │ Vnewton: Using errtol_s: 728.426056 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.879113e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.581291e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.405150e+02 │ │ │ │ Vprtstp: contraction number = 2.405150e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.418612e-04 │ │ │ │ Vprtstp: contraction number = 2.971664e-01 │ │ │ │ Vnewton: Using errtol_s: 216.463714 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.020609e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.719462e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.272000e+01 │ │ │ │ Vprtstp: contraction number = 7.272000e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.289186e-05 │ │ │ │ Vprtstp: contraction number = 3.023510e-01 │ │ │ │ Vnewton: Using errtol_s: 65.448016 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.161427e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.877076e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.214460e+01 │ │ │ │ Vprtstp: contraction number = 2.214460e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.306137e-05 │ │ │ │ Vprtstp: contraction number = 3.045186e-01 │ │ │ │ Vnewton: Using errtol_s: 19.930141 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.301255e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003195e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.772692e+00 │ │ │ │ Vprtstp: contraction number = 6.772692e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.994682e-06 │ │ │ │ Vprtstp: contraction number = 3.058394e-01 │ │ │ │ Vnewton: Using errtol_s: 6.095423 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.442531e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019256e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.077475e+00 │ │ │ │ Vprtstp: contraction number = 2.077475e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.225341e-06 │ │ │ │ Vprtstp: contraction number = 3.067429e-01 │ │ │ │ Vnewton: Using errtol_s: 1.869728 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.583083e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034897e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.386558e-01 │ │ │ │ Vprtstp: contraction number = 6.386558e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.766932e-07 │ │ │ │ Vprtstp: contraction number = 3.074192e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.635373e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.697473e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.793173e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.857625e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -17695,15 +17695,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.069846752513E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.873729752993E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.358408005729E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.416560e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.386820e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ @@ -17752,160 +17752,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00434174 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.502368 │ │ │ │ +Vacc_SASA: Time elapsed: 0.482777 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.299835e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.305577e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.382460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.356650e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.229830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.731910e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.898563e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068280e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1557370.209900 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.975133e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.076228e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.714539e+05 │ │ │ │ Vprtstp: contraction number = 2.714539e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.204551 │ │ │ │ Vnewton: Attempting damping, relres = 0.578965 │ │ │ │ Vnewton: Damping accepted, relres = 0.204551 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.045506e-01 │ │ │ │ Vprtstp: contraction number = 2.045506e-01 │ │ │ │ Vnewton: Using errtol_s: 318560.936336 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014652e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095250e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.592903e+04 │ │ │ │ Vprtstp: contraction number = 5.592903e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.183467e-02 │ │ │ │ Vprtstp: contraction number = 2.045200e-01 │ │ │ │ Vnewton: Using errtol_s: 65152.068354 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.028853e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111698e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.489191e+04 │ │ │ │ Vprtstp: contraction number = 1.489191e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.724338e-03 │ │ │ │ Vprtstp: contraction number = 2.324469e-01 │ │ │ │ Vnewton: Using errtol_s: 15144.393716 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042915e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.127463e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.311238e+03 │ │ │ │ Vprtstp: contraction number = 4.311238e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.516326e-03 │ │ │ │ Vprtstp: contraction number = 2.587658e-01 │ │ │ │ Vnewton: Using errtol_s: 3918.850513 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057005e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.143397e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.290056e+03 │ │ │ │ Vprtstp: contraction number = 1.290056e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.455704e-04 │ │ │ │ Vprtstp: contraction number = 2.962933e-01 │ │ │ │ Vnewton: Using errtol_s: 1161.129054 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.070869e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.159304e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.045979e+02 │ │ │ │ Vprtstp: contraction number = 4.045979e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.338163e-04 │ │ │ │ Vprtstp: contraction number = 3.136073e-01 │ │ │ │ Vnewton: Using errtol_s: 364.138497 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.084643e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.175027e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.295599e+02 │ │ │ │ Vprtstp: contraction number = 1.295599e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.487232e-05 │ │ │ │ Vprtstp: contraction number = 3.202186e-01 │ │ │ │ Vnewton: Using errtol_s: 116.603918 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.098377e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190914e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.202377e+01 │ │ │ │ Vprtstp: contraction number = 4.202377e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.428543e-05 │ │ │ │ Vprtstp: contraction number = 3.243579e-01 │ │ │ │ Vnewton: Using errtol_s: 37.821402 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112223e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206488e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.376584e+01 │ │ │ │ Vprtstp: contraction number = 1.376584e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 7.955244e-06 │ │ │ │ Vprtstp: contraction number = 3.275727e-01 │ │ │ │ Vnewton: Using errtol_s: 12.389260 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.126130e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222563e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.544810e+00 │ │ │ │ Vprtstp: contraction number = 4.544810e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.626434e-06 │ │ │ │ Vprtstp: contraction number = 3.301512e-01 │ │ │ │ Vnewton: Using errtol_s: 4.090329 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.140030e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.238545e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.509859e+00 │ │ │ │ Vprtstp: contraction number = 1.509859e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.725435e-07 │ │ │ │ Vprtstp: contraction number = 3.322161e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.609686e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.670758e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.828468e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.893066e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -17915,29 +17915,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 8.058985499757E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135468016715E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066711397255E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.382030e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.392990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.180090e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.280608e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:51:32 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:52:55 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -18207,151 +18207,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.906380 │ │ │ │ +Vacc_SASA: Time elapsed: 0.881586 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.618740e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.582295e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.369910e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.357000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.192310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.634740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306695e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.295113e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2191468.217175 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.081741e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.095942e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.835462e+05 │ │ │ │ Vprtstp: contraction number = 2.835462e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.130770 │ │ │ │ Vnewton: Attempting damping, relres = 0.556143 │ │ │ │ Vnewton: Damping accepted, relres = 0.130770 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.307700e-01 │ │ │ │ Vprtstp: contraction number = 1.307700e-01 │ │ │ │ Vnewton: Using errtol_s: 286578.355364 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.818556e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.086515e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.106806e+04 │ │ │ │ Vprtstp: contraction number = 5.106806e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.314467e-02 │ │ │ │ Vprtstp: contraction number = 1.769876e-01 │ │ │ │ Vnewton: Using errtol_s: 50720.810223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.231080e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.807486e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.199262e+04 │ │ │ │ Vprtstp: contraction number = 1.199262e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.100754e-03 │ │ │ │ Vprtstp: contraction number = 2.203857e-01 │ │ │ │ Vnewton: Using errtol_s: 11178.140515 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.638425e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.460933e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.172798e+03 │ │ │ │ Vprtstp: contraction number = 3.172798e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.305202e-03 │ │ │ │ Vprtstp: contraction number = 2.558841e-01 │ │ │ │ Vnewton: Using errtol_s: 2860.308039 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.055707e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010442e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.902300e+02 │ │ │ │ Vprtstp: contraction number = 8.902300e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.656064e-04 │ │ │ │ Vprtstp: contraction number = 2.801149e-01 │ │ │ │ Vnewton: Using errtol_s: 801.214793 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.046963e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.178053e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.587695e+02 │ │ │ │ Vprtstp: contraction number = 2.587695e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.062725e-04 │ │ │ │ Vprtstp: contraction number = 2.906745e-01 │ │ │ │ Vnewton: Using errtol_s: 232.892741 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188227e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.346239e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.672901e+01 │ │ │ │ Vprtstp: contraction number = 7.672901e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.151135e-05 │ │ │ │ Vprtstp: contraction number = 2.965147e-01 │ │ │ │ Vnewton: Using errtol_s: 69.056118 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.328918e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.514086e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.307099e+01 │ │ │ │ Vprtstp: contraction number = 2.307099e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.474878e-06 │ │ │ │ Vprtstp: contraction number = 3.006815e-01 │ │ │ │ Vnewton: Using errtol_s: 20.763894 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.476338e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.682080e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.011582e+00 │ │ │ │ Vprtstp: contraction number = 7.011582e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.879541e-06 │ │ │ │ Vprtstp: contraction number = 3.039133e-01 │ │ │ │ Vnewton: Using errtol_s: 6.310424 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.617488e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.850310e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.149903e+00 │ │ │ │ Vprtstp: contraction number = 2.149903e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.829299e-07 │ │ │ │ Vprtstp: contraction number = 3.066217e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.495864e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.556380e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.754426e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.818224e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -18361,17 +18361,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.760186349323E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566917500477E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282812157004E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.372590e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.379980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.325 │ │ │ │ Vpbe_ctor2: xkappa = 0.185636 │ │ │ │ @@ -18418,160 +18418,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0160678 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.894816 │ │ │ │ +Vacc_SASA: Time elapsed: 0.871280 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.869595e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.877604e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.386380e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.395760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.372250e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.696580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.992086e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.253286e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2243053.741102 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.068930e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.332908e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.528083e+05 │ │ │ │ Vprtstp: contraction number = 3.528083e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.155339 │ │ │ │ Vnewton: Attempting damping, relres = 0.568910 │ │ │ │ Vnewton: Damping accepted, relres = 0.155339 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.553392e-01 │ │ │ │ Vprtstp: contraction number = 1.553392e-01 │ │ │ │ Vnewton: Using errtol_s: 348434.112950 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.242933e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.536992e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.998444e+04 │ │ │ │ Vprtstp: contraction number = 6.998444e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.017800e-02 │ │ │ │ Vprtstp: contraction number = 1.942717e-01 │ │ │ │ Vnewton: Using errtol_s: 67690.878524 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.384276e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.711059e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.750872e+04 │ │ │ │ Vprtstp: contraction number = 1.750872e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.184752e-03 │ │ │ │ Vprtstp: contraction number = 2.380791e-01 │ │ │ │ Vnewton: Using errtol_s: 16115.784303 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.527293e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.884307e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.850206e+03 │ │ │ │ Vprtstp: contraction number = 4.850206e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.947538e-03 │ │ │ │ Vprtstp: contraction number = 2.710655e-01 │ │ │ │ Vnewton: Using errtol_s: 4368.432326 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.671533e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.056770e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.421336e+03 │ │ │ │ Vprtstp: contraction number = 1.421336e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.702989e-04 │ │ │ │ Vprtstp: contraction number = 2.928307e-01 │ │ │ │ Vnewton: Using errtol_s: 1279.211122 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.814447e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.231329e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.327691e+02 │ │ │ │ Vprtstp: contraction number = 4.327691e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.736439e-04 │ │ │ │ Vprtstp: contraction number = 3.044787e-01 │ │ │ │ Vnewton: Using errtol_s: 389.492590 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.955885e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.405969e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.351326e+02 │ │ │ │ Vprtstp: contraction number = 1.351326e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.422045e-05 │ │ │ │ Vprtstp: contraction number = 3.122508e-01 │ │ │ │ Vnewton: Using errtol_s: 121.619374 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.094862e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.579174e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.301940e+01 │ │ │ │ Vprtstp: contraction number = 4.301940e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.726105e-05 │ │ │ │ Vprtstp: contraction number = 3.183495e-01 │ │ │ │ Vnewton: Using errtol_s: 38.717465 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.235167e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.752468e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.392593e+01 │ │ │ │ Vprtstp: contraction number = 1.392593e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.587625e-06 │ │ │ │ Vprtstp: contraction number = 3.237129e-01 │ │ │ │ Vnewton: Using errtol_s: 12.533342 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.375983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.925999e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.570574e+00 │ │ │ │ Vprtstp: contraction number = 4.570574e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.833891e-06 │ │ │ │ Vprtstp: contraction number = 3.282059e-01 │ │ │ │ Vnewton: Using errtol_s: 4.113517 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.517315e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.099194e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.517041e+00 │ │ │ │ Vprtstp: contraction number = 1.517041e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.086957e-07 │ │ │ │ Vprtstp: contraction number = 3.319148e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.633339e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.695859e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.983978e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.049233e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -18581,17 +18581,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.747143888593E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951532357684E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475121024223E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.348710e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.355330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -18618,151 +18618,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.310335 │ │ │ │ +Vacc_SASA: Time elapsed: 0.303925 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.063540e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.190820e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.387750e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.359390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.295200e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.668990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.056852e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.670248e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 651047.049796 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.134052e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.750073e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.764819e+04 │ │ │ │ Vprtstp: contraction number = 8.764819e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.129306 │ │ │ │ Vnewton: Attempting damping, relres = 0.558102 │ │ │ │ Vnewton: Damping accepted, relres = 0.129306 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.293065e-01 │ │ │ │ Vprtstp: contraction number = 1.293065e-01 │ │ │ │ Vnewton: Using errtol_s: 84184.596649 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.308334e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.940803e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.647823e+04 │ │ │ │ Vprtstp: contraction number = 1.647823e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.304786e-02 │ │ │ │ Vprtstp: contraction number = 1.782421e-01 │ │ │ │ Vnewton: Using errtol_s: 15005.240621 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.451285e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.096623e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.775815e+03 │ │ │ │ Vprtstp: contraction number = 3.775815e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.220699e-03 │ │ │ │ Vprtstp: contraction number = 2.265156e-01 │ │ │ │ Vnewton: Using errtol_s: 3398.920946 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.592034e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.254563e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.635341e+02 │ │ │ │ Vprtstp: contraction number = 9.635341e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.331987e-03 │ │ │ │ Vprtstp: contraction number = 2.551357e-01 │ │ │ │ Vnewton: Using errtol_s: 867.186094 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.733114e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.411405e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.598155e+02 │ │ │ │ Vprtstp: contraction number = 2.598155e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.591665e-04 │ │ │ │ Vprtstp: contraction number = 2.696472e-01 │ │ │ │ Vnewton: Using errtol_s: 233.834272 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.874112e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.570467e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.221080e+01 │ │ │ │ Vprtstp: contraction number = 7.221080e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 9.982341e-05 │ │ │ │ Vprtstp: contraction number = 2.779308e-01 │ │ │ │ Vnewton: Using errtol_s: 64.989737 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.015901e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.729041e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.048426e+01 │ │ │ │ Vprtstp: contraction number = 2.048426e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.831721e-05 │ │ │ │ Vprtstp: contraction number = 2.836731e-01 │ │ │ │ Vnewton: Using errtol_s: 18.435838 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.157762e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.886864e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.905744e+00 │ │ │ │ Vprtstp: contraction number = 5.905744e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.164034e-06 │ │ │ │ Vprtstp: contraction number = 2.883064e-01 │ │ │ │ Vnewton: Using errtol_s: 5.315170 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.298949e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.045454e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.726219e+00 │ │ │ │ Vprtstp: contraction number = 1.726219e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.386306e-06 │ │ │ │ Vprtstp: contraction number = 2.922949e-01 │ │ │ │ Vnewton: Using errtol_s: 1.553597 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.439117e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.203006e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.103781e-01 │ │ │ │ Vprtstp: contraction number = 5.103781e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.055409e-07 │ │ │ │ Vprtstp: contraction number = 2.956624e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.490210e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.551789e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.653197e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.717320e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -18772,17 +18772,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.829422361663E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.830982023597E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.413426199926E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.397290e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.404350e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.325 │ │ │ │ Vpbe_ctor2: xkappa = 0.185636 │ │ │ │ @@ -18829,160 +18829,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00263165 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.309610 │ │ │ │ +Vacc_SASA: Time elapsed: 0.302694 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.681640e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.914980e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.378730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.361160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.343260e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.801000e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.712224e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.494367e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 676873.511924 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.789151e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.573791e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.089080e+05 │ │ │ │ Vprtstp: contraction number = 1.089080e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.152173 │ │ │ │ Vnewton: Attempting damping, relres = 0.570027 │ │ │ │ Vnewton: Damping accepted, relres = 0.152173 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.521734e-01 │ │ │ │ Vprtstp: contraction number = 1.521734e-01 │ │ │ │ Vnewton: Using errtol_s: 103002.176045 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.960886e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.763889e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.224678e+04 │ │ │ │ Vprtstp: contraction number = 2.224678e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.982235e-02 │ │ │ │ Vprtstp: contraction number = 1.959760e-01 │ │ │ │ Vnewton: Using errtol_s: 20185.957327 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.101407e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.919159e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.434268e+03 │ │ │ │ Vprtstp: contraction number = 5.434268e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.226895e-03 │ │ │ │ Vprtstp: contraction number = 2.423315e-01 │ │ │ │ Vnewton: Using errtol_s: 4891.693818 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.241013e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.077421e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.431460e+03 │ │ │ │ Vprtstp: contraction number = 1.431460e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.903352e-03 │ │ │ │ Vprtstp: contraction number = 2.633707e-01 │ │ │ │ Vnewton: Using errtol_s: 1288.328715 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.381537e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.233844e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.959616e+02 │ │ │ │ Vprtstp: contraction number = 3.959616e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.264891e-04 │ │ │ │ Vprtstp: contraction number = 2.766115e-01 │ │ │ │ Vnewton: Using errtol_s: 356.366550 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.520380e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.390631e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.131619e+02 │ │ │ │ Vprtstp: contraction number = 1.131619e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.504650e-04 │ │ │ │ Vprtstp: contraction number = 2.857895e-01 │ │ │ │ Vnewton: Using errtol_s: 101.845804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.658834e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.546102e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.312512e+01 │ │ │ │ Vprtstp: contraction number = 3.312512e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.404458e-05 │ │ │ │ Vprtstp: contraction number = 2.927230e-01 │ │ │ │ Vnewton: Using errtol_s: 29.812613 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.798335e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.702423e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.896913e+00 │ │ │ │ Vprtstp: contraction number = 9.896913e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.315936e-05 │ │ │ │ Vprtstp: contraction number = 2.987736e-01 │ │ │ │ Vnewton: Using errtol_s: 8.907223 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.936908e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.858813e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.015572e+00 │ │ │ │ Vprtstp: contraction number = 3.015572e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.009634e-06 │ │ │ │ Vprtstp: contraction number = 3.046983e-01 │ │ │ │ Vnewton: Using errtol_s: 2.714015 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.076814e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.016412e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.348798e-01 │ │ │ │ Vprtstp: contraction number = 9.348798e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.243056e-06 │ │ │ │ Vprtstp: contraction number = 3.100174e-01 │ │ │ │ Vnewton: Using errtol_s: 0.841392 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.217186e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.173989e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.940173e-01 │ │ │ │ Vprtstp: contraction number = 2.940173e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.909380e-07 │ │ │ │ Vprtstp: contraction number = 3.144974e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.612224e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.674257e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.801205e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.866513e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -18992,17 +18992,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.821085170706E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.063512300781E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.029703319589E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.391980e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.409290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -19029,162 +19029,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.490851 │ │ │ │ +Vacc_SASA: Time elapsed: 0.484136 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.075050e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.085354e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.370870e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.348730e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.244010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.762560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.777621e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.757284e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1509004.572180 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.854423e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.836546e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.143767e+05 │ │ │ │ Vprtstp: contraction number = 2.143767e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.173607 │ │ │ │ Vnewton: Attempting damping, relres = 0.564075 │ │ │ │ Vnewton: Damping accepted, relres = 0.173607 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.736069e-01 │ │ │ │ Vprtstp: contraction number = 1.736069e-01 │ │ │ │ Vnewton: Using errtol_s: 261973.588074 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.027121e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.025450e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.041338e+04 │ │ │ │ Vprtstp: contraction number = 4.041338e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.283481e-02 │ │ │ │ Vprtstp: contraction number = 1.891331e-01 │ │ │ │ Vnewton: Using errtol_s: 49547.880487 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.166659e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.188827e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.021814e+04 │ │ │ │ Vprtstp: contraction number = 1.021814e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.057379e-03 │ │ │ │ Vprtstp: contraction number = 2.149359e-01 │ │ │ │ Vnewton: Using errtol_s: 10649.617829 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.307722e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.349554e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.824157e+03 │ │ │ │ Vprtstp: contraction number = 2.824157e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.703748e-03 │ │ │ │ Vprtstp: contraction number = 2.414137e-01 │ │ │ │ Vnewton: Using errtol_s: 2570.963479 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.446784e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.506568e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.035455e+02 │ │ │ │ Vprtstp: contraction number = 8.035455e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.792870e-04 │ │ │ │ Vprtstp: contraction number = 2.813133e-01 │ │ │ │ Vnewton: Using errtol_s: 723.246303 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.586876e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.662339e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.394281e+02 │ │ │ │ Vprtstp: contraction number = 2.394281e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.427997e-04 │ │ │ │ Vprtstp: contraction number = 2.979420e-01 │ │ │ │ Vnewton: Using errtol_s: 215.485426 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.726487e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.825631e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.242618e+01 │ │ │ │ Vprtstp: contraction number = 7.242618e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.319641e-05 │ │ │ │ Vprtstp: contraction number = 3.024964e-01 │ │ │ │ Vnewton: Using errtol_s: 65.183576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.865367e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.985884e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.205930e+01 │ │ │ │ Vprtstp: contraction number = 2.205930e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.315660e-05 │ │ │ │ Vprtstp: contraction number = 3.045762e-01 │ │ │ │ Vnewton: Using errtol_s: 19.853369 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.004490e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014684e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.747262e+00 │ │ │ │ Vprtstp: contraction number = 6.747262e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.024200e-06 │ │ │ │ Vprtstp: contraction number = 3.058693e-01 │ │ │ │ Vnewton: Using errtol_s: 6.072536 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.143506e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.030655e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.069809e+00 │ │ │ │ Vprtstp: contraction number = 2.069809e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.234475e-06 │ │ │ │ Vprtstp: contraction number = 3.067629e-01 │ │ │ │ Vnewton: Using errtol_s: 1.862829 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.283173e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.046788e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.363291e-01 │ │ │ │ Vprtstp: contraction number = 6.363291e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.795192e-07 │ │ │ │ Vprtstp: contraction number = 3.074337e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.610947e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.671937e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.833836e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.898860e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19194,17 +19194,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.932901630700E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.873629019341E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.358152654068E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.385930e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.325 │ │ │ │ Vpbe_ctor2: xkappa = 0.185636 │ │ │ │ @@ -19251,160 +19251,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00380956 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.496104 │ │ │ │ +Vacc_SASA: Time elapsed: 0.487504 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.292581e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.322600e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.367450e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.416690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.315610e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.846320e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.595098e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.080641e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1539412.424593 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.671868e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.088679e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.684916e+05 │ │ │ │ Vprtstp: contraction number = 2.684916e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.201455 │ │ │ │ Vnewton: Attempting damping, relres = 0.578827 │ │ │ │ Vnewton: Damping accepted, relres = 0.201455 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.014550e-01 │ │ │ │ Vprtstp: contraction number = 2.014550e-01 │ │ │ │ Vnewton: Using errtol_s: 310122.358535 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.842919e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108118e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.524646e+04 │ │ │ │ Vprtstp: contraction number = 5.524646e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 4.083558e-02 │ │ │ │ Vprtstp: contraction number = 2.027032e-01 │ │ │ │ Vnewton: Using errtol_s: 62862.800070 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.982859e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.125011e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.470940e+04 │ │ │ │ Vprtstp: contraction number = 1.470940e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.510864e-03 │ │ │ │ Vprtstp: contraction number = 2.329063e-01 │ │ │ │ Vnewton: Using errtol_s: 14641.142976 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.012246e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.141496e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.258026e+03 │ │ │ │ Vprtstp: contraction number = 4.258026e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.506079e-03 │ │ │ │ Vprtstp: contraction number = 2.634965e-01 │ │ │ │ Vnewton: Using errtol_s: 3857.889813 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026217e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.157790e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.281004e+03 │ │ │ │ Vprtstp: contraction number = 1.281004e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.489530e-04 │ │ │ │ Vprtstp: contraction number = 2.988545e-01 │ │ │ │ Vnewton: Using errtol_s: 1152.947571 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040203e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.174180e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.026096e+02 │ │ │ │ Vprtstp: contraction number = 4.026096e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.353814e-04 │ │ │ │ Vprtstp: contraction number = 3.142806e-01 │ │ │ │ Vnewton: Using errtol_s: 362.348997 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.054080e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.190455e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.290278e+02 │ │ │ │ Vprtstp: contraction number = 1.290278e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.543469e-05 │ │ │ │ Vprtstp: contraction number = 3.204786e-01 │ │ │ │ Vnewton: Using errtol_s: 116.125091 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067970e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.206557e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.187301e+01 │ │ │ │ Vprtstp: contraction number = 4.187301e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.448058e-05 │ │ │ │ Vprtstp: contraction number = 3.245269e-01 │ │ │ │ Vnewton: Using errtol_s: 37.685715 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.081747e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.222966e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.372141e+01 │ │ │ │ Vprtstp: contraction number = 1.372141e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.022069e-06 │ │ │ │ Vprtstp: contraction number = 3.276911e-01 │ │ │ │ Vnewton: Using errtol_s: 12.349273 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.095710e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.239233e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.531250e+00 │ │ │ │ Vprtstp: contraction number = 4.531250e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.649144e-06 │ │ │ │ Vprtstp: contraction number = 3.302320e-01 │ │ │ │ Vnewton: Using errtol_s: 4.078125 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109785e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.255340e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.505606e+00 │ │ │ │ Vprtstp: contraction number = 1.505606e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.802356e-07 │ │ │ │ Vprtstp: contraction number = 3.322717e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.608911e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.669976e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.876976e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.943411e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19414,29 +19414,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.922197679692E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135367311591E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066685879920E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.375180e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.377830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.149669e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.298144e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:52:27 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:56:29 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -19706,151 +19706,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.903084 │ │ │ │ +Vacc_SASA: Time elapsed: 0.884512 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.617216e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.584941e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.369800e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.359760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.271830e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.814960e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.311029e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.316461e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2152094.716706 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.080086e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.109366e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.782066e+05 │ │ │ │ Vprtstp: contraction number = 2.782066e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.128497 │ │ │ │ Vnewton: Attempting damping, relres = 0.555913 │ │ │ │ Vnewton: Damping accepted, relres = 0.128497 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.284973e-01 │ │ │ │ Vprtstp: contraction number = 1.284973e-01 │ │ │ │ Vnewton: Using errtol_s: 276538.353939 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.822222e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.074767e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.023327e+04 │ │ │ │ Vprtstp: contraction number = 5.023327e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.262924e-02 │ │ │ │ Vprtstp: contraction number = 1.761067e-01 │ │ │ │ Vnewton: Using errtol_s: 48700.264198 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.231559e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.755424e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.183043e+04 │ │ │ │ Vprtstp: contraction number = 1.183043e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.048628e-03 │ │ │ │ Vprtstp: contraction number = 2.231020e-01 │ │ │ │ Vnewton: Using errtol_s: 10865.126461 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.643454e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.444810e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.142996e+03 │ │ │ │ Vprtstp: contraction number = 3.142996e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.315159e-03 │ │ │ │ Vprtstp: contraction number = 2.604983e-01 │ │ │ │ Vnewton: Using errtol_s: 2830.346955 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.065656e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.014041e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.861041e+02 │ │ │ │ Vprtstp: contraction number = 8.861041e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.705677e-04 │ │ │ │ Vprtstp: contraction number = 2.817665e-01 │ │ │ │ Vnewton: Using errtol_s: 797.496893 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047622e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.183842e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.579465e+02 │ │ │ │ Vprtstp: contraction number = 2.579465e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.078726e-04 │ │ │ │ Vprtstp: contraction number = 2.911008e-01 │ │ │ │ Vnewton: Using errtol_s: 232.151972 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188671e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.350053e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.653069e+01 │ │ │ │ Vprtstp: contraction number = 7.653069e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.200493e-05 │ │ │ │ Vprtstp: contraction number = 2.966920e-01 │ │ │ │ Vnewton: Using errtol_s: 68.877633 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.331326e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.517354e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.301874e+01 │ │ │ │ Vprtstp: contraction number = 2.301874e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.626375e-06 │ │ │ │ Vprtstp: contraction number = 3.007779e-01 │ │ │ │ Vnewton: Using errtol_s: 20.716870 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.472120e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.687996e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.996910e+00 │ │ │ │ Vprtstp: contraction number = 6.996910e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.926088e-06 │ │ │ │ Vprtstp: contraction number = 3.039658e-01 │ │ │ │ Vnewton: Using errtol_s: 6.297219 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.613583e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.852382e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.145621e+00 │ │ │ │ Vprtstp: contraction number = 2.145621e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 8.972926e-07 │ │ │ │ Vprtstp: contraction number = 3.066526e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.491898e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.553208e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.753233e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.818712e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -19860,17 +19860,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.527227679472E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566736557939E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282759892518E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.387930e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.386680e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.4 │ │ │ │ Vpbe_ctor2: xkappa = 0.205945 │ │ │ │ @@ -19917,160 +19917,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0146503 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.880708 │ │ │ │ +Vacc_SASA: Time elapsed: 0.880780 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.925141e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.885646e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.369370e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.420330e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.273790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.703530e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.993284e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.255277e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2200727.622444 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.069995e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.333470e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.461855e+05 │ │ │ │ Vprtstp: contraction number = 3.461855e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153259 │ │ │ │ Vnewton: Attempting damping, relres = 0.568747 │ │ │ │ Vnewton: Damping accepted, relres = 0.153259 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.532593e-01 │ │ │ │ Vprtstp: contraction number = 1.532593e-01 │ │ │ │ Vnewton: Using errtol_s: 337281.994589 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.242647e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.528712e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.878964e+04 │ │ │ │ Vprtstp: contraction number = 6.878964e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.969348e-02 │ │ │ │ Vprtstp: contraction number = 1.937467e-01 │ │ │ │ Vnewton: Using errtol_s: 65347.260012 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.384567e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.699908e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.723760e+04 │ │ │ │ Vprtstp: contraction number = 1.723760e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.139932e-03 │ │ │ │ Vprtstp: contraction number = 2.404545e-01 │ │ │ │ Vnewton: Using errtol_s: 15713.045576 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.525230e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.872253e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.791285e+03 │ │ │ │ Vprtstp: contraction number = 4.791285e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.959957e-03 │ │ │ │ Vprtstp: contraction number = 2.745064e-01 │ │ │ │ Vnewton: Using errtol_s: 4313.331787 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.665921e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.038870e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.410218e+03 │ │ │ │ Vprtstp: contraction number = 1.410218e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.767187e-04 │ │ │ │ Vprtstp: contraction number = 2.942507e-01 │ │ │ │ Vnewton: Using errtol_s: 1269.200854 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.808110e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.210067e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.302153e+02 │ │ │ │ Vprtstp: contraction number = 4.302153e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.759391e-04 │ │ │ │ Vprtstp: contraction number = 3.050692e-01 │ │ │ │ Vnewton: Using errtol_s: 387.194118 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.950264e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.380622e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.344961e+02 │ │ │ │ Vprtstp: contraction number = 1.344961e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.500295e-05 │ │ │ │ Vprtstp: contraction number = 3.126248e-01 │ │ │ │ Vnewton: Using errtol_s: 121.046502 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.092068e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.554889e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.285292e+01 │ │ │ │ Vprtstp: contraction number = 4.285292e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.752495e-05 │ │ │ │ Vprtstp: contraction number = 3.186183e-01 │ │ │ │ Vnewton: Using errtol_s: 38.567632 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.232829e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.729299e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.387951e+01 │ │ │ │ Vprtstp: contraction number = 1.387951e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.676104e-06 │ │ │ │ Vprtstp: contraction number = 3.238871e-01 │ │ │ │ Vnewton: Using errtol_s: 12.491560 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.375613e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.903183e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.556799e+00 │ │ │ │ Vprtstp: contraction number = 4.556799e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.863529e-06 │ │ │ │ Vprtstp: contraction number = 3.283112e-01 │ │ │ │ Vnewton: Using errtol_s: 4.101119 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.516912e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.077004e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.512689e+00 │ │ │ │ Vprtstp: contraction number = 1.512689e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.186225e-07 │ │ │ │ Vprtstp: contraction number = 3.319630e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.632711e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.694001e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.963772e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.029219e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -20080,17 +20080,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.514675732237E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951351537778E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475068873214E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.351330e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.377980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -20117,151 +20117,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.306627 │ │ │ │ +Vacc_SASA: Time elapsed: 0.309056 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.059250e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.267110e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.354550e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.391150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.259170e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.869990e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.055656e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.662903e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 642085.519744 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.133029e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.743523e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.625055e+04 │ │ │ │ Vprtstp: contraction number = 8.625055e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.128656 │ │ │ │ Vnewton: Attempting damping, relres = 0.557901 │ │ │ │ Vnewton: Damping accepted, relres = 0.128656 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.286562e-01 │ │ │ │ Vprtstp: contraction number = 1.286562e-01 │ │ │ │ Vnewton: Using errtol_s: 82608.252849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.306034e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.938767e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.628118e+04 │ │ │ │ Vprtstp: contraction number = 1.628118e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.304734e-02 │ │ │ │ Vprtstp: contraction number = 1.791390e-01 │ │ │ │ Vnewton: Using errtol_s: 14798.361839 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.447630e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.102079e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.747143e+03 │ │ │ │ Vprtstp: contraction number = 3.747143e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.253150e-03 │ │ │ │ Vprtstp: contraction number = 2.279287e-01 │ │ │ │ Vnewton: Using errtol_s: 3372.971529 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.588995e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.262780e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.592593e+02 │ │ │ │ Vprtstp: contraction number = 9.592593e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.344585e-03 │ │ │ │ Vprtstp: contraction number = 2.559579e-01 │ │ │ │ Vnewton: Using errtol_s: 863.338654 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.728888e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.423705e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.591357e+02 │ │ │ │ Vprtstp: contraction number = 2.591357e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.632264e-04 │ │ │ │ Vprtstp: contraction number = 2.701401e-01 │ │ │ │ Vnewton: Using errtol_s: 233.222386 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.870854e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.583259e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.209902e+01 │ │ │ │ Vprtstp: contraction number = 7.209902e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.010600e-04 │ │ │ │ Vprtstp: contraction number = 2.782286e-01 │ │ │ │ Vnewton: Using errtol_s: 64.889141 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.017404e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.744566e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.046499e+01 │ │ │ │ Vprtstp: contraction number = 2.046499e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.868541e-05 │ │ │ │ Vprtstp: contraction number = 2.838455e-01 │ │ │ │ Vnewton: Using errtol_s: 18.418489 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.158398e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.908288e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.902147e+00 │ │ │ │ Vprtstp: contraction number = 5.902147e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.272935e-06 │ │ │ │ Vprtstp: contraction number = 2.884022e-01 │ │ │ │ Vnewton: Using errtol_s: 5.311932 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.299457e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.069838e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.725476e+00 │ │ │ │ Vprtstp: contraction number = 1.725476e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.418570e-06 │ │ │ │ Vprtstp: contraction number = 2.923472e-01 │ │ │ │ Vnewton: Using errtol_s: 1.552929 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.440559e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.231461e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.102067e-01 │ │ │ │ Vprtstp: contraction number = 5.102067e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.151478e-07 │ │ │ │ Vprtstp: contraction number = 2.956904e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.492484e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.553615e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.694710e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.761146e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -20271,17 +20271,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.836319274152E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.830295346260E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.413099848091E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.415060e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.423630e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.4 │ │ │ │ Vpbe_ctor2: xkappa = 0.205945 │ │ │ │ @@ -20328,160 +20328,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00207488 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.306461 │ │ │ │ +Vacc_SASA: Time elapsed: 0.305114 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.753010e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 9.004610e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.378550e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.399850e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.309240e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.844400e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.713906e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.530790e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 667195.414501 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.791402e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.611100e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.070575e+05 │ │ │ │ Vprtstp: contraction number = 1.070575e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.151420 │ │ │ │ Vnewton: Attempting damping, relres = 0.569765 │ │ │ │ Vnewton: Damping accepted, relres = 0.151420 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.514203e-01 │ │ │ │ Vprtstp: contraction number = 1.514203e-01 │ │ │ │ Vnewton: Using errtol_s: 101026.941605 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.964066e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.809071e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.191459e+04 │ │ │ │ Vprtstp: contraction number = 2.191459e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.976400e-02 │ │ │ │ Vprtstp: contraction number = 1.965654e-01 │ │ │ │ Vnewton: Using errtol_s: 19858.405232 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.104329e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.971467e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.366842e+03 │ │ │ │ Vprtstp: contraction number = 5.366842e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.240542e-03 │ │ │ │ Vprtstp: contraction number = 2.432651e-01 │ │ │ │ Vnewton: Using errtol_s: 4830.856278 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.245658e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.132725e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.417443e+03 │ │ │ │ Vprtstp: contraction number = 1.417443e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.912054e-03 │ │ │ │ Vprtstp: contraction number = 2.640761e-01 │ │ │ │ Vnewton: Using errtol_s: 1275.713735 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.390476e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.295248e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.929589e+02 │ │ │ │ Vprtstp: contraction number = 3.929589e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.300759e-04 │ │ │ │ Vprtstp: contraction number = 2.772285e-01 │ │ │ │ Vnewton: Using errtol_s: 353.664179 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.528284e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.457145e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.125096e+02 │ │ │ │ Vprtstp: contraction number = 1.125096e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.517678e-04 │ │ │ │ Vprtstp: contraction number = 2.863133e-01 │ │ │ │ Vnewton: Using errtol_s: 101.258773 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.669968e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.621930e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.298207e+01 │ │ │ │ Vprtstp: contraction number = 3.298207e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.449052e-05 │ │ │ │ Vprtstp: contraction number = 2.931486e-01 │ │ │ │ Vnewton: Using errtol_s: 29.683870 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.810746e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.784748e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.865288e+00 │ │ │ │ Vprtstp: contraction number = 9.865288e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.330759e-05 │ │ │ │ Vprtstp: contraction number = 2.991106e-01 │ │ │ │ Vnewton: Using errtol_s: 8.878760 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.950546e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.947894e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.008494e+00 │ │ │ │ Vprtstp: contraction number = 3.008494e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.058248e-06 │ │ │ │ Vprtstp: contraction number = 3.049575e-01 │ │ │ │ Vnewton: Using errtol_s: 2.707645 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.091593e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.111158e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.332652e-01 │ │ │ │ Vprtstp: contraction number = 9.332652e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.258910e-06 │ │ │ │ Vprtstp: contraction number = 3.102101e-01 │ │ │ │ Vnewton: Using errtol_s: 0.839939 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.231177e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.274017e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.936402e-01 │ │ │ │ Vprtstp: contraction number = 2.936402e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.961001e-07 │ │ │ │ Vprtstp: contraction number = 3.146374e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624575e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.686320e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.872993e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.939346e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -20491,15 +20491,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.827843084018E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.062828524213E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.029378526105E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.383720e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.407200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -20528,162 +20528,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.499269 │ │ │ │ +Vacc_SASA: Time elapsed: 0.482082 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.092656e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.084567e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.399790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.311140e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.740500e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.796795e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.861172e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1471319.117079 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.875311e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.941813e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.089888e+05 │ │ │ │ Vprtstp: contraction number = 2.089888e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.165808 │ │ │ │ Vnewton: Attempting damping, relres = 0.563564 │ │ │ │ Vnewton: Damping accepted, relres = 0.165808 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.658082e-01 │ │ │ │ Vprtstp: contraction number = 1.658082e-01 │ │ │ │ Vnewton: Using errtol_s: 243956.756463 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.049517e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.135581e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.927783e+04 │ │ │ │ Vprtstp: contraction number = 3.927783e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.048323e-02 │ │ │ │ Vprtstp: contraction number = 1.838464e-01 │ │ │ │ Vnewton: Using errtol_s: 44850.563282 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.192551e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.302271e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.923271e+03 │ │ │ │ Vprtstp: contraction number = 9.923271e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.609400e-03 │ │ │ │ Vprtstp: contraction number = 2.168208e-01 │ │ │ │ Vnewton: Using errtol_s: 9724.536863 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.333198e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.464356e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.744656e+03 │ │ │ │ Vprtstp: contraction number = 2.744656e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.685430e-03 │ │ │ │ Vprtstp: contraction number = 2.550050e-01 │ │ │ │ Vnewton: Using errtol_s: 2479.805360 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.475659e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.624290e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.927726e+02 │ │ │ │ Vprtstp: contraction number = 7.927726e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.849448e-04 │ │ │ │ Vprtstp: contraction number = 2.877276e-01 │ │ │ │ Vnewton: Using errtol_s: 713.508521 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.616769e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.785693e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.371902e+02 │ │ │ │ Vprtstp: contraction number = 2.371902e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.450884e-04 │ │ │ │ Vprtstp: contraction number = 2.991854e-01 │ │ │ │ Vnewton: Using errtol_s: 213.471337 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.759552e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.943513e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.181744e+01 │ │ │ │ Vprtstp: contraction number = 7.181744e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.393045e-05 │ │ │ │ Vprtstp: contraction number = 3.027840e-01 │ │ │ │ Vnewton: Using errtol_s: 64.635706 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.901889e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.010515e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.188269e+01 │ │ │ │ Vprtstp: contraction number = 2.188269e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.338555e-05 │ │ │ │ Vprtstp: contraction number = 3.046988e-01 │ │ │ │ Vnewton: Using errtol_s: 19.694422 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.042733e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026534e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.694672e+00 │ │ │ │ Vprtstp: contraction number = 6.694672e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.095104e-06 │ │ │ │ Vprtstp: contraction number = 3.059346e-01 │ │ │ │ Vnewton: Using errtol_s: 6.025205 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.181066e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.042108e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.053963e+00 │ │ │ │ Vprtstp: contraction number = 2.053963e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.256401e-06 │ │ │ │ Vprtstp: contraction number = 3.068056e-01 │ │ │ │ Vnewton: Using errtol_s: 1.848567 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.322038e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.058126e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.315192e-01 │ │ │ │ Vprtstp: contraction number = 6.315192e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.862977e-07 │ │ │ │ Vprtstp: contraction number = 3.074637e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.633360e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.695744e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.844160e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.909170e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -20693,17 +20693,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.577297422192E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.873373018987E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.357495652952E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.402270e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403810e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.4 │ │ │ │ Vpbe_ctor2: xkappa = 0.205945 │ │ │ │ @@ -20750,160 +20750,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00276825 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.493450 │ │ │ │ +Vacc_SASA: Time elapsed: 0.472157 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.293154e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.295610e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.359700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.363200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.269490e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.595640e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.636932e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.091491e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1499432.159358 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.715623e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.099469e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.618100e+05 │ │ │ │ Vprtstp: contraction number = 2.618100e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.194105 │ │ │ │ Vnewton: Attempting damping, relres = 0.578438 │ │ │ │ Vnewton: Damping accepted, relres = 0.194105 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.941047e-01 │ │ │ │ Vprtstp: contraction number = 1.941047e-01 │ │ │ │ Vnewton: Using errtol_s: 291046.875702 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.889936e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.119241e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.372130e+04 │ │ │ │ Vprtstp: contraction number = 5.372130e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.856178e-02 │ │ │ │ Vprtstp: contraction number = 1.986648e-01 │ │ │ │ Vnewton: Using errtol_s: 57820.773992 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.003278e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.136081e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.429172e+04 │ │ │ │ Vprtstp: contraction number = 1.429172e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 9.088822e-03 │ │ │ │ Vprtstp: contraction number = 2.356951e-01 │ │ │ │ Vnewton: Using errtol_s: 13628.071398 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.017407e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.152623e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.146951e+03 │ │ │ │ Vprtstp: contraction number = 4.146951e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.494923e-03 │ │ │ │ Vprtstp: contraction number = 2.745046e-01 │ │ │ │ Vnewton: Using errtol_s: 3740.967765 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.031564e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.168775e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.262928e+03 │ │ │ │ Vprtstp: contraction number = 1.262928e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.580508e-04 │ │ │ │ Vprtstp: contraction number = 3.038374e-01 │ │ │ │ Vnewton: Using errtol_s: 1136.645774 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045879e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.185521e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.984728e+02 │ │ │ │ Vprtstp: contraction number = 3.984728e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.391744e-04 │ │ │ │ Vprtstp: contraction number = 3.155124e-01 │ │ │ │ Vnewton: Using errtol_s: 358.625830 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.060307e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.201944e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.279297e+02 │ │ │ │ Vprtstp: contraction number = 1.279297e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.678689e-05 │ │ │ │ Vprtstp: contraction number = 3.210497e-01 │ │ │ │ Vnewton: Using errtol_s: 115.136728 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.074877e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.218193e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.156614e+01 │ │ │ │ Vprtstp: contraction number = 4.156614e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.494913e-05 │ │ │ │ Vprtstp: contraction number = 3.249140e-01 │ │ │ │ Vnewton: Using errtol_s: 37.409531 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.089257e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.234571e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.363199e+01 │ │ │ │ Vprtstp: contraction number = 1.363199e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.182289e-06 │ │ │ │ Vprtstp: contraction number = 3.279589e-01 │ │ │ │ Vnewton: Using errtol_s: 12.268788 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103534e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.250626e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.504209e+00 │ │ │ │ Vprtstp: contraction number = 4.504209e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.703549e-06 │ │ │ │ Vprtstp: contraction number = 3.304147e-01 │ │ │ │ Vnewton: Using errtol_s: 4.053788 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.118028e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.266792e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.497181e+00 │ │ │ │ Vprtstp: contraction number = 1.497181e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 8.986490e-07 │ │ │ │ Vprtstp: contraction number = 3.323961e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.655060e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.716166e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.881170e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.944617e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -20913,29 +20913,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.566888561677E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.135111393094E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066620211340E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.381950e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.429800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.158647e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.308657e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:53:22 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 22:00:03 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -21205,151 +21205,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.894734 │ │ │ │ +Vacc_SASA: Time elapsed: 0.879185 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.624556e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.582148e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.370170e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.376370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.421720e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.736150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.333736e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306593e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2117021.813584 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.127760e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.114744e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.733993e+05 │ │ │ │ Vprtstp: contraction number = 2.733993e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.126346 │ │ │ │ Vnewton: Attempting damping, relres = 0.555677 │ │ │ │ Vnewton: Damping accepted, relres = 0.126346 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.263459e-01 │ │ │ │ Vprtstp: contraction number = 1.263459e-01 │ │ │ │ Vnewton: Using errtol_s: 267477.104304 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.874408e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.184661e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.948638e+04 │ │ │ │ Vprtstp: contraction number = 4.948638e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.218275e-02 │ │ │ │ Vprtstp: contraction number = 1.755716e-01 │ │ │ │ Vnewton: Using errtol_s: 46961.371226 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.377687e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.925078e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.168877e+04 │ │ │ │ Vprtstp: contraction number = 1.168877e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.021324e-03 │ │ │ │ Vprtstp: contraction number = 2.263616e-01 │ │ │ │ Vnewton: Using errtol_s: 10630.252373 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.835541e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.679417e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.120176e+03 │ │ │ │ Vprtstp: contraction number = 3.120176e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.326708e-03 │ │ │ │ Vprtstp: contraction number = 2.642148e-01 │ │ │ │ Vnewton: Using errtol_s: 2808.669489 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.288608e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045685e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.828690e+02 │ │ │ │ Vprtstp: contraction number = 8.828690e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.753310e-04 │ │ │ │ Vprtstp: contraction number = 2.829040e-01 │ │ │ │ Vnewton: Using errtol_s: 794.583820 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.072213e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.221727e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.573077e+02 │ │ │ │ Vprtstp: contraction number = 2.573077e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.093881e-04 │ │ │ │ Vprtstp: contraction number = 2.914445e-01 │ │ │ │ Vnewton: Using errtol_s: 231.577068 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.215691e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.398286e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.638166e+01 │ │ │ │ Vprtstp: contraction number = 7.638166e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.247180e-05 │ │ │ │ Vprtstp: contraction number = 2.968494e-01 │ │ │ │ Vnewton: Using errtol_s: 68.743505 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.356799e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.573991e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.298047e+01 │ │ │ │ Vprtstp: contraction number = 2.298047e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.769584e-06 │ │ │ │ Vprtstp: contraction number = 3.008636e-01 │ │ │ │ Vnewton: Using errtol_s: 20.682422 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.498465e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.744225e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.986364e+00 │ │ │ │ Vprtstp: contraction number = 6.986364e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.970082e-06 │ │ │ │ Vprtstp: contraction number = 3.040131e-01 │ │ │ │ Vnewton: Using errtol_s: 6.287728 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.642428e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.916551e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.142572e+00 │ │ │ │ Vprtstp: contraction number = 2.142572e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.108619e-07 │ │ │ │ Vprtstp: contraction number = 3.066791e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.517717e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.580470e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.825744e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.890878e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21359,15 +21359,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.282938613188E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566547142826E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282703574681E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.363780e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.371700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ @@ -21416,160 +21416,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0133684 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.886086 │ │ │ │ +Vacc_SASA: Time elapsed: 0.863577 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.867509e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.862724e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.450850e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.371440e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.346590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.655520e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.016734e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.322915e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2163354.564593 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.094506e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.403059e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.401998e+05 │ │ │ │ Vprtstp: contraction number = 3.401998e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.151250 │ │ │ │ Vnewton: Attempting damping, relres = 0.568556 │ │ │ │ Vnewton: Damping accepted, relres = 0.151250 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.512496e-01 │ │ │ │ Vprtstp: contraction number = 1.512496e-01 │ │ │ │ Vnewton: Using errtol_s: 327206.577099 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.269254e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.604339e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.770698e+04 │ │ │ │ Vprtstp: contraction number = 6.770698e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.926462e-02 │ │ │ │ Vprtstp: contraction number = 1.934856e-01 │ │ │ │ Vnewton: Using errtol_s: 63309.757927 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.412067e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.775156e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.699399e+04 │ │ │ │ Vprtstp: contraction number = 1.699399e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.115656e-03 │ │ │ │ Vprtstp: contraction number = 2.431487e-01 │ │ │ │ Vnewton: Using errtol_s: 15393.687585 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.554543e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.950201e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.742003e+03 │ │ │ │ Vprtstp: contraction number = 4.742003e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.972961e-03 │ │ │ │ Vprtstp: contraction number = 2.772704e-01 │ │ │ │ Vnewton: Using errtol_s: 4268.214485 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.698095e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.119240e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.400571e+03 │ │ │ │ Vprtstp: contraction number = 1.400571e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.826678e-04 │ │ │ │ Vprtstp: contraction number = 2.953265e-01 │ │ │ │ Vnewton: Using errtol_s: 1260.517005 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.838734e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.286441e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.279978e+02 │ │ │ │ Vprtstp: contraction number = 4.279978e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.780560e-04 │ │ │ │ Vprtstp: contraction number = 3.055876e-01 │ │ │ │ Vnewton: Using errtol_s: 385.198337 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.980843e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.456486e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.339544e+02 │ │ │ │ Vprtstp: contraction number = 1.339544e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.572782e-05 │ │ │ │ Vprtstp: contraction number = 3.129791e-01 │ │ │ │ Vnewton: Using errtol_s: 120.559033 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.123145e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.629142e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.271452e+01 │ │ │ │ Vprtstp: contraction number = 4.271452e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.777012e-05 │ │ │ │ Vprtstp: contraction number = 3.188734e-01 │ │ │ │ Vnewton: Using errtol_s: 38.443069 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.265379e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.803755e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.384186e+01 │ │ │ │ Vprtstp: contraction number = 1.384186e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.758498e-06 │ │ │ │ Vprtstp: contraction number = 3.240551e-01 │ │ │ │ Vnewton: Using errtol_s: 12.457672 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.408506e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.973243e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.545889e+00 │ │ │ │ Vprtstp: contraction number = 4.545889e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.891183e-06 │ │ │ │ Vprtstp: contraction number = 3.284161e-01 │ │ │ │ Vnewton: Using errtol_s: 4.091300 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.549999e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.140180e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.509299e+00 │ │ │ │ Vprtstp: contraction number = 1.509299e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.278996e-07 │ │ │ │ Vprtstp: contraction number = 3.320141e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.643119e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.706051e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.957594e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.021651e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21579,15 +21579,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.270848264537E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951162263981E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.475012659776E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.383620e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.389480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -21616,151 +21616,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.319160 │ │ │ │ +Vacc_SASA: Time elapsed: 0.307703 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.074270e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.227560e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.315840e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.794840e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.088862e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.709301e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 634193.792999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.166897e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.791216e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.499222e+04 │ │ │ │ Vprtstp: contraction number = 8.499222e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.127890 │ │ │ │ Vnewton: Attempting damping, relres = 0.557688 │ │ │ │ Vnewton: Damping accepted, relres = 0.127890 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.278898e-01 │ │ │ │ Vprtstp: contraction number = 1.278898e-01 │ │ │ │ Vnewton: Using errtol_s: 81106.914272 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.343130e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.988133e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.610090e+04 │ │ │ │ Vprtstp: contraction number = 1.610090e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.303084e-02 │ │ │ │ Vprtstp: contraction number = 1.800835e-01 │ │ │ │ Vnewton: Using errtol_s: 14606.018111 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.486342e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.150281e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.721077e+03 │ │ │ │ Vprtstp: contraction number = 3.721077e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.281325e-03 │ │ │ │ Vprtstp: contraction number = 2.293153e-01 │ │ │ │ Vnewton: Using errtol_s: 3349.383286 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.627133e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.315432e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.553498e+02 │ │ │ │ Vprtstp: contraction number = 9.553498e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.355768e-03 │ │ │ │ Vprtstp: contraction number = 2.567099e-01 │ │ │ │ Vnewton: Using errtol_s: 859.819863 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.769894e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.479352e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.585067e+02 │ │ │ │ Vprtstp: contraction number = 2.585067e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.668537e-04 │ │ │ │ Vprtstp: contraction number = 2.705873e-01 │ │ │ │ Vnewton: Using errtol_s: 232.656331 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.911616e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.645951e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.199407e+01 │ │ │ │ Vprtstp: contraction number = 7.199407e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.021686e-04 │ │ │ │ Vprtstp: contraction number = 2.784995e-01 │ │ │ │ Vnewton: Using errtol_s: 64.794682 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.054795e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.809942e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.044636e+01 │ │ │ │ Vprtstp: contraction number = 2.044636e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.901594e-05 │ │ │ │ Vprtstp: contraction number = 2.840006e-01 │ │ │ │ Vnewton: Using errtol_s: 18.401729 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.198474e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.971401e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.898540e+00 │ │ │ │ Vprtstp: contraction number = 5.898540e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.370763e-06 │ │ │ │ Vprtstp: contraction number = 2.884884e-01 │ │ │ │ Vnewton: Using errtol_s: 5.308686 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.338866e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.132422e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.724703e+00 │ │ │ │ Vprtstp: contraction number = 1.724703e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.447569e-06 │ │ │ │ Vprtstp: contraction number = 2.923949e-01 │ │ │ │ Vnewton: Using errtol_s: 1.552233 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.480081e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.295882e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.100216e-01 │ │ │ │ Vprtstp: contraction number = 5.100216e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.237842e-07 │ │ │ │ Vprtstp: contraction number = 2.957156e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.498372e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.560066e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.709760e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.774766e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21770,15 +21770,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.835376083091E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.829553004280E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.412753768634E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390800e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.408360e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ @@ -21827,160 +21827,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00156468 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.312185 │ │ │ │ +Vacc_SASA: Time elapsed: 0.300818 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.672930e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.777350e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.372980e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.408850e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.279270e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.863870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.751481e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.590039e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 658696.826144 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.828116e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.672219e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.053855e+05 │ │ │ │ Vprtstp: contraction number = 1.053855e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.150549 │ │ │ │ Vnewton: Attempting damping, relres = 0.569486 │ │ │ │ Vnewton: Damping accepted, relres = 0.150549 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.505490e-01 │ │ │ │ Vprtstp: contraction number = 1.505490e-01 │ │ │ │ Vnewton: Using errtol_s: 99166.139789 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.002591e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.871507e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.161238e+04 │ │ │ │ Vprtstp: contraction number = 2.161238e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.969136e-02 │ │ │ │ Vprtstp: contraction number = 1.972206e-01 │ │ │ │ Vnewton: Using errtol_s: 19557.601485 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.145380e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.039965e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.305338e+03 │ │ │ │ Vprtstp: contraction number = 5.305338e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.249717e-03 │ │ │ │ Vprtstp: contraction number = 2.441693e-01 │ │ │ │ Vnewton: Using errtol_s: 4775.365541 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.287620e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.206386e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.404636e+03 │ │ │ │ Vprtstp: contraction number = 1.404636e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.919225e-03 │ │ │ │ Vprtstp: contraction number = 2.647311e-01 │ │ │ │ Vnewton: Using errtol_s: 1264.187582 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.430523e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.372397e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.902078e+02 │ │ │ │ Vprtstp: contraction number = 3.902078e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.331561e-04 │ │ │ │ Vprtstp: contraction number = 2.777976e-01 │ │ │ │ Vnewton: Using errtol_s: 351.188214 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.573833e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.538460e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.119096e+02 │ │ │ │ Vprtstp: contraction number = 1.119096e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.529061e-04 │ │ │ │ Vprtstp: contraction number = 2.867943e-01 │ │ │ │ Vnewton: Using errtol_s: 100.718769 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.717070e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.708245e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.284972e+01 │ │ │ │ Vprtstp: contraction number = 3.284972e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.488371e-05 │ │ │ │ Vprtstp: contraction number = 2.935377e-01 │ │ │ │ Vnewton: Using errtol_s: 29.564758 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.860093e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.873914e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.835792e+00 │ │ │ │ Vprtstp: contraction number = 9.835792e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.343898e-05 │ │ │ │ Vprtstp: contraction number = 2.994178e-01 │ │ │ │ Vnewton: Using errtol_s: 8.852214 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.002977e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.038430e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.001834e+00 │ │ │ │ Vprtstp: contraction number = 3.001834e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.101508e-06 │ │ │ │ Vprtstp: contraction number = 3.051949e-01 │ │ │ │ Vnewton: Using errtol_s: 2.701650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.145832e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.203458e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.317265e-01 │ │ │ │ Vprtstp: contraction number = 9.317265e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.273050e-06 │ │ │ │ Vprtstp: contraction number = 3.103858e-01 │ │ │ │ Vnewton: Using errtol_s: 0.838554 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.286623e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.368689e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.932750e-01 │ │ │ │ Vprtstp: contraction number = 2.932750e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.007117e-07 │ │ │ │ Vprtstp: contraction number = 3.147651e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.643433e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.704709e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.904795e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.971531e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -21990,15 +21990,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.826778540566E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.062089331006E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.029034062463E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.391050e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.396450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -22027,162 +22027,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.496257 │ │ │ │ +Vacc_SASA: Time elapsed: 0.482449 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.091557e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.081192e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.445110e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.374020e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.499690e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.637200e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.850991e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.947031e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1439349.266881 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.928396e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.024068e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.043544e+05 │ │ │ │ Vprtstp: contraction number = 2.043544e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.158631 │ │ │ │ Vnewton: Attempting damping, relres = 0.563029 │ │ │ │ Vnewton: Damping accepted, relres = 0.158631 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.586310e-01 │ │ │ │ Vprtstp: contraction number = 1.586310e-01 │ │ │ │ Vnewton: Using errtol_s: 228325.431602 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.103744e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.216370e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.831785e+04 │ │ │ │ Vprtstp: contraction number = 3.831785e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.847279e-02 │ │ │ │ Vprtstp: contraction number = 1.794907e-01 │ │ │ │ Vnewton: Using errtol_s: 40982.294833 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.246885e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.378576e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.668291e+03 │ │ │ │ Vprtstp: contraction number = 9.668291e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.314045e-03 │ │ │ │ Vprtstp: contraction number = 2.217571e-01 │ │ │ │ Vnewton: Using errtol_s: 9088.116327 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.388681e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.539955e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.688849e+03 │ │ │ │ Vprtstp: contraction number = 2.688849e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.683268e-03 │ │ │ │ Vprtstp: contraction number = 2.665910e-01 │ │ │ │ Vnewton: Using errtol_s: 2422.810315 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.529960e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.703068e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.856129e+02 │ │ │ │ Vprtstp: contraction number = 7.856129e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.912324e-04 │ │ │ │ Vprtstp: contraction number = 2.918326e-01 │ │ │ │ Vnewton: Using errtol_s: 707.055007 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.671889e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.863978e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.356112e+02 │ │ │ │ Vprtstp: contraction number = 2.356112e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.473237e-04 │ │ │ │ Vprtstp: contraction number = 2.999062e-01 │ │ │ │ Vnewton: Using errtol_s: 212.050207 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.812667e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.002697e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.139103e+01 │ │ │ │ Vprtstp: contraction number = 7.139103e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.463957e-05 │ │ │ │ Vprtstp: contraction number = 3.030034e-01 │ │ │ │ Vnewton: Using errtol_s: 64.251934 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.953547e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.019045e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.175983e+01 │ │ │ │ Vprtstp: contraction number = 2.175983e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.360604e-05 │ │ │ │ Vprtstp: contraction number = 3.047978e-01 │ │ │ │ Vnewton: Using errtol_s: 19.583846 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.095933e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.035587e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.658230e+00 │ │ │ │ Vprtstp: contraction number = 6.658230e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.163275e-06 │ │ │ │ Vprtstp: contraction number = 3.059873e-01 │ │ │ │ Vnewton: Using errtol_s: 5.992407 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.237895e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052210e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.042996e+00 │ │ │ │ Vprtstp: contraction number = 2.042996e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.277450e-06 │ │ │ │ Vprtstp: contraction number = 3.068378e-01 │ │ │ │ Vnewton: Using errtol_s: 1.838697 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.380959e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068288e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.281914e-01 │ │ │ │ Vprtstp: contraction number = 6.281914e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.927971e-07 │ │ │ │ Vprtstp: contraction number = 3.074853e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.637670e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.701884e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.865151e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.929198e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -22192,17 +22192,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.196840922494E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.873106662838E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.356799948261E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.407650e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.443280e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.5 │ │ │ │ Vpbe_ctor2: xkappa = 0.230253 │ │ │ │ @@ -22249,160 +22249,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00202496 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.484065 │ │ │ │ +Vacc_SASA: Time elapsed: 0.492581 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.289578e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.319051e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.372930e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.401640e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.354150e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.793040e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.696128e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.102692e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1465724.452340 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.773361e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.111002e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.560590e+05 │ │ │ │ Vprtstp: contraction number = 2.560590e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.187284 │ │ │ │ Vnewton: Attempting damping, relres = 0.577996 │ │ │ │ Vnewton: Damping accepted, relres = 0.187284 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.872842e-01 │ │ │ │ Vprtstp: contraction number = 1.872842e-01 │ │ │ │ Vnewton: Using errtol_s: 274507.063571 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.947771e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.130849e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.241855e+04 │ │ │ │ Vprtstp: contraction number = 5.241855e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.660510e-02 │ │ │ │ Vprtstp: contraction number = 1.954521e-01 │ │ │ │ Vnewton: Using errtol_s: 53652.984086 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008968e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.147937e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.392830e+04 │ │ │ │ Vprtstp: contraction number = 1.392830e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.808972e-03 │ │ │ │ Vprtstp: contraction number = 2.406488e-01 │ │ │ │ Vnewton: Using errtol_s: 12911.525544 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023066e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.164257e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.064869e+03 │ │ │ │ Vprtstp: contraction number = 4.064869e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.497826e-03 │ │ │ │ Vprtstp: contraction number = 2.835548e-01 │ │ │ │ Vnewton: Using errtol_s: 3661.124985 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.037247e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.180395e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.249555e+03 │ │ │ │ Vprtstp: contraction number = 1.249555e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.672679e-04 │ │ │ │ Vprtstp: contraction number = 3.071743e-01 │ │ │ │ Vnewton: Using errtol_s: 1124.603371 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.051375e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.196705e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.953417e+02 │ │ │ │ Vprtstp: contraction number = 3.953417e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.427522e-04 │ │ │ │ Vprtstp: contraction number = 3.163852e-01 │ │ │ │ Vnewton: Using errtol_s: 355.807819 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.065457e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.213047e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.271192e+02 │ │ │ │ Vprtstp: contraction number = 1.271192e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.805515e-05 │ │ │ │ Vprtstp: contraction number = 3.215425e-01 │ │ │ │ Vnewton: Using errtol_s: 114.407339 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.079676e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229357e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.134607e+01 │ │ │ │ Vprtstp: contraction number = 4.134607e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.538777e-05 │ │ │ │ Vprtstp: contraction number = 3.252542e-01 │ │ │ │ Vnewton: Using errtol_s: 37.211468 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094478e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.245811e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.356940e+01 │ │ │ │ Vprtstp: contraction number = 1.356940e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.332028e-06 │ │ │ │ Vprtstp: contraction number = 3.281907e-01 │ │ │ │ Vnewton: Using errtol_s: 12.212457 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109330e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.261763e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.485660e+00 │ │ │ │ Vprtstp: contraction number = 4.485660e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.754334e-06 │ │ │ │ Vprtstp: contraction number = 3.305718e-01 │ │ │ │ Vnewton: Using errtol_s: 4.037094 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.124088e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.278073e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.491490e+00 │ │ │ │ Vprtstp: contraction number = 1.491490e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 9.158205e-07 │ │ │ │ Vprtstp: contraction number = 3.325017e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.657192e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.719284e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.881171e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.947104e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -22412,29 +22412,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 7.186606092212E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.134845139455E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066550655218E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.407330e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.375690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.164277e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.319154e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:54:18 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 22:02:51 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -22704,151 +22704,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.891170 │ │ │ │ +Vacc_SASA: Time elapsed: 0.846294 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.609146e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.536188e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.361570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.361450e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.282440e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.697950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.306105e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.254714e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2093191.031761 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.084495e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.053952e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.700910e+05 │ │ │ │ Vprtstp: contraction number = 2.700910e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.124805 │ │ │ │ Vnewton: Attempting damping, relres = 0.555496 │ │ │ │ Vnewton: Damping accepted, relres = 0.124805 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.248046e-01 │ │ │ │ Vprtstp: contraction number = 1.248046e-01 │ │ │ │ Vnewton: Using errtol_s: 261239.913592 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.822252e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.070569e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.897400e+04 │ │ │ │ Vprtstp: contraction number = 4.897400e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.189435e-02 │ │ │ │ Vprtstp: contraction number = 1.754290e-01 │ │ │ │ Vnewton: Using errtol_s: 45829.056358 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.238126e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.857972e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.159488e+04 │ │ │ │ Vprtstp: contraction number = 1.159488e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.014196e-03 │ │ │ │ Vprtstp: contraction number = 2.290178e-01 │ │ │ │ Vnewton: Using errtol_s: 10495.669115 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.660450e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.601039e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.106549e+03 │ │ │ │ Vprtstp: contraction number = 3.106549e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.335806e-03 │ │ │ │ Vprtstp: contraction number = 2.664048e-01 │ │ │ │ Vnewton: Using errtol_s: 2796.096256 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.099357e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.029525e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.808235e+02 │ │ │ │ Vprtstp: contraction number = 8.808235e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.787243e-04 │ │ │ │ Vprtstp: contraction number = 2.835176e-01 │ │ │ │ Vnewton: Using errtol_s: 792.742402 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.053551e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.196507e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.569082e+02 │ │ │ │ Vprtstp: contraction number = 2.569082e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.104617e-04 │ │ │ │ Vprtstp: contraction number = 2.916679e-01 │ │ │ │ Vnewton: Using errtol_s: 231.217496 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.194574e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.364632e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.629035e+01 │ │ │ │ Vprtstp: contraction number = 7.629035e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.280223e-05 │ │ │ │ Vprtstp: contraction number = 2.969556e-01 │ │ │ │ Vnewton: Using errtol_s: 68.661328 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.336402e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.539304e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.295748e+01 │ │ │ │ Vprtstp: contraction number = 2.295748e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.870924e-06 │ │ │ │ Vprtstp: contraction number = 3.009224e-01 │ │ │ │ Vnewton: Using errtol_s: 20.661731 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.478999e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.709981e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.980126e+00 │ │ │ │ Vprtstp: contraction number = 6.980126e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.001214e-06 │ │ │ │ Vprtstp: contraction number = 3.040459e-01 │ │ │ │ Vnewton: Using errtol_s: 6.282114 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.620366e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.878120e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.140783e+00 │ │ │ │ Vprtstp: contraction number = 2.140783e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.204627e-07 │ │ │ │ Vprtstp: contraction number = 3.066968e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.498940e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.560372e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.790615e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.855005e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -22858,17 +22858,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.091310515028E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566396275850E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282657451494E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.370550e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.353690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.6 │ │ │ │ Vpbe_ctor2: xkappa = 0.25223 │ │ │ │ @@ -22915,160 +22915,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0123549 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.880277 │ │ │ │ +Vacc_SASA: Time elapsed: 0.854447 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.854806e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.826826e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.384810e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.337720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.317600e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.520030e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.993111e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.276999e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2138246.077963 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.070473e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.356706e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.360784e+05 │ │ │ │ Vprtstp: contraction number = 3.360784e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.149785 │ │ │ │ Vnewton: Attempting damping, relres = 0.568394 │ │ │ │ Vnewton: Damping accepted, relres = 0.149785 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.497849e-01 │ │ │ │ Vprtstp: contraction number = 1.497849e-01 │ │ │ │ Vnewton: Using errtol_s: 320277.019000 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.245702e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.554500e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.696106e+04 │ │ │ │ Vprtstp: contraction number = 6.696106e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.898319e-02 │ │ │ │ Vprtstp: contraction number = 1.934987e-01 │ │ │ │ Vnewton: Using errtol_s: 61973.189490 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.389586e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.721420e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.682773e+04 │ │ │ │ Vprtstp: contraction number = 1.682773e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.107594e-03 │ │ │ │ Vprtstp: contraction number = 2.452316e-01 │ │ │ │ Vnewton: Using errtol_s: 15197.785187 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.532167e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.888302e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.709721e+03 │ │ │ │ Vprtstp: contraction number = 4.709721e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.982435e-03 │ │ │ │ Vprtstp: contraction number = 2.789179e-01 │ │ │ │ Vnewton: Using errtol_s: 4238.934308 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.675740e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.061933e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.393997e+03 │ │ │ │ Vprtstp: contraction number = 1.393997e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.867426e-04 │ │ │ │ Vprtstp: contraction number = 2.959706e-01 │ │ │ │ Vnewton: Using errtol_s: 1254.599967 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.819487e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.229363e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.264850e+02 │ │ │ │ Vprtstp: contraction number = 4.264850e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.795101e-04 │ │ │ │ Vprtstp: contraction number = 3.059436e-01 │ │ │ │ Vnewton: Using errtol_s: 383.836806 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.962961e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.400025e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.335898e+02 │ │ │ │ Vprtstp: contraction number = 1.335898e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.622871e-05 │ │ │ │ Vprtstp: contraction number = 3.132342e-01 │ │ │ │ Vnewton: Using errtol_s: 120.230819 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.106454e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.571495e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.262294e+01 │ │ │ │ Vprtstp: contraction number = 4.262294e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.794024e-05 │ │ │ │ Vprtstp: contraction number = 3.190584e-01 │ │ │ │ Vnewton: Using errtol_s: 38.360650 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.249905e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.743233e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.381744e+01 │ │ │ │ Vprtstp: contraction number = 1.381744e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.815841e-06 │ │ │ │ Vprtstp: contraction number = 3.241785e-01 │ │ │ │ Vnewton: Using errtol_s: 12.435699 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.392441e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.916373e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.538963e+00 │ │ │ │ Vprtstp: contraction number = 4.538963e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.910476e-06 │ │ │ │ Vprtstp: contraction number = 3.284952e-01 │ │ │ │ Vnewton: Using errtol_s: 4.085067 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.534673e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.096169e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.507189e+00 │ │ │ │ Vprtstp: contraction number = 1.507189e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.343844e-07 │ │ │ │ Vprtstp: contraction number = 3.320557e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.651445e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.713471e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.954027e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.016379e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -23078,17 +23078,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 5.079562127761E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.951011518926E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.474966609512E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.369770e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.363980e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -23115,151 +23115,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.308587 │ │ │ │ +Vacc_SASA: Time elapsed: 0.298776 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.129660e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.047800e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.365790e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.353290e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.261480e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.628560e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.071114e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.654017e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 628877.747769 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.149358e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.734694e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.412647e+04 │ │ │ │ Vprtstp: contraction number = 8.412647e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.127232 │ │ │ │ Vnewton: Attempting damping, relres = 0.557518 │ │ │ │ Vnewton: Damping accepted, relres = 0.127232 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.272321e-01 │ │ │ │ Vprtstp: contraction number = 1.272321e-01 │ │ │ │ Vnewton: Using errtol_s: 80013.454014 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.323844e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.923946e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.597434e+04 │ │ │ │ Vprtstp: contraction number = 1.597434e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.300878e-02 │ │ │ │ Vprtstp: contraction number = 1.808409e-01 │ │ │ │ Vnewton: Using errtol_s: 14469.707458 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.464979e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.079925e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.702955e+03 │ │ │ │ Vprtstp: contraction number = 3.702955e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.299891e-03 │ │ │ │ Vprtstp: contraction number = 2.303422e-01 │ │ │ │ Vnewton: Using errtol_s: 3332.983791 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.605718e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.239881e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.526036e+02 │ │ │ │ Vprtstp: contraction number = 9.526036e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.363298e-03 │ │ │ │ Vprtstp: contraction number = 2.572314e-01 │ │ │ │ Vnewton: Using errtol_s: 857.348085 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.746800e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.398648e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.580584e+02 │ │ │ │ Vprtstp: contraction number = 2.580584e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.693131e-04 │ │ │ │ Vprtstp: contraction number = 2.708968e-01 │ │ │ │ Vnewton: Using errtol_s: 232.252814 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.886957e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.556966e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.191756e+01 │ │ │ │ Vprtstp: contraction number = 7.191756e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.029227e-04 │ │ │ │ Vprtstp: contraction number = 2.786869e-01 │ │ │ │ Vnewton: Using errtol_s: 64.725819 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.027714e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.712280e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.043225e+01 │ │ │ │ Vprtstp: contraction number = 2.043225e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.924102e-05 │ │ │ │ Vprtstp: contraction number = 2.841066e-01 │ │ │ │ Vnewton: Using errtol_s: 18.389029 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.167419e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.867022e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.895681e+00 │ │ │ │ Vprtstp: contraction number = 5.895681e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.437431e-06 │ │ │ │ Vprtstp: contraction number = 2.885477e-01 │ │ │ │ Vnewton: Using errtol_s: 5.306113 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.311938e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.023215e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.724061e+00 │ │ │ │ Vprtstp: contraction number = 1.724061e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.467339e-06 │ │ │ │ Vprtstp: contraction number = 2.924277e-01 │ │ │ │ Vnewton: Using errtol_s: 1.551655 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.451515e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.180557e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.098608e-01 │ │ │ │ Vprtstp: contraction number = 5.098608e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.296724e-07 │ │ │ │ Vprtstp: contraction number = 2.957325e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.487704e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.548943e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.647913e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.711475e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -23269,17 +23269,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.828142417011E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.828945138010E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.412475614010E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.399960e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.406260e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.6 │ │ │ │ Vpbe_ctor2: xkappa = 0.25223 │ │ │ │ @@ -23326,160 +23326,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0012176 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.307327 │ │ │ │ +Vacc_SASA: Time elapsed: 0.296796 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.683760e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.643760e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.382460e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.435780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.331520e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.580060e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.724037e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.469131e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 653003.444935 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.801695e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.548467e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.042328e+05 │ │ │ │ Vprtstp: contraction number = 1.042328e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.149810 │ │ │ │ Vnewton: Attempting damping, relres = 0.569263 │ │ │ │ Vnewton: Damping accepted, relres = 0.149810 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.498099e-01 │ │ │ │ Vprtstp: contraction number = 1.498099e-01 │ │ │ │ Vnewton: Using errtol_s: 97826.408096 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.974519e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.740750e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.140231e+04 │ │ │ │ Vprtstp: contraction number = 2.140231e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.962843e-02 │ │ │ │ Vprtstp: contraction number = 1.977735e-01 │ │ │ │ Vnewton: Using errtol_s: 19347.468430 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.116327e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.901656e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.262567e+03 │ │ │ │ Vprtstp: contraction number = 5.262567e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.253840e-03 │ │ │ │ Vprtstp: contraction number = 2.448270e-01 │ │ │ │ Vnewton: Using errtol_s: 4736.782334 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.258915e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.064109e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.395696e+03 │ │ │ │ Vprtstp: contraction number = 1.395696e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.923638e-03 │ │ │ │ Vprtstp: contraction number = 2.651889e-01 │ │ │ │ Vnewton: Using errtol_s: 1256.142167 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.401072e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.225668e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.882795e+02 │ │ │ │ Vprtstp: contraction number = 3.882795e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.351469e-04 │ │ │ │ Vprtstp: contraction number = 2.781952e-01 │ │ │ │ Vnewton: Using errtol_s: 349.452740 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.543507e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.388753e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.114868e+02 │ │ │ │ Vprtstp: contraction number = 1.114868e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.536566e-04 │ │ │ │ Vprtstp: contraction number = 2.871297e-01 │ │ │ │ Vnewton: Using errtol_s: 100.338262 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.685048e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.554760e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.275571e+01 │ │ │ │ Vprtstp: contraction number = 3.275571e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.514547e-05 │ │ │ │ Vprtstp: contraction number = 2.938077e-01 │ │ │ │ Vnewton: Using errtol_s: 29.480150 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.826355e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.714130e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.814633e+00 │ │ │ │ Vprtstp: contraction number = 9.814633e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.352699e-05 │ │ │ │ Vprtstp: contraction number = 2.996311e-01 │ │ │ │ Vnewton: Using errtol_s: 8.833170 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.967939e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.873575e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.996998e+00 │ │ │ │ Vprtstp: contraction number = 2.996998e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.130604e-06 │ │ │ │ Vprtstp: contraction number = 3.053602e-01 │ │ │ │ Vnewton: Using errtol_s: 2.697298 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.109474e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.032036e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.305904e-01 │ │ │ │ Vprtstp: contraction number = 9.305904e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.282583e-06 │ │ │ │ Vprtstp: contraction number = 3.105075e-01 │ │ │ │ Vnewton: Using errtol_s: 0.837531 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.251920e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.190182e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.929997e-01 │ │ │ │ Vprtstp: contraction number = 2.929997e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.038259e-07 │ │ │ │ Vprtstp: contraction number = 3.148535e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.636637e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.698675e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.847596e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.911948e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -23489,17 +23489,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.819478148872E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.061484049390E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.028757163114E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.412160e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.390490e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -23526,162 +23526,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.496247 │ │ │ │ +Vacc_SASA: Time elapsed: 0.476094 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.075538e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.071181e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.371660e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.377140e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.294410e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.671600e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.809219e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.767560e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1418682.220089 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.886269e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.847220e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.013102e+05 │ │ │ │ Vprtstp: contraction number = 2.013102e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.153624 │ │ │ │ Vnewton: Attempting damping, relres = 0.562616 │ │ │ │ Vnewton: Damping accepted, relres = 0.153624 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.536244e-01 │ │ │ │ Vprtstp: contraction number = 1.536244e-01 │ │ │ │ Vnewton: Using errtol_s: 217944.143405 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.059605e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.038217e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.768720e+04 │ │ │ │ Vprtstp: contraction number = 3.768720e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.718554e-02 │ │ │ │ Vprtstp: contraction number = 1.769611e-01 │ │ │ │ Vnewton: Using errtol_s: 38567.641801 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.198731e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.203604e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.503404e+03 │ │ │ │ Vprtstp: contraction number = 9.503404e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.173770e-03 │ │ │ │ Vprtstp: contraction number = 2.270976e-01 │ │ │ │ Vnewton: Using errtol_s: 8758.617788 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.338787e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.362580e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.660166e+03 │ │ │ │ Vprtstp: contraction number = 2.660166e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.688330e-03 │ │ │ │ Vprtstp: contraction number = 2.734683e-01 │ │ │ │ Vnewton: Using errtol_s: 2395.204376 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.478678e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.525156e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.818054e+02 │ │ │ │ Vprtstp: contraction number = 7.818054e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.959721e-04 │ │ │ │ Vprtstp: contraction number = 2.937648e-01 │ │ │ │ Vnewton: Using errtol_s: 703.626776 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.618336e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.685430e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.347603e+02 │ │ │ │ Vprtstp: contraction number = 2.347603e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.489300e-04 │ │ │ │ Vprtstp: contraction number = 3.002790e-01 │ │ │ │ Vnewton: Using errtol_s: 211.284321 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.759087e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.843653e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.116445e+01 │ │ │ │ Vprtstp: contraction number = 7.116445e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.514613e-05 │ │ │ │ Vprtstp: contraction number = 3.031366e-01 │ │ │ │ Vnewton: Using errtol_s: 64.048016 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.899870e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000573e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.169522e+01 │ │ │ │ Vprtstp: contraction number = 2.169522e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.376326e-05 │ │ │ │ Vprtstp: contraction number = 3.048603e-01 │ │ │ │ Vnewton: Using errtol_s: 19.525698 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.040024e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016646e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.639132e+00 │ │ │ │ Vprtstp: contraction number = 6.639132e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.211809e-06 │ │ │ │ Vprtstp: contraction number = 3.060182e-01 │ │ │ │ Vnewton: Using errtol_s: 5.975219 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.183463e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032703e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.037255e+00 │ │ │ │ Vprtstp: contraction number = 2.037255e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.292417e-06 │ │ │ │ Vprtstp: contraction number = 3.068556e-01 │ │ │ │ Vnewton: Using errtol_s: 1.833530 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.323311e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.048535e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.264492e-01 │ │ │ │ Vprtstp: contraction number = 6.264492e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 3.974141e-07 │ │ │ │ Vprtstp: contraction number = 3.074967e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.621304e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.682854e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.842836e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.907231e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -23691,17 +23691,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.888929472568E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.872895947241E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.356241018508E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.388350e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.384800e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.6 │ │ │ │ Vpbe_ctor2: xkappa = 0.25223 │ │ │ │ @@ -23748,160 +23748,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00159488 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.493531 │ │ │ │ +Vacc_SASA: Time elapsed: 0.481587 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.290266e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.298800e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.362210e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368720e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.292180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.722750e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.637252e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.082119e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1444108.030883 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.716589e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.090116e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.522925e+05 │ │ │ │ Vprtstp: contraction number = 2.522925e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.182497 │ │ │ │ Vnewton: Attempting damping, relres = 0.577636 │ │ │ │ Vnewton: Damping accepted, relres = 0.182497 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.824967e-01 │ │ │ │ Vprtstp: contraction number = 1.824967e-01 │ │ │ │ Vnewton: Using errtol_s: 263544.898395 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.893869e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.109533e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.156495e+04 │ │ │ │ Vprtstp: contraction number = 5.156495e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.534743e-02 │ │ │ │ Vprtstp: contraction number = 1.936881e-01 │ │ │ │ Vnewton: Using errtol_s: 51045.503065 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.005669e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.125960e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.369160e+04 │ │ │ │ Vprtstp: contraction number = 1.369160e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.672608e-03 │ │ │ │ Vprtstp: contraction number = 2.453533e-01 │ │ │ │ Vnewton: Using errtol_s: 12524.182385 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.020205e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.142943e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.019157e+03 │ │ │ │ Vprtstp: contraction number = 4.019157e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.505566e-03 │ │ │ │ Vprtstp: contraction number = 2.889057e-01 │ │ │ │ Vnewton: Using errtol_s: 3618.307619 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.034771e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.160190e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.241608e+03 │ │ │ │ Vprtstp: contraction number = 1.241608e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.737990e-04 │ │ │ │ Vprtstp: contraction number = 3.088321e-01 │ │ │ │ Vnewton: Using errtol_s: 1117.449365 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.050441e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.177275e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.934907e+02 │ │ │ │ Vprtstp: contraction number = 3.934907e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.452323e-04 │ │ │ │ Vprtstp: contraction number = 3.169199e-01 │ │ │ │ Vnewton: Using errtol_s: 354.141922 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.064523e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.194769e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.266527e+02 │ │ │ │ Vprtstp: contraction number = 1.266527e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.893280e-05 │ │ │ │ Vprtstp: contraction number = 3.218695e-01 │ │ │ │ Vnewton: Using errtol_s: 113.987497 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.078815e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.211879e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.122303e+01 │ │ │ │ Vprtstp: contraction number = 4.122303e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.569111e-05 │ │ │ │ Vprtstp: contraction number = 3.254807e-01 │ │ │ │ Vnewton: Using errtol_s: 37.100733 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.092938e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.229138e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.353532e+01 │ │ │ │ Vprtstp: contraction number = 1.353532e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.435513e-06 │ │ │ │ Vprtstp: contraction number = 3.283437e-01 │ │ │ │ Vnewton: Using errtol_s: 12.181792 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107282e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.246438e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.475781e+00 │ │ │ │ Vprtstp: contraction number = 4.475781e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.789406e-06 │ │ │ │ Vprtstp: contraction number = 3.306741e-01 │ │ │ │ Vnewton: Using errtol_s: 4.028203 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.122309e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.263691e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.488509e+00 │ │ │ │ Vprtstp: contraction number = 1.488509e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 9.276717e-07 │ │ │ │ Vprtstp: contraction number = 3.325696e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.693380e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.754843e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.953363e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.018080e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -23911,29 +23911,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.878772494899E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.134634520141E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066494761685E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.377420e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.467810e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.161811e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.307857e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:55:14 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 22:05:42 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -24203,151 +24203,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.884631 │ │ │ │ +Vacc_SASA: Time elapsed: 0.895745 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.689102e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.601410e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.360290e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.430150e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.282630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.841070e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.385551e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.345087e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2075985.759525 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.153646e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.167577e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.676742e+05 │ │ │ │ Vprtstp: contraction number = 2.676742e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.123645 │ │ │ │ Vnewton: Attempting damping, relres = 0.555352 │ │ │ │ Vnewton: Damping accepted, relres = 0.123645 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.236446e-01 │ │ │ │ Vprtstp: contraction number = 1.236446e-01 │ │ │ │ Vnewton: Using errtol_s: 256684.416130 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.869567e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.300477e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.859973e+04 │ │ │ │ Vprtstp: contraction number = 4.859973e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.169836e-02 │ │ │ │ Vprtstp: contraction number = 1.754897e-01 │ │ │ │ Vnewton: Using errtol_s: 45045.483798 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.268375e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.126398e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.152870e+04 │ │ │ │ Vprtstp: contraction number = 1.152870e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.014779e-03 │ │ │ │ Vprtstp: contraction number = 2.311133e-01 │ │ │ │ Vnewton: Using errtol_s: 10410.609915 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.658538e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.915262e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.097422e+03 │ │ │ │ Vprtstp: contraction number = 3.097422e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.342870e-03 │ │ │ │ Vprtstp: contraction number = 2.677824e-01 │ │ │ │ Vnewton: Using errtol_s: 2787.778355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.049656e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.068539e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.793803e+02 │ │ │ │ Vprtstp: contraction number = 8.793803e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.812374e-04 │ │ │ │ Vprtstp: contraction number = 2.838975e-01 │ │ │ │ Vnewton: Using errtol_s: 791.443333 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047854e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.247290e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.566243e+02 │ │ │ │ Vprtstp: contraction number = 2.566243e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.112541e-04 │ │ │ │ Vprtstp: contraction number = 2.918238e-01 │ │ │ │ Vnewton: Using errtol_s: 230.962017 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.193004e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427039e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.622598e+01 │ │ │ │ Vprtstp: contraction number = 7.622598e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.304618e-05 │ │ │ │ Vprtstp: contraction number = 2.970332e-01 │ │ │ │ Vnewton: Using errtol_s: 68.603390 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.330704e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.604757e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.294139e+01 │ │ │ │ Vprtstp: contraction number = 2.294139e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 9.945756e-06 │ │ │ │ Vprtstp: contraction number = 3.009654e-01 │ │ │ │ Vnewton: Using errtol_s: 20.647248 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.468498e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.784021e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.975781e+00 │ │ │ │ Vprtstp: contraction number = 6.975781e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.024203e-06 │ │ │ │ Vprtstp: contraction number = 3.040697e-01 │ │ │ │ Vnewton: Using errtol_s: 6.278203 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.606994e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.962427e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.139542e+00 │ │ │ │ Vprtstp: contraction number = 2.139542e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.275536e-07 │ │ │ │ Vprtstp: contraction number = 3.067101e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.473380e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.534776e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.870731e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.937415e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24357,17 +24357,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.936418090820E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566271448852E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282618425876E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.379450e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.405640e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.7 │ │ │ │ Vpbe_ctor2: xkappa = 0.272439 │ │ │ │ @@ -24414,160 +24414,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0114665 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.875809 │ │ │ │ +Vacc_SASA: Time elapsed: 0.927367 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.856120e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.955462e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.365310e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.413320e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.212390e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.818740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.974175e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.383592e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2120327.174672 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.050341e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.463882e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.330788e+05 │ │ │ │ Vprtstp: contraction number = 3.330788e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.148670 │ │ │ │ Vnewton: Attempting damping, relres = 0.568259 │ │ │ │ Vnewton: Damping accepted, relres = 0.148670 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.486698e-01 │ │ │ │ Vprtstp: contraction number = 1.486698e-01 │ │ │ │ Vnewton: Using errtol_s: 315228.684259 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.219919e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.667979e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.641464e+04 │ │ │ │ Vprtstp: contraction number = 6.641464e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.878895e-02 │ │ │ │ Vprtstp: contraction number = 1.936435e-01 │ │ │ │ Vnewton: Using errtol_s: 61041.990934 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.357954e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.844861e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.670744e+04 │ │ │ │ Vprtstp: contraction number = 1.670744e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.105637e-03 │ │ │ │ Vprtstp: contraction number = 2.468182e-01 │ │ │ │ Vnewton: Using errtol_s: 15066.274957 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.497564e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.022974e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.686665e+03 │ │ │ │ Vprtstp: contraction number = 4.686665e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.989361e-03 │ │ │ │ Vprtstp: contraction number = 2.799694e-01 │ │ │ │ Vnewton: Using errtol_s: 4218.095910 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.637276e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.199880e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.389137e+03 │ │ │ │ Vprtstp: contraction number = 1.389137e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.896382e-04 │ │ │ │ Vprtstp: contraction number = 2.963958e-01 │ │ │ │ Vnewton: Using errtol_s: 1250.225849 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.777718e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.371532e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.253662e+02 │ │ │ │ Vprtstp: contraction number = 4.253662e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.805523e-04 │ │ │ │ Vprtstp: contraction number = 3.062086e-01 │ │ │ │ Vnewton: Using errtol_s: 382.829903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.917821e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.543686e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.333214e+02 │ │ │ │ Vprtstp: contraction number = 1.333214e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.659001e-05 │ │ │ │ Vprtstp: contraction number = 3.134273e-01 │ │ │ │ Vnewton: Using errtol_s: 119.989327 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.057833e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.714437e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.255612e+01 │ │ │ │ Vprtstp: contraction number = 4.255612e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.806349e-05 │ │ │ │ Vprtstp: contraction number = 3.191993e-01 │ │ │ │ Vnewton: Using errtol_s: 38.300511 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.199452e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.884192e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.379985e+01 │ │ │ │ Vprtstp: contraction number = 1.379985e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.857525e-06 │ │ │ │ Vprtstp: contraction number = 3.242742e-01 │ │ │ │ Vnewton: Using errtol_s: 12.419869 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.339266e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.057826e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.534043e+00 │ │ │ │ Vprtstp: contraction number = 4.534043e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.924533e-06 │ │ │ │ Vprtstp: contraction number = 3.285573e-01 │ │ │ │ Vnewton: Using errtol_s: 4.080639 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.479012e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.226388e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.505713e+00 │ │ │ │ Vprtstp: contraction number = 1.505713e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.391193e-07 │ │ │ │ Vprtstp: contraction number = 3.320906e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.612082e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.672565e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.980794e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.047047e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24577,15 +24577,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.924946278586E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.950886798741E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.474927636785E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.364150e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.379610e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ @@ -24614,151 +24614,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.301051 │ │ │ │ +Vacc_SASA: Time elapsed: 0.298395 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.972590e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.123530e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.356820e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.379090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.301480e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.864580e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.008744e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.797710e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 625058.556229 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.085653e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.878677e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.349434e+04 │ │ │ │ Vprtstp: contraction number = 8.349434e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.126666 │ │ │ │ Vnewton: Attempting damping, relres = 0.557380 │ │ │ │ Vnewton: Damping accepted, relres = 0.126666 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.266665e-01 │ │ │ │ Vprtstp: contraction number = 1.266665e-01 │ │ │ │ Vnewton: Using errtol_s: 79173.978566 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.258504e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.072436e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.587988e+04 │ │ │ │ Vprtstp: contraction number = 1.587988e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.298610e-02 │ │ │ │ Vprtstp: contraction number = 1.814695e-01 │ │ │ │ Vnewton: Using errtol_s: 14367.659528 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.396988e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.233759e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.689543e+03 │ │ │ │ Vprtstp: contraction number = 3.689543e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.312865e-03 │ │ │ │ Vprtstp: contraction number = 2.311338e-01 │ │ │ │ Vnewton: Using errtol_s: 3320.851989 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.535602e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.393118e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.505518e+02 │ │ │ │ Vprtstp: contraction number = 9.505518e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.368674e-03 │ │ │ │ Vprtstp: contraction number = 2.576150e-01 │ │ │ │ Vnewton: Using errtol_s: 855.501271 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.674574e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.550688e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.577170e+02 │ │ │ │ Vprtstp: contraction number = 2.577170e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.710781e-04 │ │ │ │ Vprtstp: contraction number = 2.711224e-01 │ │ │ │ Vnewton: Using errtol_s: 231.945545 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.814964e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.710406e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.185767e+01 │ │ │ │ Vprtstp: contraction number = 7.185767e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.034654e-04 │ │ │ │ Vprtstp: contraction number = 2.788237e-01 │ │ │ │ Vnewton: Using errtol_s: 64.671921 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.955287e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.869705e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.042074e+01 │ │ │ │ Vprtstp: contraction number = 2.042074e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.940311e-05 │ │ │ │ Vprtstp: contraction number = 2.841831e-01 │ │ │ │ Vnewton: Using errtol_s: 18.378664 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.095802e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.027785e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.893233e+00 │ │ │ │ Vprtstp: contraction number = 5.893233e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.485461e-06 │ │ │ │ Vprtstp: contraction number = 2.885906e-01 │ │ │ │ Vnewton: Using errtol_s: 5.303910 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.238289e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.187013e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.723486e+00 │ │ │ │ Vprtstp: contraction number = 1.723486e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.481587e-06 │ │ │ │ Vprtstp: contraction number = 2.924517e-01 │ │ │ │ Vnewton: Using errtol_s: 1.551137 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.378967e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.346723e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.097109e-01 │ │ │ │ Vprtstp: contraction number = 5.097109e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.339149e-07 │ │ │ │ Vprtstp: contraction number = 2.957442e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.479167e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.540683e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.673621e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.739877e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24768,17 +24768,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.817512164844E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.828431655726E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.412244339074E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.415640e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.446130e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.7 │ │ │ │ Vpbe_ctor2: xkappa = 0.272439 │ │ │ │ @@ -24825,160 +24825,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.000971631 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.309945 │ │ │ │ +Vacc_SASA: Time elapsed: 0.306086 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.732340e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.908610e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.371350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.410460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.287280e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.796700e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.653332e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.643262e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 648940.820048 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.731718e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.725020e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.033896e+05 │ │ │ │ Vprtstp: contraction number = 1.033896e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.149178 │ │ │ │ Vnewton: Attempting damping, relres = 0.569081 │ │ │ │ Vnewton: Damping accepted, relres = 0.149178 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.491779e-01 │ │ │ │ Vprtstp: contraction number = 1.491779e-01 │ │ │ │ Vnewton: Using errtol_s: 96807.596825 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.909173e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.923462e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.124753e+04 │ │ │ │ Vprtstp: contraction number = 2.124753e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.957488e-02 │ │ │ │ Vprtstp: contraction number = 1.982525e-01 │ │ │ │ Vnewton: Using errtol_s: 19192.349469 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.052817e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.086098e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.231045e+03 │ │ │ │ Vprtstp: contraction number = 5.231045e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.255435e-03 │ │ │ │ Vprtstp: contraction number = 2.453242e-01 │ │ │ │ Vnewton: Using errtol_s: 4708.348197 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.196140e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.252234e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.389072e+03 │ │ │ │ Vprtstp: contraction number = 1.389072e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.926494e-03 │ │ │ │ Vprtstp: contraction number = 2.655242e-01 │ │ │ │ Vnewton: Using errtol_s: 1250.180442 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.339097e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.416733e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.868439e+02 │ │ │ │ Vprtstp: contraction number = 3.868439e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.365061e-04 │ │ │ │ Vprtstp: contraction number = 2.784884e-01 │ │ │ │ Vnewton: Using errtol_s: 348.160728 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.481558e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.579663e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.111703e+02 │ │ │ │ Vprtstp: contraction number = 1.111703e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.541795e-04 │ │ │ │ Vprtstp: contraction number = 2.873769e-01 │ │ │ │ Vnewton: Using errtol_s: 100.053355 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.624624e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.741783e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.268464e+01 │ │ │ │ Vprtstp: contraction number = 3.268464e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.532954e-05 │ │ │ │ Vprtstp: contraction number = 2.940050e-01 │ │ │ │ Vnewton: Using errtol_s: 29.416189 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.767874e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.908631e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.798450e+00 │ │ │ │ Vprtstp: contraction number = 9.798450e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.358923e-05 │ │ │ │ Vprtstp: contraction number = 2.997875e-01 │ │ │ │ Vnewton: Using errtol_s: 8.818606 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.908910e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.077812e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.993247e+00 │ │ │ │ Vprtstp: contraction number = 2.993247e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.151261e-06 │ │ │ │ Vprtstp: contraction number = 3.054817e-01 │ │ │ │ Vnewton: Using errtol_s: 2.693923 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.051155e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.241778e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.296932e-01 │ │ │ │ Vprtstp: contraction number = 9.296932e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.289368e-06 │ │ │ │ Vprtstp: contraction number = 3.105968e-01 │ │ │ │ Vnewton: Using errtol_s: 0.836724 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.192786e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.405088e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.927772e-01 │ │ │ │ Vprtstp: contraction number = 2.927772e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.060455e-07 │ │ │ │ Vprtstp: contraction number = 3.149181e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.647299e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.708900e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.888367e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.954340e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -24988,17 +24988,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.808821595407E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.060972751461E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.028526891385E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.402110e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.420740e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -25025,162 +25025,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.490984 │ │ │ │ +Vacc_SASA: Time elapsed: 0.498328 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.083344e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.103087e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.368120e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.462460e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.263160e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.040420e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.752646e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.995055e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1404398.831107 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.830864e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.076043e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.991752e+05 │ │ │ │ Vprtstp: contraction number = 1.991752e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.149937 │ │ │ │ Vnewton: Attempting damping, relres = 0.562289 │ │ │ │ Vnewton: Damping accepted, relres = 0.149937 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.499366e-01 │ │ │ │ Vprtstp: contraction number = 1.499366e-01 │ │ │ │ Vnewton: Using errtol_s: 210570.777586 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.003401e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.271902e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.724441e+04 │ │ │ │ Vprtstp: contraction number = 3.724441e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.631656e-02 │ │ │ │ Vprtstp: contraction number = 1.755180e-01 │ │ │ │ Vnewton: Using errtol_s: 36958.952617 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.143450e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.437179e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.392042e+03 │ │ │ │ Vprtstp: contraction number = 9.392042e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.102282e-03 │ │ │ │ Vprtstp: contraction number = 2.318799e-01 │ │ │ │ Vnewton: Using errtol_s: 8570.037199 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.284073e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.599662e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.643900e+03 │ │ │ │ Vprtstp: contraction number = 2.643900e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.694653e-03 │ │ │ │ Vprtstp: contraction number = 2.777081e-01 │ │ │ │ Vnewton: Using errtol_s: 2379.968912 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.424596e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.760680e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.795002e+02 │ │ │ │ Vprtstp: contraction number = 7.795002e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 4.995386e-04 │ │ │ │ Vprtstp: contraction number = 2.947734e-01 │ │ │ │ Vnewton: Using errtol_s: 701.551412 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.563407e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.921578e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.342462e+02 │ │ │ │ Vprtstp: contraction number = 2.342462e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.501153e-04 │ │ │ │ Vprtstp: contraction number = 3.005079e-01 │ │ │ │ Vnewton: Using errtol_s: 210.821708 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.704382e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008273e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.102938e+01 │ │ │ │ Vprtstp: contraction number = 7.102938e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.551873e-05 │ │ │ │ Vprtstp: contraction number = 3.032252e-01 │ │ │ │ Vnewton: Using errtol_s: 63.926447 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.847542e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.024616e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.165701e+01 │ │ │ │ Vprtstp: contraction number = 2.165701e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.387876e-05 │ │ │ │ Vprtstp: contraction number = 3.049021e-01 │ │ │ │ Vnewton: Using errtol_s: 19.491311 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.990278e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.040640e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.627865e+00 │ │ │ │ Vprtstp: contraction number = 6.627865e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.247425e-06 │ │ │ │ Vprtstp: contraction number = 3.060378e-01 │ │ │ │ Vnewton: Using errtol_s: 5.965078 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.129529e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.056671e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.033869e+00 │ │ │ │ Vprtstp: contraction number = 2.033869e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.303392e-06 │ │ │ │ Vprtstp: contraction number = 3.068664e-01 │ │ │ │ Vnewton: Using errtol_s: 1.830482 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.270435e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.072870e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.254212e-01 │ │ │ │ Vprtstp: contraction number = 6.254212e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.007972e-07 │ │ │ │ Vprtstp: contraction number = 3.075032e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.624946e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.686132e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.860465e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.929517e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -25190,17 +25190,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.631424094606E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.872722745686E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.355776117184E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.414050e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.410410e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.7 │ │ │ │ Vpbe_ctor2: xkappa = 0.272439 │ │ │ │ @@ -25247,160 +25247,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00130951 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.491320 │ │ │ │ +Vacc_SASA: Time elapsed: 0.495506 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.298034e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.323104e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.369670e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.401230e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.325040e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.848950e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.585859e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.107080e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1429289.662203 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.664145e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.115178e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.496624e+05 │ │ │ │ Vprtstp: contraction number = 2.496624e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.178955 │ │ │ │ Vnewton: Attempting damping, relres = 0.577343 │ │ │ │ Vnewton: Damping accepted, relres = 0.178955 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.789551e-01 │ │ │ │ Vprtstp: contraction number = 1.789551e-01 │ │ │ │ Vnewton: Using errtol_s: 255778.622825 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.839475e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.134840e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.096661e+04 │ │ │ │ Vprtstp: contraction number = 5.096661e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.449699e-02 │ │ │ │ Vprtstp: contraction number = 1.927690e-01 │ │ │ │ Vnewton: Using errtol_s: 49306.188432 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.982644e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.151481e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.352983e+04 │ │ │ │ Vprtstp: contraction number = 1.352983e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.601027e-03 │ │ │ │ Vprtstp: contraction number = 2.493269e-01 │ │ │ │ Vnewton: Using errtol_s: 12293.359097 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.012503e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.167908e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.990835e+03 │ │ │ │ Vprtstp: contraction number = 3.990835e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.513298e-03 │ │ │ │ Vprtstp: contraction number = 2.922090e-01 │ │ │ │ Vnewton: Using errtol_s: 3592.230783 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.026740e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.184249e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.236351e+03 │ │ │ │ Vprtstp: contraction number = 1.236351e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.785110e-04 │ │ │ │ Vprtstp: contraction number = 3.097567e-01 │ │ │ │ Vnewton: Using errtol_s: 1112.717700 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.041009e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200791e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.922762e+02 │ │ │ │ Vprtstp: contraction number = 3.922762e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.470100e-04 │ │ │ │ Vprtstp: contraction number = 3.172852e-01 │ │ │ │ Vnewton: Using errtol_s: 353.048870 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.055191e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.217376e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.263525e+02 │ │ │ │ Vprtstp: contraction number = 1.263525e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 7.956210e-05 │ │ │ │ Vprtstp: contraction number = 3.221007e-01 │ │ │ │ Vnewton: Using errtol_s: 113.717282 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.069332e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.233793e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.114546e+01 │ │ │ │ Vprtstp: contraction number = 4.114546e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.590862e-05 │ │ │ │ Vprtstp: contraction number = 3.256402e-01 │ │ │ │ Vnewton: Using errtol_s: 37.030918 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.083497e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.250348e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.351428e+01 │ │ │ │ Vprtstp: contraction number = 1.351428e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.509716e-06 │ │ │ │ Vprtstp: contraction number = 3.284512e-01 │ │ │ │ Vnewton: Using errtol_s: 12.162848 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.097724e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.267089e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.469783e+00 │ │ │ │ Vprtstp: contraction number = 4.469783e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.814548e-06 │ │ │ │ Vprtstp: contraction number = 3.307453e-01 │ │ │ │ Vnewton: Using errtol_s: 4.022804 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.112035e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.283746e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.486721e+00 │ │ │ │ Vprtstp: contraction number = 1.486721e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 9.361638e-07 │ │ │ │ Vprtstp: contraction number = 3.326161e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.644742e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.706715e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.898382e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.964856e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -25410,29 +25410,29 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.621321814807E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.134461409198E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066448263473E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.396150e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.408240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.152187e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.326270e+02 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:56:09 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 22:09:28 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path model_outNB.pqr │ │ │ │ @@ -25702,151 +25702,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.889422 │ │ │ │ +Vacc_SASA: Time elapsed: 0.890993 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.615513e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.601716e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.378350e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.369300e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.296860e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 5.003710e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.315531e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.362347e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2063009.659222 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.095182e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.169097e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.658306e+05 │ │ │ │ Vprtstp: contraction number = 2.658306e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.122739 │ │ │ │ Vnewton: Attempting damping, relres = 0.555235 │ │ │ │ Vnewton: Damping accepted, relres = 0.122739 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.227391e-01 │ │ │ │ Vprtstp: contraction number = 1.227391e-01 │ │ │ │ Vnewton: Using errtol_s: 253211.880914 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.857003e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.253751e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.831485e+04 │ │ │ │ Vprtstp: contraction number = 4.831485e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.156033e-02 │ │ │ │ Vprtstp: contraction number = 1.756599e-01 │ │ │ │ Vnewton: Using errtol_s: 44479.169236 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.275067e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.053014e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.148001e+04 │ │ │ │ Vprtstp: contraction number = 1.148001e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.018325e-03 │ │ │ │ Vprtstp: contraction number = 2.327573e-01 │ │ │ │ Vnewton: Using errtol_s: 10352.852780 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.711915e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.863676e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.090763e+03 │ │ │ │ Vprtstp: contraction number = 3.090763e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.348386e-03 │ │ │ │ Vprtstp: contraction number = 2.686924e-01 │ │ │ │ Vnewton: Using errtol_s: 2781.733245 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.138817e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.067154e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.782780e+02 │ │ │ │ Vprtstp: contraction number = 8.782780e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.831544e-04 │ │ │ │ Vprtstp: contraction number = 2.841578e-01 │ │ │ │ Vnewton: Using errtol_s: 790.451228 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.057453e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.249574e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.564053e+02 │ │ │ │ Vprtstp: contraction number = 2.564053e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.118584e-04 │ │ │ │ Vprtstp: contraction number = 2.919407e-01 │ │ │ │ Vnewton: Using errtol_s: 230.764871 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.200575e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.427113e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.617617e+01 │ │ │ │ Vprtstp: contraction number = 7.617617e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 3.323230e-05 │ │ │ │ Vprtstp: contraction number = 2.970927e-01 │ │ │ │ Vnewton: Using errtol_s: 68.558559 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.345114e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.604284e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.292888e+01 │ │ │ │ Vprtstp: contraction number = 2.292888e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.000286e-05 │ │ │ │ Vprtstp: contraction number = 3.009981e-01 │ │ │ │ Vnewton: Using errtol_s: 20.635996 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.488945e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.777075e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.972403e+00 │ │ │ │ Vprtstp: contraction number = 6.972403e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 3.041752e-06 │ │ │ │ Vprtstp: contraction number = 3.040882e-01 │ │ │ │ Vnewton: Using errtol_s: 6.275163 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.632701e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.951800e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.138578e+00 │ │ │ │ Vprtstp: contraction number = 2.138578e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 9.329670e-07 │ │ │ │ Vprtstp: contraction number = 3.067203e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.510942e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.572519e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.854523e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.922849e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -25856,15 +25856,15 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.808172570835E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.566165331536E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.282584652691E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.389190e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.399430e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 25.8477 │ │ │ │ Vpbe_ctor2: solute dimensions = 26.666 x 32.3234 x 48.3902 │ │ │ │ Vpbe_ctor2: solute charge = -14 │ │ │ │ @@ -25913,160 +25913,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.0106595 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.882434 │ │ │ │ +Vacc_SASA: Time elapsed: 0.881557 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.871196e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.903462e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.373340e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.459510e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.295660e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.932970e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.007395e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.365681e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 2106967.008420 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.084569e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.446430e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.308151e+05 │ │ │ │ Vprtstp: contraction number = 3.308151e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.147795 │ │ │ │ Vnewton: Attempting damping, relres = 0.568147 │ │ │ │ Vnewton: Damping accepted, relres = 0.147795 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.477951e-01 │ │ │ │ Vprtstp: contraction number = 1.477951e-01 │ │ │ │ Vnewton: Using errtol_s: 311399.390533 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.260268e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.656532e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.599748e+04 │ │ │ │ Vprtstp: contraction number = 6.599748e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.864948e-02 │ │ │ │ Vprtstp: contraction number = 1.938459e-01 │ │ │ │ Vnewton: Using errtol_s: 60363.499136 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.403533e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.834855e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.661676e+04 │ │ │ │ Vprtstp: contraction number = 1.661676e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.106188e-03 │ │ │ │ Vprtstp: contraction number = 2.480390e-01 │ │ │ │ Vnewton: Using errtol_s: 14972.503442 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.546709e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.019415e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.669116e+03 │ │ │ │ Vprtstp: contraction number = 4.669116e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.994461e-03 │ │ │ │ Vprtstp: contraction number = 2.806653e-01 │ │ │ │ Vnewton: Using errtol_s: 4202.262595 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.690329e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.195494e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.385353e+03 │ │ │ │ Vprtstp: contraction number = 1.385353e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.917609e-04 │ │ │ │ Vprtstp: contraction number = 2.967022e-01 │ │ │ │ Vnewton: Using errtol_s: 1246.820661 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.835344e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.373466e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.244924e+02 │ │ │ │ Vprtstp: contraction number = 4.244924e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.813239e-04 │ │ │ │ Vprtstp: contraction number = 3.064141e-01 │ │ │ │ Vnewton: Using errtol_s: 382.043458 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.980949e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.548994e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.331120e+02 │ │ │ │ Vprtstp: contraction number = 1.331120e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.685939e-05 │ │ │ │ Vprtstp: contraction number = 3.135792e-01 │ │ │ │ Vnewton: Using errtol_s: 119.800865 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.124891e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.722795e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.250410e+01 │ │ │ │ Vprtstp: contraction number = 4.250410e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.815581e-05 │ │ │ │ Vprtstp: contraction number = 3.193107e-01 │ │ │ │ Vnewton: Using errtol_s: 38.253693 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.267847e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.898158e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.378625e+01 │ │ │ │ Vprtstp: contraction number = 1.378625e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 5.888858e-06 │ │ │ │ Vprtstp: contraction number = 3.243511e-01 │ │ │ │ Vnewton: Using errtol_s: 12.407629 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.409947e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.073549e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.530276e+00 │ │ │ │ Vprtstp: contraction number = 4.530276e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.935127e-06 │ │ │ │ Vprtstp: contraction number = 3.286082e-01 │ │ │ │ Vnewton: Using errtol_s: 4.077249 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.553032e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.247933e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.504596e+00 │ │ │ │ Vprtstp: contraction number = 1.504596e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.426945e-07 │ │ │ │ Vprtstp: contraction number = 3.321201e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.656305e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.717848e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 2.021357e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.089252e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -26076,17 +26076,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 4.796939220773E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.950780776080E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.474893902492E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.360890e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.346630e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -26113,151 +26113,151 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.314431 │ │ │ │ +Vacc_SASA: Time elapsed: 0.308034 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.116680e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 7.222660e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.380590e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.359690e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.292010e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.707160e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.095582e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.816817e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 622184.484743 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.173001e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.896910e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 8.301310e+04 │ │ │ │ Vprtstp: contraction number = 8.301310e+04 │ │ │ │ Vnewton: Attempting damping, relres = 0.126177 │ │ │ │ Vnewton: Attempting damping, relres = 0.557265 │ │ │ │ Vnewton: Damping accepted, relres = 0.126177 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.261770e-01 │ │ │ │ Vprtstp: contraction number = 1.261770e-01 │ │ │ │ Vnewton: Using errtol_s: 78505.344097 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.345033e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.093494e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.580629e+04 │ │ │ │ Vprtstp: contraction number = 1.580629e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.296474e-02 │ │ │ │ Vprtstp: contraction number = 1.820042e-01 │ │ │ │ Vnewton: Using errtol_s: 14288.305999 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.486340e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.254802e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.679149e+03 │ │ │ │ Vprtstp: contraction number = 3.679149e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 5.322303e-03 │ │ │ │ Vprtstp: contraction number = 2.317597e-01 │ │ │ │ Vnewton: Using errtol_s: 3311.454085 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.626875e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.411938e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.489453e+02 │ │ │ │ Vprtstp: contraction number = 9.489453e+02 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.372672e-03 │ │ │ │ Vprtstp: contraction number = 2.579095e-01 │ │ │ │ Vnewton: Using errtol_s: 854.055318 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.769482e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.569130e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.574445e+02 │ │ │ │ Vprtstp: contraction number = 2.574445e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 3.723980e-04 │ │ │ │ Vprtstp: contraction number = 2.712942e-01 │ │ │ │ Vnewton: Using errtol_s: 231.700267 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.916190e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.725931e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.180833e+01 │ │ │ │ Vprtstp: contraction number = 7.180833e+01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.038719e-04 │ │ │ │ Vprtstp: contraction number = 2.789272e-01 │ │ │ │ Vnewton: Using errtol_s: 64.627514 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.060478e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.883817e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.041084e+01 │ │ │ │ Vprtstp: contraction number = 2.041084e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.952461e-05 │ │ │ │ Vprtstp: contraction number = 2.842404e-01 │ │ │ │ Vnewton: Using errtol_s: 18.369753 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.201983e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.040167e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.891035e+00 │ │ │ │ Vprtstp: contraction number = 5.891035e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 8.521479e-06 │ │ │ │ Vprtstp: contraction number = 2.886229e-01 │ │ │ │ Vnewton: Using errtol_s: 5.301932 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.339982e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.198131e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.722947e+00 │ │ │ │ Vprtstp: contraction number = 1.722947e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 2.492271e-06 │ │ │ │ Vprtstp: contraction number = 2.924694e-01 │ │ │ │ Vnewton: Using errtol_s: 1.550653 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.478391e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.355754e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.095658e-01 │ │ │ │ Vprtstp: contraction number = 5.095658e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 7.370953e-07 │ │ │ │ Vprtstp: contraction number = 2.957524e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.488603e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.550135e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.661575e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.726029e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -26267,17 +26267,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.805001041922E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 6.827988101886E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 3.412047294485E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.403520e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.411940e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 19.3778 │ │ │ │ Vpbe_ctor2: solute dimensions = 19.082 x 18.3114 x 35.7654 │ │ │ │ Vpbe_ctor2: solute charge = 4 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.8 │ │ │ │ Vpbe_ctor2: xkappa = 0.29125 │ │ │ │ @@ -26324,160 +26324,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.000791536 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.311903 │ │ │ │ +Vacc_SASA: Time elapsed: 0.307780 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.761230e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 8.883260e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.346450e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.350390e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.237290e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.704520e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.748681e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.648104e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 645906.037357 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.826376e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.727011e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.027473e+05 │ │ │ │ Vprtstp: contraction number = 1.027473e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.148634 │ │ │ │ Vnewton: Attempting damping, relres = 0.568930 │ │ │ │ Vnewton: Damping accepted, relres = 0.148634 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.486339e-01 │ │ │ │ Vprtstp: contraction number = 1.486339e-01 │ │ │ │ Vnewton: Using errtol_s: 96003.523693 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.001621e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.919684e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.112857e+04 │ │ │ │ Vprtstp: contraction number = 2.112857e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.952923e-02 │ │ │ │ Vprtstp: contraction number = 1.986709e-01 │ │ │ │ Vnewton: Using errtol_s: 19073.107408 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.142822e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.082255e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.206787e+03 │ │ │ │ Vprtstp: contraction number = 5.206787e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 7.255653e-03 │ │ │ │ Vprtstp: contraction number = 2.457109e-01 │ │ │ │ Vnewton: Using errtol_s: 4686.469778 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.284008e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.244156e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.383944e+03 │ │ │ │ Vprtstp: contraction number = 1.383944e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.928400e-03 │ │ │ │ Vprtstp: contraction number = 2.657790e-01 │ │ │ │ Vnewton: Using errtol_s: 1245.565289 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.425186e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.405660e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.857274e+02 │ │ │ │ Vprtstp: contraction number = 3.857274e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.374712e-04 │ │ │ │ Vprtstp: contraction number = 2.787135e-01 │ │ │ │ Vnewton: Using errtol_s: 347.155903 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.567065e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.569010e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.109221e+02 │ │ │ │ Vprtstp: contraction number = 1.109221e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.545581e-04 │ │ │ │ Vprtstp: contraction number = 2.875654e-01 │ │ │ │ Vnewton: Using errtol_s: 99.830021 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.706838e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.731268e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.262844e+01 │ │ │ │ Vprtstp: contraction number = 3.262844e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.546421e-05 │ │ │ │ Vprtstp: contraction number = 2.941561e-01 │ │ │ │ Vnewton: Using errtol_s: 29.365605 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.846364e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.891524e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.785490e+00 │ │ │ │ Vprtstp: contraction number = 9.785490e+00 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.363502e-05 │ │ │ │ Vprtstp: contraction number = 2.999067e-01 │ │ │ │ Vnewton: Using errtol_s: 8.806942 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.987367e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.051109e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.990197e+00 │ │ │ │ Vprtstp: contraction number = 2.990197e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.166516e-06 │ │ │ │ Vprtstp: contraction number = 3.055746e-01 │ │ │ │ Vnewton: Using errtol_s: 2.691178 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.130632e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.210767e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.289503e-01 │ │ │ │ Vprtstp: contraction number = 9.289503e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.294392e-06 │ │ │ │ Vprtstp: contraction number = 3.106652e-01 │ │ │ │ Vnewton: Using errtol_s: 0.836055 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.277418e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.372557e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.925887e-01 │ │ │ │ Vprtstp: contraction number = 2.925887e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.076906e-07 │ │ │ │ Vprtstp: contraction number = 3.149670e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.635467e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.695958e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.850451e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.914843e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -26487,17 +26487,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 1.796314557167E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 8.060531082527E+03 kT │ │ │ │ Vpmg_energy: dielEnergy = 4.028330665485E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.395630e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.394760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ @@ -26524,162 +26524,162 @@ │ │ │ │ Vpmp_ctor2: Using meth = 1, mgsolv = 0 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.495682 │ │ │ │ +Vacc_SASA: Time elapsed: 0.469212 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.080800e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.068784e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.365570e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.383210e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.218630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.712830e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.838170e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.946736e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1394036.370554 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.916360e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.025783e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.976078e+05 │ │ │ │ Vprtstp: contraction number = 1.976078e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.147111 │ │ │ │ Vnewton: Attempting damping, relres = 0.562025 │ │ │ │ Vnewton: Damping accepted, relres = 0.147111 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.471110e-01 │ │ │ │ Vprtstp: contraction number = 1.471110e-01 │ │ │ │ Vnewton: Using errtol_s: 205078.018083 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.090256e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.216640e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.691787e+04 │ │ │ │ Vprtstp: contraction number = 3.691787e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 2.570682e-02 │ │ │ │ Vprtstp: contraction number = 1.747444e-01 │ │ │ │ Vnewton: Using errtol_s: 35836.239165 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.232771e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.374345e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 9.313783e+03 │ │ │ │ Vprtstp: contraction number = 9.313783e+03 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 6.063883e-03 │ │ │ │ Vprtstp: contraction number = 2.358862e-01 │ │ │ │ Vnewton: Using errtol_s: 8453.273025 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.373839e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.530816e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.633660e+03 │ │ │ │ Vprtstp: contraction number = 2.633660e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 1.700470e-03 │ │ │ │ Vprtstp: contraction number = 2.804259e-01 │ │ │ │ Vnewton: Using errtol_s: 2370.516473 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.514722e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.686351e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.779603e+02 │ │ │ │ Vprtstp: contraction number = 7.779603e+02 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 5.022576e-04 │ │ │ │ Vprtstp: contraction number = 2.953640e-01 │ │ │ │ Vnewton: Using errtol_s: 700.165343 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.658684e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.843364e+01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.339032e+02 │ │ │ │ Vprtstp: contraction number = 2.339032e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.510097e-04 │ │ │ │ Vprtstp: contraction number = 3.006618e-01 │ │ │ │ Vnewton: Using errtol_s: 210.512957 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.804290e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.000372e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 7.094002e+01 │ │ │ │ Vprtstp: contraction number = 7.094002e+01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 4.579940e-05 │ │ │ │ Vprtstp: contraction number = 3.032879e-01 │ │ │ │ Vnewton: Using errtol_s: 63.846030 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.949775e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016239e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.163184e+01 │ │ │ │ Vprtstp: contraction number = 2.163184e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 1.396567e-05 │ │ │ │ Vprtstp: contraction number = 3.049313e-01 │ │ │ │ Vnewton: Using errtol_s: 19.468652 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.094040e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.032016e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.620444e+00 │ │ │ │ Vprtstp: contraction number = 6.620444e+00 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 4.274207e-06 │ │ │ │ Vprtstp: contraction number = 3.060510e-01 │ │ │ │ Vnewton: Using errtol_s: 5.958400 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.236374e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.047690e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.031637e+00 │ │ │ │ Vprtstp: contraction number = 2.031637e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 1.311640e-06 │ │ │ │ Vprtstp: contraction number = 3.068733e-01 │ │ │ │ Vnewton: Using errtol_s: 1.828474 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.378760e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.063688e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 6.247427e-01 │ │ │ │ Vprtstp: contraction number = 6.247427e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 4.033384e-07 │ │ │ │ Vprtstp: contraction number = 3.075070e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.650057e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.710680e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.811268e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.876015e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -22.1914, -32.8742) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 32.7584, 49.3892) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -26689,17 +26689,17 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.410814502422E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 1.872576445438E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 9.355379703968E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.421230e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.377480e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 20.7943 │ │ │ │ Vpbe_ctor2: solute dimensions = 25.3482 x 27.3592 x 40.136 │ │ │ │ Vpbe_ctor2: solute charge = -18 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0.8 │ │ │ │ Vpbe_ctor2: xkappa = 0.29125 │ │ │ │ @@ -26746,160 +26746,160 @@ │ │ │ │ VPMG::extEnergy: extQfEnergy = 0 kT │ │ │ │ VPMG::extEnergy: extDiEnergy = 0.00110224 kT │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline2... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.499473 │ │ │ │ +Vacc_SASA: Time elapsed: 0.478597 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.298684e+00 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.296630e+00 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 097, 129) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.374970e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup). CPU TIME = 1.383090e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 049, 065) │ │ │ │ Vbuildops: Galer: (017, 025, 033) │ │ │ │ Vbuildops: Galer: (009, 013, 017) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.246020e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup). CPU TIME = 4.645380e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vnewdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.695807e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.096820e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vnewton: Damping enabled │ │ │ │ Vnewton: Using errtol_s: 1418623.682815 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.773422e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.104764e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.477376e+05 │ │ │ │ Vprtstp: contraction number = 2.477376e+05 │ │ │ │ Vnewton: Attempting damping, relres = 0.176231 │ │ │ │ Vnewton: Attempting damping, relres = 0.577102 │ │ │ │ Vnewton: Damping accepted, relres = 0.176231 │ │ │ │ Vnewton: Damping disabled │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.762312e-01 │ │ │ │ Vprtstp: contraction number = 1.762312e-01 │ │ │ │ Vnewton: Using errtol_s: 250005.771686 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.946688e+01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123865e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 5.052668e+04 │ │ │ │ Vprtstp: contraction number = 5.052668e+04 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ Vprtstp: relative residual = 3.389791e-02 │ │ │ │ Vprtstp: contraction number = 1.923491e-01 │ │ │ │ Vnewton: Using errtol_s: 48088.378660 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.008899e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.139893e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.341451e+04 │ │ │ │ Vprtstp: contraction number = 1.341451e+04 │ │ │ │ Vprtstp: iteration = 3 │ │ │ │ Vprtstp: relative residual = 8.561128e-03 │ │ │ │ Vprtstp: contraction number = 2.525562e-01 │ │ │ │ Vnewton: Using errtol_s: 12145.019085 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.023786e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.155929e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.971688e+03 │ │ │ │ Vprtstp: contraction number = 3.971688e+03 │ │ │ │ Vprtstp: iteration = 4 │ │ │ │ Vprtstp: relative residual = 2.519877e-03 │ │ │ │ Vprtstp: contraction number = 2.943394e-01 │ │ │ │ Vnewton: Using errtol_s: 3574.757814 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.037968e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.171916e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.232605e+03 │ │ │ │ Vprtstp: contraction number = 1.232605e+03 │ │ │ │ Vprtstp: iteration = 5 │ │ │ │ Vprtstp: relative residual = 7.819875e-04 │ │ │ │ Vprtstp: contraction number = 3.103276e-01 │ │ │ │ Vnewton: Using errtol_s: 1109.346049 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.052115e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.188333e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 3.914134e+02 │ │ │ │ Vprtstp: contraction number = 3.914134e+02 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 2.483197e-04 │ │ │ │ Vprtstp: contraction number = 3.175495e-01 │ │ │ │ Vnewton: Using errtol_s: 352.272271 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.066356e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.204421e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.261412e+02 │ │ │ │ Vprtstp: contraction number = 1.261412e+02 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 8.002626e-05 │ │ │ │ Vprtstp: contraction number = 3.222710e-01 │ │ │ │ Vnewton: Using errtol_s: 113.527152 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.080472e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.220339e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.109151e+01 │ │ │ │ Vprtstp: contraction number = 4.109151e+01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 2.606919e-05 │ │ │ │ Vprtstp: contraction number = 3.257579e-01 │ │ │ │ Vnewton: Using errtol_s: 36.982365 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.094779e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.236304e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.349979e+01 │ │ │ │ Vprtstp: contraction number = 1.349979e+01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 8.564509e-06 │ │ │ │ Vprtstp: contraction number = 3.285300e-01 │ │ │ │ Vnewton: Using errtol_s: 12.149816 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.108948e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.252285e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 4.465689e+00 │ │ │ │ Vprtstp: contraction number = 4.465689e+00 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.833112e-06 │ │ │ │ Vprtstp: contraction number = 3.307968e-01 │ │ │ │ Vnewton: Using errtol_s: 4.019120 │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.123127e+02 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.268594e+02 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.485509e+00 │ │ │ │ Vprtstp: contraction number = 1.485509e+00 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 9.424331e-07 │ │ │ │ Vprtstp: contraction number = 3.326494e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.643592e+01 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.704749e+01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vnewdrv2: solve). CPU TIME = 1.844059e+01 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.908444e+01 │ │ │ │ Vpmg_setPart: lower corner = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: upper corner = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: actual minima = (-8.8441, -20.8782, -25.9376) │ │ │ │ Vpmg_setPart: actual maxima = (36.4881, 31.4452, 42.4526) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ @@ -26909,19 +26909,19 @@ │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating full PBE energy │ │ │ │ Vpmg_qmEnergy: Calculating nonlinear energy │ │ │ │ Vpmg_energy: qmEnergy = 6.400773657781E+00 kT │ │ │ │ Vpmg_qfEnergyVolume: Calculating energy │ │ │ │ Vpmg_energy: qfEnergy = 2.134315194179E+04 kT │ │ │ │ Vpmg_energy: dielEnergy = 1.066408609760E+04 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.375630e-01 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.376240e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ Vgrid_writeDX: Opening virtual socket... │ │ │ │ Vgrid_writeDX: Writing to virtual socket... │ │ │ │ Vgrid_writeDX: Writing comments for ASC format. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.163207e+02 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.310271e+02 │ │ │ ├── ./usr/share/apbs/examples/solv/io.mc │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:19 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:24:32 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path methanol.pqr │ │ │ │ @@ -245,32 +245,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002947 │ │ │ │ +Vacc_SASA: Time elapsed: 0.002318 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.247100e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.774500e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.762500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.765800e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.280180e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.857960e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.656170e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.193980e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.930795e-01 │ │ │ │ Vprtstp: contraction number = 2.930795e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -299,32 +299,32 @@ │ │ │ │ Vprtstp: contraction number = 3.064107e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 2.158998e-06 │ │ │ │ Vprtstp: contraction number = 3.114698e-01 │ │ │ │ Vprtstp: iteration = 11 │ │ │ │ Vprtstp: relative residual = 6.836605e-07 │ │ │ │ Vprtstp: contraction number = 3.166565e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.896289e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.095100e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.357879e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.625319e+00 │ │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.481476875907E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.120000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.060000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2.83039 │ │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.8153 │ │ │ │ Vpbe_ctor2: solute charge = 5.55112e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -345,32 +345,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.001173 │ │ │ │ +Vacc_SASA: Time elapsed: 0.002262 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.648200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.936200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.978000e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.871700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.447430e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.868870e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.455371e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.992766e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.518468e-01 │ │ │ │ Vprtstp: contraction number = 1.518468e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -387,30 +387,30 @@ │ │ │ │ Vprtstp: contraction number = 1.057725e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.782567e-06 │ │ │ │ Vprtstp: contraction number = 1.074900e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.936135e-07 │ │ │ │ Vprtstp: contraction number = 1.086150e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.918833e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.156505e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.098594e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.365878e+00 │ │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.510541428496E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.700000e-05 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.010000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ @@ -433,32 +433,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.000777 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001260 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.554200e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.790200e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.999600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.830300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.424920e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.733780e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.650536e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.390724e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.228747e-01 │ │ │ │ Vprtstp: contraction number = 1.228747e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -484,30 +484,30 @@ │ │ │ │ Vprtstp: contraction number = 3.196112e-01 │ │ │ │ Vprtstp: iteration = 9 │ │ │ │ Vprtstp: relative residual = 1.915327e-06 │ │ │ │ Vprtstp: contraction number = 3.214910e-01 │ │ │ │ Vprtstp: iteration = 10 │ │ │ │ Vprtstp: relative residual = 6.179105e-07 │ │ │ │ Vprtstp: contraction number = 3.226135e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.555707e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.777733e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.015737e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.268309e+00 │ │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.191047608004E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.870000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.130000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ @@ -530,32 +530,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002736 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001356 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.155300e-02 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.723600e-02 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.371500e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.830100e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.243880e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.774370e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.462106e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.707444e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.134958e-01 │ │ │ │ Vprtstp: contraction number = 1.134958e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -572,42 +572,42 @@ │ │ │ │ Vprtstp: contraction number = 1.069805e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.498256e-06 │ │ │ │ Vprtstp: contraction number = 1.078455e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.625625e-07 │ │ │ │ Vprtstp: contraction number = 1.085012e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.774575e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.980143e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.076026e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.330940e+00 │ │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.504084363930E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.040000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.060000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 6.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.024025e+01 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.179155e+01 │ │ │ │ ############################################################################## │ │ │ │ # MC-shell I/O capture file. │ │ │ │ -# Creation Date and Time: Sun Jan 7 16:40:24 2024 │ │ │ │ +# Creation Date and Time: Mon Jan 8 21:24:39 2024 │ │ │ │ │ │ │ │ ############################################################################## │ │ │ │ Hello world from PE 0 │ │ │ │ Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. │ │ │ │ NOsh_parseInput: Starting file parsing... │ │ │ │ NOsh: Parsing READ section │ │ │ │ NOsh: Storing molecule 0 path methanol.pqr │ │ │ │ @@ -848,32 +848,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.003493 │ │ │ │ +Vacc_SASA: Time elapsed: 0.002336 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.666540e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.520330e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 5.191700e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.749200e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.433730e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.748120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.225500e-01 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.243300e-01 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 2.392714e-01 │ │ │ │ Vprtstp: contraction number = 2.392714e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -893,32 +893,32 @@ │ │ │ │ Vprtstp: contraction number = 1.556589e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 2.217054e-06 │ │ │ │ Vprtstp: contraction number = 1.639311e-01 │ │ │ │ Vprtstp: iteration = 8 │ │ │ │ Vprtstp: relative residual = 3.821154e-07 │ │ │ │ Vprtstp: contraction number = 1.723528e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.032340e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.263669e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.464709e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.714929e+00 │ │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.481634746029E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.080000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.110000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 4.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2.83039 │ │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.8153 │ │ │ │ Vpbe_ctor2: solute charge = 5.55112e-17 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -939,32 +939,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.003056 │ │ │ │ +Vacc_SASA: Time elapsed: 0.002134 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.698690e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.643040e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.926600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.814000e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.266740e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.796170e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.833519e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.325175e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.514442e-01 │ │ │ │ Vprtstp: contraction number = 1.514442e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -981,32 +981,32 @@ │ │ │ │ Vprtstp: contraction number = 1.045560e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.694780e-06 │ │ │ │ Vprtstp: contraction number = 1.061179e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.817099e-07 │ │ │ │ Vprtstp: contraction number = 1.072174e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.696457e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.896351e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.124304e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.378286e+00 │ │ │ │ Vpmg_setPart: lower corner = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: upper corner = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: actual minima = (-7.69135, -8, -8.2417) │ │ │ │ Vpmg_setPart: actual maxima = (8.30865, 8, 7.7583) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 1.511763544580E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.080000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.900000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1027,32 +1027,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002587 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001267 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.670090e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.605360e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.856800e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.856700e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.258700e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.870120e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.895220e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.880520e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.159916e-01 │ │ │ │ Vprtstp: contraction number = 1.159916e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1069,32 +1069,32 @@ │ │ │ │ Vprtstp: contraction number = 1.378576e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 3.539643e-06 │ │ │ │ Vprtstp: contraction number = 1.515814e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 5.760895e-07 │ │ │ │ Vprtstp: contraction number = 1.627536e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.773759e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.963291e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.086239e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.347789e+00 │ │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.192183682119E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.020000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 8.400000e-05 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ Vnm_tstart: starting timer 27 (Setup timer).. │ │ │ │ Setting up PBE object... │ │ │ │ Vpbe_ctor2: solute radius = 2.54275 │ │ │ │ Vpbe_ctor2: solute dimensions = 3.775 x 3.775 x 4.733 │ │ │ │ Vpbe_ctor2: solute charge = -1 │ │ │ │ Vpbe_ctor2: bulk ionic strength = 0 │ │ │ │ Vpbe_ctor2: xkappa = 0 │ │ │ │ @@ -1115,32 +1115,32 @@ │ │ │ │ Vpmp_ctor2: Using meth = 2, mgsolv = 1 │ │ │ │ Setting PDE center to local center... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ fillcoCharge: Calling fillcoChargeSpline1... │ │ │ │ Vpmg_fillco: filling in source term. │ │ │ │ Vpmg_fillco: marking ion and solvent accessibility. │ │ │ │ fillcoCoef: Calling fillcoCoefMol... │ │ │ │ -Vacc_SASA: Time elapsed: 0.002927 │ │ │ │ +Vacc_SASA: Time elapsed: 0.001242 │ │ │ │ Vpmg_fillco: done filling coefficient arrays │ │ │ │ Vpmg_fillco: filling boundary arrays │ │ │ │ Vpmg_fillco: done filling boundary arrays │ │ │ │ -Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.666600e-01 │ │ │ │ +Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.601830e-01 │ │ │ │ Vnm_tstart: starting timer 28 (Solver timer).. │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. │ │ │ │ Vbuildops: Fine: (065, 065, 065) │ │ │ │ Vbuildops: Operator stencil (lev, numdia) = (1, 4) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.845600e-02 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.761300e-02 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. │ │ │ │ Vbuildops: Galer: (033, 033, 033) │ │ │ │ Vbuildops: Galer: (017, 017, 017) │ │ │ │ Vbuildops: Galer: (009, 009, 009) │ │ │ │ Vbuildops: Galer: (005, 005, 005) │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.234630e-01 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 1.797760e-01 │ │ │ │ Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. │ │ │ │ -Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.031104e+00 │ │ │ │ +Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.391808e+00 │ │ │ │ Vprtstp: iteration = 0 │ │ │ │ Vprtstp: relative residual = 1.000000e+00 │ │ │ │ Vprtstp: contraction number = 1.000000e+00 │ │ │ │ Vprtstp: iteration = 1 │ │ │ │ Vprtstp: relative residual = 1.128724e-01 │ │ │ │ Vprtstp: contraction number = 1.128724e-01 │ │ │ │ Vprtstp: iteration = 2 │ │ │ │ @@ -1157,32 +1157,32 @@ │ │ │ │ Vprtstp: contraction number = 1.067766e-01 │ │ │ │ Vprtstp: iteration = 6 │ │ │ │ Vprtstp: relative residual = 1.477665e-06 │ │ │ │ Vprtstp: contraction number = 1.075719e-01 │ │ │ │ Vprtstp: iteration = 7 │ │ │ │ Vprtstp: relative residual = 1.598211e-07 │ │ │ │ Vprtstp: contraction number = 1.081578e-01 │ │ │ │ -Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.699737e+00 │ │ │ │ -Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.886240e+00 │ │ │ │ +Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 2.252304e+00 │ │ │ │ +Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 2.508506e+00 │ │ │ │ Vpmg_setPart: lower corner = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: upper corner = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: actual minima = (-8, -8, -8.12785) │ │ │ │ Vpmg_setPart: actual maxima = (8, 8, 7.87215) │ │ │ │ Vpmg_setPart: bflag[FRONT] = 0 │ │ │ │ Vpmg_setPart: bflag[BACK] = 0 │ │ │ │ Vpmg_setPart: bflag[LEFT] = 0 │ │ │ │ Vpmg_setPart: bflag[RIGHT] = 0 │ │ │ │ Vpmg_setPart: bflag[UP] = 0 │ │ │ │ Vpmg_setPart: bflag[DOWN] = 0 │ │ │ │ Vnm_tstart: starting timer 29 (Energy timer).. │ │ │ │ Vpmg_energy: calculating only q-phi energy │ │ │ │ Vpmg_energy: qfEnergy = 2.505883286802E+03 kT │ │ │ │ -Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.160000e-04 │ │ │ │ +Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.070000e-04 │ │ │ │ Vnm_tstart: starting timer 30 (Force timer).. │ │ │ │ -Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 5.000000e-06 │ │ │ │ +Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 3.000000e-06 │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ printEnergy: Performing global reduction (sum) │ │ │ │ Vcom_reduce: Not compiled with MPI, doing simple copy. │ │ │ │ -Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 8.734378e+00 │ │ │ │ +Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.065301e+01