From cd9d7e46aee64fc125c3bf9871d05eee81cc2a13 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 22 Jul 2015 16:14:45 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13686 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 6 +++--- doc/Section_packages.html | 28 ++++++++++++++++++++++++++++ doc/Section_packages.txt | 28 ++++++++++++++++++++++++++++ doc/compute_saed.html | 6 +++++- doc/compute_xrd.html | 6 +++++- doc/fix_saed_vtk.html | 4 ++++ 6 files changed, 73 insertions(+), 5 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index aa264663f9..cad8cdfffa 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -436,9 +436,9 @@ package. adapt/fepaddtorqueatcave/spatial/spherecolvarsgle imdipilangevin/efflb/fluidlb/momentumlb/pc lb/rigid/pc/spherelb/viscousmesomeso/stationarynph/effnpt/eff -nve/effnvt/effnvt/sllod/effphononpimdqeq/reax -qmmmreax/c/bondsreax/c/speciessaed/vtksmdtemp/rescale/eff -ti/rsti/springttm/mod +nve/effnvt/effnvt/sllod/effphononpimdqbmsst +qeq/reaxqmmmqtbreax/c/bondsreax/c/speciessaed/vtk +smdtemp/rescale/effti/rsti/springttm/mod
diff --git a/doc/Section_packages.html b/doc/Section_packages.html index 9295269d8f..733294f656 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -136,6 +136,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries. USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate - - - USER-PHONON phonon dynamical matrix Ling-Ti Kong (Shanghai Jiao Tong U) fix phonon USER/phonon - - USER-QMMM QM/MM coupling Axel Kohlmeyer (Temple U) fix qmmm USER/qmmm - lib/qmmm +USER-QTB quantum nuclear effects Yuan Shen (Stanford) fix qtb fix_qbmsst qtb - - USER-QUIP QM/MM coupling Albert Bartok-Partay (U Cambridge) fix quip USER/quip - lib/quip USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc reax - - USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf USER/sph sph - @@ -548,6 +549,33 @@ without changes to LAMMPS itself.

+

USER-QTB package +

+

This package provides a self-consistent quantum treatment of the +vibrational modes in a classical molecular dynamics simulation. By +coupling the MD simulation to a colored thermostat, it introduces zero +point energy into the system, alter the energy power spectrum and the +heat capacity towards their quantum nature. This package could be of +interest if one wants to model systems at temperatures lower than +their classical limits or when temperatures ramp up across the +classical limits in the simulation. +

+

See these two doc pages to get started: +

+

fix qtb provides quantum nulcear correction through a +colored thermostat and can be used with other time integration schemes +like fix nve or fix nph. +

+

fix qbmsst enables quantum nuclear correction of a +multi-scale shock technique simulation by coupling the quantum thermal +bath with the shocked system. +

+

The person who created this package is Yuan Shen (sy0302 at +stanford.edu) at Stanford University. Contact him directly if you +have questions. +

+
+

USER-REAXC package

This package contains a implementation for LAMMPS of the ReaxFF force diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 13182ac008..fec4b5d8e1 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -128,6 +128,7 @@ USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfi USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, - USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, - USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm +USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, - USER-QUIP, QM/MM coupling, Albert Bartok-Partay (U Cambridge), "fix quip"_fix_quip.html, USER/quip, -, lib/quip USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, - USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - @@ -535,6 +536,33 @@ The person who created this package is Axel Kohlmeyer at Temple U :line +USER-QTB package :h4 + +This package provides a self-consistent quantum treatment of the +vibrational modes in a classical molecular dynamics simulation. By +coupling the MD simulation to a colored thermostat, it introduces zero +point energy into the system, alter the energy power spectrum and the +heat capacity towards their quantum nature. This package could be of +interest if one wants to model systems at temperatures lower than +their classical limits or when temperatures ramp up across the +classical limits in the simulation. + +See these two doc pages to get started: + +"fix qtb"_fix_qtb.html provides quantum nulcear correction through a +colored thermostat and can be used with other time integration schemes +like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html. + +"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a +multi-scale shock technique simulation by coupling the quantum thermal +bath with the shocked system. + +The person who created this package is Yuan Shen (sy0302 at +stanford.edu) at Stanford University. Contact him directly if you +have questions. + +:line + USER-REAXC package :h4 This package contains a implementation for LAMMPS of the ReaxFF force diff --git a/doc/compute_saed.html b/doc/compute_saed.html index c8f4ad0cec..88a2fbb521 100644 --- a/doc/compute_saed.html +++ b/doc/compute_saed.html @@ -160,7 +160,11 @@ options.

Restrictions:

-

The compute_saed command does not work for triclinic cells. +

This command is part of the USER-DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the Making +LAMMPS section for more info. +

+

This command does not work for triclinic cells.

Related commands:

diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html index 253f936a21..be78543107 100644 --- a/doc/compute_xrd.html +++ b/doc/compute_xrd.html @@ -182,7 +182,11 @@ options.

Restrictions:

-

The compute_xrd command does not work for triclinic cells. +

This command is part of the USER-DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the Making +LAMMPS section for more info. +

+

This command does not work for triclinic cells.

Related commands:

diff --git a/doc/fix_saed_vtk.html b/doc/fix_saed_vtk.html index 370ebe7856..233444c6d7 100644 --- a/doc/fix_saed_vtk.html +++ b/doc/fix_saed_vtk.html @@ -170,6 +170,10 @@ minimization.

Restrictions:

+

This command is part of the USER-DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the Making +LAMMPS section for more info. +

The attributes for fix_saed_vtk must match the values assigned in the associated compute_saed command.