From e70a48dc85ab67e9485a4cbc3e4e17ce12e90b1e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 9 May 2014 16:33:05 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11962 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 96 ++++++++++++++++++++------------------- doc/Section_commands.txt | 18 +++++++- doc/Section_packages.html | 26 ++++++++++- doc/Section_packages.txt | 26 ++++++++++- 4 files changed, 115 insertions(+), 51 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 2bec1769e9..0888116918 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -413,11 +413,11 @@ of each style or click on the style itself for a full description: package.

- - - - - + + + +
addtorqueatccolvarsimdlangevin/efflb/fluid
lb/momentumlb/pclb/rigid/pc/spherelb/viscousmesomeso/stationary
nph/effnpt/effnve/effnvt/effnvt/sllod/effphonon
qeq/reaxqmmmreax/c/bondsreax/c/speciessmdtemp/rescale/eff
ti/rsti/spring +
adapt/fepaddtorqueatccolvarsimdlangevin/eff
lb/fluidlb/momentumlb/pclb/rigid/pc/spherelb/viscousmeso
meso/stationarynph/effnpt/effnve/effnvt/effnvt/sllod/eff
phononqeq/reaxqmmmreax/c/bondsreax/c/speciessmd
temp/rescale/effti/rsti/spring

These are accelerated fix styles, which can be used if LAMMPS is @@ -458,8 +458,8 @@ each style or click on the style itself for a full description: package.

- - +
ackland/atombasal/atomke/effke/atom/effmeso_e/atommeso_rho/atom
meso_t/atomtemp/efftemp/deform/efftemp/region/efftemp/rotate +
ackland/atombasal/atomfepke/effke/atom/effmeso_e/atom
meso_rho/atommeso_t/atomtemp/efftemp/deform/efftemp/region/efftemp/rotate

These are accelerated compute styles, which can be used if LAMMPS is @@ -511,12 +511,14 @@ potentials. Click on the style itself for a full description: package.

- - - - - - + + + + + + +
awpmd/cutcoul/dieleam/cdedip
eff/cutgauss/cutlistlj/cut/dipole/sf
lj/sdklj/sdk/coul/longlj/sdk/coul/msmlj/sf
meam/splinemeam/sw/splinereax/csph/heatconduction
sph/idealgassph/ljsph/rhosumsph/taitwater
sph/taitwater/morristersoff/table +
awpmd/cutcoul/cut/softcoul/dielcoul/long/soft
eam/cdedipeff/cutgauss/cut
listlj/cut/coul/cut/softlj/cut/coul/long/softlj/cut/dipole/sf
lj/cut/softlj/cut/tip4p/long/softlj/sdklj/sdk/coul/long
lj/sdk/coul/msmlj/sfmeam/splinemeam/sw/spline
reax/csph/heatconductionsph/idealgassph/lj
sph/rhosumsph/taitwatersph/taitwater/morristersoff/table
tip4p/long/soft

These are accelerated pair styles, which can be used if LAMMPS is @@ -531,41 +533,43 @@ package. buck/coul/cut/ompbuck/coul/long/cudabuck/coul/long/gpubuck/coul/long/omp buck/coul/msm/ompbuck/cudabuck/long/coul/long/ompbuck/gpu buck/ompcolloid/gpucolloid/ompcomb/omp -coul/cut/ompcoul/debye/ompcoul/dsf/gpucoul/dsf/omp -coul/long/gpucoul/long/ompcoul/msm/ompcoul/wolf -dpd/ompdpd/tstat/ompeam/alloy/cudaeam/alloy/gpu -eam/alloy/ompeam/alloy/opteam/cd/ompeam/cuda -eam/fs/cudaeam/fs/gpueam/fs/ompeam/fs/opt -eam/gpueam/ompeam/optedip/omp -eim/ompgauss/gpugauss/ompgayberne/gpu -gayberne/ompgran/hertz/history/ompgran/hooke/cudagran/hooke/history/omp -gran/hooke/omphbond/dreiding/lj/omphbond/dreiding/morse/ompline/lj/omp -lj/charmm/coul/charmm/cudalj/charmm/coul/charmm/omplj/charmm/coul/charmm/implicit/cudalj/charmm/coul/charmm/implicit/omp -lj/charmm/coul/long/cudalj/charmm/coul/long/gpulj/charmm/coul/long/omplj/charmm/coul/long/opt -lj/class2/coul/cut/cudalj/class2/coul/cut/omplj/class2/coul/long/cudalj/class2/coul/long/gpu -lj/class2/coul/long/omplj/class2/coul/msm/omplj/class2/cudalj/class2/gpu -lj/class2/omplj/long/coul/long/omplj/cut/coul/cut/cudalj/cut/coul/cut/gpu -lj/cut/coul/cut/omplj/cut/coul/debye/cudalj/cut/coul/debye/gpulj/cut/coul/debye/omp -lj/cut/coul/dsf/gpulj/cut/coul/dsf/omplj/cut/coul/long/cudalj/cut/coul/long/gpu -lj/cut/coul/long/omplj/cut/coul/long/optlj/cut/coul/msm/gpulj/cut/coul/msm/opt +coul/cut/ompcoul/cut/soft/ompcoul/debye/ompcoul/dsf/gpu +coul/dsf/ompcoul/long/gpucoul/long/ompcoul/long/soft/omp +coul/msm/ompcoul/wolfdpd/ompdpd/tstat/omp +eam/alloy/cudaeam/alloy/gpueam/alloy/ompeam/alloy/opt +eam/cd/ompeam/cudaeam/fs/cudaeam/fs/gpu +eam/fs/ompeam/fs/opteam/gpueam/omp +eam/optedip/ompeim/ompgauss/gpu +gauss/ompgayberne/gpugayberne/ompgran/hertz/history/omp +gran/hooke/cudagran/hooke/history/ompgran/hooke/omphbond/dreiding/lj/omp +hbond/dreiding/morse/ompline/lj/omplj/charmm/coul/charmm/cudalj/charmm/coul/charmm/omp +lj/charmm/coul/charmm/implicit/cudalj/charmm/coul/charmm/implicit/omplj/charmm/coul/long/cudalj/charmm/coul/long/gpu +lj/charmm/coul/long/omplj/charmm/coul/long/optlj/class2/coul/cut/cudalj/class2/coul/cut/omp +lj/class2/coul/long/cudalj/class2/coul/long/gpulj/class2/coul/long/omplj/class2/coul/msm/omp +lj/class2/cudalj/class2/gpulj/class2/omplj/long/coul/long/omp +lj/cut/coul/cut/cudalj/cut/coul/cut/gpulj/cut/coul/cut/omplj/cut/coul/cut/soft/omp +lj/cut/coul/debye/cudalj/cut/coul/debye/gpulj/cut/coul/debye/omplj/cut/coul/dsf/gpu +lj/cut/coul/dsf/omplj/cut/coul/long/cudalj/cut/coul/long/gpulj/cut/coul/long/omp +lj/cut/coul/long/optlj/cut/coul/msm/gpulj/cut/coul/msm/optlj/cut/coul/long/soft/omp lj/cut/cudalj/cut/dipole/cut/gpulj/cut/dipole/cut/omplj/cut/dipole/sf/gpu lj/cut/dipole/sf/omplj/cut/experimental/cudalj/cut/gpulj/cut/omp -lj/cut/optlj/cut/tip4p/cut/omplj/cut/tip4p/long/omplj/cut/tip4p/long/opt -lj/expand/cudalj/expand/gpulj/expand/omplj/gromacs/coul/gromacs/cuda -lj/gromacs/coul/gromacs/omplj/gromacs/cudalj/gromacs/gpulj/gromacs/omp -lj/long/coul/long/optlj/sdk/gpulj/sdk/omplj/sdk/coul/long/gpu -lj/sdk/coul/long/omplj/sdk/coul/msm/omplj/sf/omplj/smooth/cuda -lj/smooth/omplj/smooth/linear/omplj96/cut/cudalj96/cut/gpu -lj96/cut/omplubricate/omplubricate/poly/ompmeam/spline/omp -mie/cut/gpumorse/cudamorse/gpumorse/omp -morse/optnb3b/harmonic/ompnm/cut/ompnm/cut/coul/cut/omp -nm/cut/coul/long/ompperi/lps/ompperi/pmb/omprebo/omp -resquared/gpuresquared/ompsoft/gpusoft/omp -sw/cudasw/gpusw/omptable/gpu -table/omptersoff/cudatersoff/omptersoff/mod/omp -tersoff/table/omptersoff/zbl/omptip4p/cut/omptip4p/long/omp -tri/lj/ompyukawa/gpuyukawa/ompyukawa/colloid/gpu -yukawa/colloid/ompzbl/omp +lj/cut/optlj/cut/soft/omplj/cut/tip4p/cut/omplj/cut/tip4p/long/omp +lj/cut/tip4p/long/optlj/cut/tip4p/long/soft/omplj/expand/cudalj/expand/gpu +lj/expand/omplj/gromacs/coul/gromacs/cudalj/gromacs/coul/gromacs/omplj/gromacs/cuda +lj/gromacs/gpulj/gromacs/omplj/long/coul/long/optlj/sdk/gpu +lj/sdk/omplj/sdk/coul/long/gpulj/sdk/coul/long/omplj/sdk/coul/msm/omp +lj/sf/omplj/smooth/cudalj/smooth/omplj/smooth/linear/omp +lj96/cut/cudalj96/cut/gpulj96/cut/omplubricate/omp +lubricate/poly/ompmeam/spline/ompmie/cut/gpumorse/cuda +morse/gpumorse/ompmorse/optnb3b/harmonic/omp +nm/cut/ompnm/cut/coul/cut/ompnm/cut/coul/long/ompperi/lps/omp +peri/pmb/omprebo/ompresquared/gpuresquared/omp +soft/gpusoft/ompsw/cudasw/gpu +sw/omptable/gputable/omptersoff/cuda +tersoff/omptersoff/mod/omptersoff/table/omptersoff/zbl/omp +tip4p/cut/omptip4p/long/omptip4p/long/soft/omptri/lj/omp +yukawa/gpuyukawa/ompyukawa/colloid/gpuyukawa/colloid/omp +zbl/omp

diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index e6acf39b18..c9acfcd8f4 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -568,6 +568,7 @@ These are fix styles contributed by users, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. +"adapt/fep"_fix_adapt_fep.html, "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "colvars"_fix_colvars.html, @@ -707,6 +708,7 @@ package"_Section_start.html#start_3. "ackland/atom"_compute_ackland_atom.html, "basal/atom"_compute_basal_atom.html, +"fep"_compute_fep.html, "ke/eff"_compute_ke_eff.html, "ke/atom/eff"_compute_ke_atom_eff.html, "meso_e/atom"_compute_meso_e_atom.html, @@ -840,13 +842,19 @@ These are pair styles contributed by users, which can be used if package"_Section_start.html#start_3. "awpmd/cut"_pair_awpmd.html, +"coul/cut/soft"_pair_lj_soft.html, "coul/diel"_pair_coul_diel.html, +"coul/long/soft"_pair_lj_soft.html, "eam/cd"_pair_eam.html, "edip"_pair_edip.html, "eff/cut"_pair_eff.html, "gauss/cut"_pair_gauss.html, "list"_pair_list.html, +"lj/cut/coul/cut/soft"_pair_lj_soft.html, +"lj/cut/coul/long/soft"_pair_lj_soft.html, "lj/cut/dipole/sf"_pair_dipole.html, +"lj/cut/soft"_pair_lj_soft.html, +"lj/cut/tip4p/long/soft"_pair_lj_soft.html, "lj/sdk"_pair_sdk.html, "lj/sdk/coul/long"_pair_sdk.html, "lj/sdk/coul/msm"_pair_sdk.html, @@ -860,7 +868,8 @@ package"_Section_start.html#start_3. "sph/rhosum"_pair_sph_rhosum.html, "sph/taitwater"_pair_sph_taitwater.html, "sph/taitwater/morris"_pair_sph_taitwater_morris.html, -"tersoff/table"_pair_tersoff.html :tb(c=4,ea=c) +"tersoff/table"_pair_tersoff.html, +"tip4p/long/soft"_pair_lj_soft.html :tb(c=4,ea=c) These are accelerated pair styles, which can be used if LAMMPS is built with the "appropriate accelerated @@ -895,11 +904,13 @@ package"_Section_accelerate.html. "colloid/omp"_pair_colloid.html, "comb/omp"_pair_comb.html, "coul/cut/omp"_pair_coul.html, +"coul/cut/soft/omp"_pair_lj_soft.html, "coul/debye/omp"_pair_coul.html, "coul/dsf/gpu"_pair_coul.html, "coul/dsf/omp"_pair_coul.html, "coul/long/gpu"_pair_coul.html, "coul/long/omp"_pair_coul.html, +"coul/long/soft/omp"_pair_lj_soft.html, "coul/msm/omp"_pair_coul.html, "coul/wolf"_pair_coul.html, "dpd/omp"_pair_dpd.html, @@ -951,6 +962,7 @@ package"_Section_accelerate.html. "lj/cut/coul/cut/cuda"_pair_lj.html, "lj/cut/coul/cut/gpu"_pair_lj.html, "lj/cut/coul/cut/omp"_pair_lj.html, +"lj/cut/coul/cut/soft/omp"_pair_lj_soft.html, "lj/cut/coul/debye/cuda"_pair_lj.html, "lj/cut/coul/debye/gpu"_pair_lj.html, "lj/cut/coul/debye/omp"_pair_lj.html, @@ -962,6 +974,7 @@ package"_Section_accelerate.html. "lj/cut/coul/long/opt"_pair_lj.html, "lj/cut/coul/msm/gpu"_pair_lj.html, "lj/cut/coul/msm/opt"_pair_lj.html, +"lj/cut/coul/long/soft/omp"_pair_lj_soft.html, "lj/cut/cuda"_pair_lj.html, "lj/cut/dipole/cut/gpu"_pair_dipole.html, "lj/cut/dipole/cut/omp"_pair_dipole.html, @@ -971,9 +984,11 @@ package"_Section_accelerate.html. "lj/cut/gpu"_pair_lj.html, "lj/cut/omp"_pair_lj.html, "lj/cut/opt"_pair_lj.html, +"lj/cut/soft/omp"_pair_lj_soft.html, "lj/cut/tip4p/cut/omp"_pair_lj.html, "lj/cut/tip4p/long/omp"_pair_lj.html, "lj/cut/tip4p/long/opt"_pair_lj.html, +"lj/cut/tip4p/long/soft/omp"_pair_lj_soft.html, "lj/expand/cuda"_pair_lj_expand.html, "lj/expand/gpu"_pair_lj_expand.html, "lj/expand/omp"_pair_lj_expand.html, @@ -1026,6 +1041,7 @@ package"_Section_accelerate.html. "tersoff/zbl/omp"_pair_tersoff_zbl.html, "tip4p/cut/omp"_pair_coul.html, "tip4p/long/omp"_pair_coul.html, +"tip4p/long/soft/omp"_pair_lj_soft.html, "tri/lj/omp"_pair_tri_lj.html, "yukawa/gpu"_pair_yukawa.html, "yukawa/omp"_pair_yukawa.html, diff --git a/doc/Section_packages.html b/doc/Section_packages.html index edadfad0f3..55e3901ea4 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -119,6 +119,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries. USER-COLVARS collective variables Fiorin & Henin & Kohlmeyer (3) fix colvars USER/colvars colvars lib/colvars USER-CUDA NVIDIA GPU styles Christian Trott (U Tech Ilmenau) Section accelerate USER/cuda - lib/cuda USER-EFF electron force field Andres Jaramillo-Botero (Caltech) pair_style eff/cut USER/eff eff - +USER-FEP free energy perturbation Agilio Padua (U Blaise Pascal Clermont-Ferrand) fix adapt/fep USER/fep - - USER-LB Lattice Boltzmann fluid Colin Denniston (U Western Ontario) fix lb/fluid USER/lb - - USER-MISC single-file contributions USER-MISC/README USER-MISC/README - - - USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile - - VMD-MOLFILE @@ -276,8 +277,12 @@ used in a LAMMPS input script. Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and Restraints. This code consists of two parts:

-