Another option for thermalizing the Drude model is to use the\n-temperature-grouped Nose-Hoover (TGNH) thermostat proposed by (Son).\n+temperature-grouped Nose-Hoover (TGNH) thermostat proposed by (Son).\n This is implemented as fix tgnvt/drude and fix tgnpt/drude.\n It separates the kinetic energy into three contributions:\n the molecular center of mass (COM) motion, the motion of atoms or atom-Drude pairs relative to molecular COMs,\n and the relative motion of atom-Drude pairs.\n An independent Nose-Hoover chain is applied to each type of motion.\n When TGNH is used, the temperatures of molecular, atomic and Drude motion can be printed out with thermo_style command command.
\n \n Description
\n These commands are variants of the Nose-Hoover fix styles fix nvt and fix npt for thermalized Drude polarizable\n models. They apply temperature-grouped Nose-Hoover thermostat (TGNH)\n-proposed by (Son). When there are fast vibrational\n+proposed by (Son). When there are fast vibrational\n modes with frequencies close to Drude oscillators (e.g. double bonds or\n out-of-plane torsions), this thermostat can provide better kinetic\n energy equipartitioning.
\n The difference between TGNH and the original Nose-Hoover thermostat is that,\n TGNH separates the kinetic energy of the group into three contributions:\n molecular center of mass (COM) motion,\n motion of COM of atom-Drude pairs or non-polarizable atoms relative to molecular COM,\n"}, {"source1": "./usr/share/doc/lammps/html/objects.inv", "source2": "./usr/share/doc/lammps/html/objects.inv", "unified_diff": null, "details": [{"source1": "Sphinx inventory", "source2": "Sphinx inventory", "unified_diff": "@@ -1,12 +1,13 @@\n # Sphinx inventory version 2\n # Project: LAMMPS\n # Version: 7 Feb 2024\n # The remainder of this file is compressed using zlib.\n 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[48, \"use-utils-numeric-functions-instead-of-force-numeric\"]\n ],\n- \"compute composition/atom command\": [\n- [357, \"compute-composition-atom-command\"]\n+ \"Use utils::open_potential() function to open potential files\": [\n+ [48, \"use-utils-open-potential-function-to-open-potential-files\"]\n ],\n- \"compute cna/atom command\": [\n- [353, \"compute-cna-atom-command\"]\n+ \"Use symbolic Atom and AtomVec constants instead of numerical values\": [\n+ [48, \"use-symbolic-atom-and-atomvec-constants-instead-of-numerical-values\"]\n ],\n- \"compute contact/atom command\": [\n- [358, \"compute-contact-atom-command\"]\n+ \"Simplify customized error messages\": [\n+ [48, \"simplify-customized-error-messages\"]\n ],\n- \"compute ave/sphere/atom command\": [\n- [343, \"compute-ave-sphere-atom-command\"]\n+ \"Use of \\u201coverride\\u201d instead of \\u201cvirtual\\u201d\": [\n+ [48, \"use-of-override-instead-of-virtual\"]\n ],\n- \"compute count/type command\": [\n- [360, 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instead of Output::find_dump()\": [\n+ [48, \"use-output-get-dump-by-id-instead-of-output-find-dump\"]\n ],\n- \"compute command\": [\n- [337, \"compute-command\"]\n+ \"Refactored grid communication using Grid3d/Grid2d classes instead of GridComm\": [\n+ [48, \"refactored-grid-communication-using-grid3d-grid2d-classes-instead-of-gridcomm\"]\n ],\n- \"compute angle command\": [\n- [340, \"compute-angle-command\"]\n+ \"Long-range interactions\": [\n+ [40, \"long-range-interactions\"]\n ],\n- \"compute adf command\": [\n- [339, \"compute-adf-command\"]\n+ \"Neighbor lists\": [\n+ [41, \"neighbor-lists\"]\n ],\n \"The :f:mod:`LIBLAMMPS` Fortran Module\": [\n [61, \"the-f-mod-liblammps-fortran-module\"]\n ],\n \"Fortran compiler compatibility\": [\n [61, null]\n ],\n"}]}]}]}]}]}