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Changes from Mike Changes from Mike Brown. 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5280 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
pscrozi 2010-11-23 00:51:42 +00:00
parent 64dc05333c
commit a20cc3b588
14 changed files with 700 additions and 183 deletions
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46
doc/Section_commands.html
View File

@ -311,7 +311,7 @@ included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD></TR>
@ -335,7 +335,7 @@ in the command's documentation.
<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions
of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD></TR>
@ -351,7 +351,7 @@ of each style or click on the style itself for a full description:
<P>These are fix styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
</TD></TR></TABLE></DIV>
@ -363,7 +363,7 @@ of each style or click on the style itself for a full description:
<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
@ -377,7 +377,7 @@ each style or click on the style itself for a full description:
<P>These are compute styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A>
</TD></TR></TABLE></DIV>
@ -388,7 +388,7 @@ each style or click on the style itself for a full description:
<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD></TR>
@ -400,20 +400,22 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
</TD></TR></TABLE></DIV>
<HR>
@ -423,7 +425,7 @@ potentials. Click on the style itself for a full description:
<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic</A></TD><TD WIDTH="100"><A HREF = "bond_table.html">table</A>
@ -436,7 +438,7 @@ potentials. Click on the style itself for a full description:
<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
angle potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
@ -445,7 +447,7 @@ angle potentials. Click on the style itself for a full description:
<P>These are angle styles contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_cmm.html">cg/cmm</A>
</TD></TR></TABLE></DIV>
@ -457,7 +459,7 @@ angle potentials. Click on the style itself for a full description:
of dihedral potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls</A>
</TD></TR></TABLE></DIV>
@ -470,7 +472,7 @@ description:
of improper potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
</TD></TR></TABLE></DIV>
@ -482,14 +484,14 @@ description:
<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
Kspace solvers. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
</TD></TR></TABLE></DIV>
<P>These are Kspace solvers contributed by users, which can be used if
<A HREF = "Section_start.html#2_3">LAMMPS is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/n</A>
</TD></TR></TABLE></DIV>

5
doc/Section_commands.txt
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@ -605,14 +605,17 @@ potentials. Click on the style itself for a full description:
"lj/cut/gpu"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/cut/coul/cut"_pair_lj.html,
"lj/cut/coul/cut/gpu"_pair_lj.html,
"lj/cut/coul/debye"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
"lj/cut/coul/long/tip4p"_pair_lj.html,
"lj/expand"_pair_lj_expand.html,
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/smooth"_pair_lj_smooth.html,
"lj96/cut"_pair_lj96_cut.html,
"lj96/cut/gpu"_pair_lj96_cut.html,
"lubricate"_pair_lubricate.html,
"meam"_pair_meam.html,
"morse"_pair_morse.html,
@ -634,8 +637,10 @@ These are pair styles contributed by users, which can be used if
"buck/coul"_pair_buck_coul.html,
"cg/cmm"_pair_cmm.html,
"cg/cmm/gpu"_pair_cmm.html,
"cg/cmm/coul/cut"_pair_cmm.html,
"cg/cmm/coul/long"_pair_cmm.html,
"cg/cmm/coul/long/gpu"_pair_cmm.html,
"eam/cd"_pair_eam.html,
"eff/cut"_pair_eff.html,
"lj/coul"_pair_lj_coul.html,

158
doc/Section_start.html
View File

@ -403,9 +403,9 @@ LAMMPS is built.
the files in these packages require other packages to also be
included. If this is not the case, then those subsidiary files in
"gpu" and "opt" will not be installed either. To install all the
files in package "gpu", the "asphere" package must also be installed.
To install all the files in package "opt", the "kspace" and "manybody"
packages must also be installed.
files in package "gpu", the "asphere" and "kspace" packages must also be
installed. To install all the files in package "opt", the "kspace" and
"manybody" packages must also be installed.
</P>
<P>You may wish to exclude certain packages if you will never run certain
kinds of simulations. This will keep you from having to build
@ -909,53 +909,141 @@ certain NVIDIA CUDA software on your system:
</P>
<UL><LI>Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
<LI>Go to http://www.nvidia.com/object/cuda_get.html
<LI>Install a driver and toolkit appopriate for your system (SDK is not necessary)
<LI>Run make in lammps/lib/gpu, editing a Makefile if necessary
<LI>Install a driver and toolkit appropriate for your system (SDK is not necessary)
<LI>Follow the instructions in README in lammps/lib/gpu to build the library.
<LI>Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties
</UL>
<H4>GPU hardware
<H4>GPU configuration
</H4>
<P>When using GPUs, you are restricted to one physical GPU per LAMMPS
process. This can be multiple GPUs on a single node or across
multiple nodes. For each GPU pair style, the first two arguments (GPU
mode followed by GPU ID) control how GPUs are selected. If you are
running on a single node, the mode is "one/node" and the parameter is
the ID of the first GPU to select:
process. Multiple processes can share a single GPU and in many cases it
will be more efficient to run with multiple processes per GPU. Any GPU
accelerated style requires that <A HREF = "fix_gpu.html">fix gpu</A> be used in the
input script to select and initialize the GPUs. The format for the fix
is:
</P>
<PRE>pair_style lj/cut/gpu one/node 0 2.5
<PRE>fix <I>name</I> all gpu <I>mode</I> <I>first</I> <I>last</I> <I>split</I>
</PRE>
<P>The ID is the GPU ID reported by the driver for CUDA enabled graphics
cards. For multiple GPU cards on a node, an MPI process should be run
for each graphics card. In this case, each process will grab the GPU
with ID equal to the process rank plus the GPU parameter.
<P>where <I>name</I> is the name for the fix. The gpu fix must be the first
fix specified for a given run, otherwise the program will exit
with an error. The gpu fix will not have any effect on runs
that do not use GPU acceleration; there should be no problem
with specifying the fix first in any input script.
</P>
<P>For multiple nodes with one GPU per node, the mode is "one/gpu" and
the parameter is the ID of the GPU used on every node:
<P><I>mode</I> can be either "force" or "force/neigh". In the former,
neighbor list calculation is performed on the CPU using the
standard LAMMPS routines. In the latter, the neighbor list
calculation is performed on the GPU. The GPU neighbor list
can be used for better performance, however, it
should not be used with a triclinic box.
</P>
<PRE>pair_style lj/cut/gpu one/gpu 1 2.5
<P>There are cases when it might be more efficient to select the CPU for neighbor
list builds. If a non-GPU enabled style requires a neighbor list, it will also
be built using CPU routines. Redundant CPU and GPU neighbor list calculations
will typically be less efficient. For <A HREF = "pair_hybrid.html">hybrid</A> pair
styles, GPU calculated neighbor lists might be less efficient because
no particles will be skipped in a given neighbor list.
</P>
<P><I>first</I> is the ID (as reported by lammps/lib/gpu/nvc_get_devices)
of the first GPU that will be used on each node. <I>last</I> is the
ID of the last GPU that will be used on each node. If you have
only one GPU per node, <I>first</I> and <I>last</I> will typically both be
0. Selecting a non-sequential set of GPU IDs (e.g. 0,1,3)
is not currently supported.
</P>
<P><I>split</I> is the fraction of particles whose forces, torques,
energies, and/or virials will be calculated on the GPU. This
can be used to perform CPU and GPU force calculations
simultaneously. If <I>split</I> is negative, the software will
attempt to calculate the optimal fraction automatically
every 25 timesteps based on CPU and GPU timings. Because the GPU speedups
are dependent on the number of particles, automatic calculation of the
split can be less efficient, but typically results in loop times
within 20% of an optimal fixed split.
</P>
<P>If you have two GPUs per node, 8 CPU cores per node, and
would like to run on 4 nodes with dynamic balancing of
force calculation across CPU and GPU cores, the fix
might be
</P>
<PRE>fix 0 all gpu force/neigh 0 1 -1
</PRE>
<P>In this case, MPI should be run with exactly one process per node.
<P>with LAMMPS run on 32 processes. In this case, all
CPU cores and GPU devices on the nodes would be utilized.
Each GPU device would be shared by 4 CPU cores. The
CPU cores would perform force calculations for some
fraction of the particles at the same time the GPUs
performed force calculation for the other particles.
</P>
<P>For multiple nodes with multiple GPUs, the mode is "multi/gpu" and the
parameter is the number of GPUs per node:
<P>Because of the large number of cores on each GPU
device, it might be more efficient to run on fewer
processes per GPU when the number of particles per process
is small (100's of particles); this can be necessary
to keep the GPU cores busy.
</P>
<PRE>pair_style lj/cut/gpu multi/gpu 3 2.5
</PRE>
<P>In this case, LAMMPS will attempt to grab 3 GPUs per node and this
requires that the number of processes per node be 3. The first GPU
selected must have ID zero for this mode (in the example, GPUs 0, 1,
and 2 will be selected on every node). An additional constraint is
that the MPI processes must be filled by slot on each node such that
the process ranks on each node are always sequential. This is a option
for the MPI launcher (mpirun/mpiexec) and will be the default on many
clusters.
<H4>GPU input script
</H4>
<P>In order to use GPU acceleration in LAMMPS,
<A HREF = "fix_gpu.html">fix_gpu</A>
should be used in order to initialize and configure the
GPUs for use. Additionally, GPU enabled styles must be
selected in the input script. Currently,
this is limited to a few <A HREF = "pair_style.html">pair styles</A>.
Some GPU-enabled styles have additional restrictions
listed in their documentation.
</P>
<H4>GPU asynchronous pair computation
</H4>
<P>The GPU accelerated pair styles can be used to perform
pair style force calculation on the GPU while other
calculations are
performed on the CPU. One method to do this is to specify
a <I>split</I> in the gpu fix as described above. In this case,
force calculation for the pair style will also be performed
on the CPU.
</P>
<P>When the CPU work in a GPU pair style has finished,
the next force computation will begin, possibly before the
GPU has finished. If <I>split</I> is 1.0 in the gpu fix, the next
force computation will begin almost immediately. This can
be used to run a <A HREF = "pair_hybrid.html">hybrid</A> GPU pair style at
the same time as a hybrid CPU pair style. In this case, the
GPU pair style should be first in the hybrid command in order to
perform simultaneous calculations. This also
allows <A HREF = "bond_style.html">bond</A>, <A HREF = "angle_style.html">angle</A>,
<A HREF = "dihedral_style.html">dihedral</A>, <A HREF = "improper_style.html">improper</A>,
and <A HREF = "kspace_style.html">long-range</A> force
computations to be run simultaneously with the GPU pair style.
Once all CPU force computations have completed, the gpu fix
will block until the GPU has finished all work before continuing
the run.
</P>
<H4>GPU timing
</H4>
<P>GPU accelerated pair styles can perform computations asynchronously
with CPU computations. The "Pair" time reported by LAMMPS
will be the maximum of the time required to complete the CPU
pair style computations and the time required to complete the GPU
pair style computations. Any time spent for GPU-enabled pair styles
for computations that run simultaneously with <A HREF = "bond_style.html">bond</A>,
<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A> calculations
will not be included in the "Pair" time.
</P>
<P>When <I>mode</I> for the gpu fix is force/neigh,
the time for neighbor list calculations on the GPU will be added
into the "Pair" time, not the "Neigh" time. A breakdown of the
times required for various tasks on the GPU (data copy, neighbor
calculations, force computations, etc.) are output only
with the LAMMPS screen output at the end of each run. These timings represent
total time spent on the GPU for each routine, regardless of asynchronous
CPU calculations.
</P>
<H4>GPU single vs double precision
</H4>
<P>See the lammps/lib/gpu/README file for instructions on how to build
the LAMMPS gpu library for single vs double precision. The latter
requires that your GPU card supports double precision. The lj/cut/gpu
pair style does not support double precision.
the LAMMPS gpu library for single, mixed, and double precision. The latter
requires that your GPU card supports double precision.
</P>
<HR>

156
doc/Section_start.txt
View File

@ -396,9 +396,9 @@ The two exceptions to this are the "gpu" and "opt" packages. Some of
the files in these packages require other packages to also be
included. If this is not the case, then those subsidiary files in
"gpu" and "opt" will not be installed either. To install all the
files in package "gpu", the "asphere" package must also be installed.
To install all the files in package "opt", the "kspace" and "manybody"
packages must also be installed.
files in package "gpu", the "asphere" and "kspace" packages must also be
installed. To install all the files in package "opt", the "kspace" and
"manybody" packages must also be installed.
You may wish to exclude certain packages if you will never run certain
kinds of simulations. This will keep you from having to build
@ -899,53 +899,141 @@ certain NVIDIA CUDA software on your system:
Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
Go to http://www.nvidia.com/object/cuda_get.html
Install a driver and toolkit appopriate for your system (SDK is not necessary)
Run make in lammps/lib/gpu, editing a Makefile if necessary
Install a driver and toolkit appropriate for your system (SDK is not necessary)
Follow the instructions in README in lammps/lib/gpu to build the library.
Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties :ul
GPU hardware :h4
GPU configuration :h4
When using GPUs, you are restricted to one physical GPU per LAMMPS
process. This can be multiple GPUs on a single node or across
multiple nodes. For each GPU pair style, the first two arguments (GPU
mode followed by GPU ID) control how GPUs are selected. If you are
running on a single node, the mode is "one/node" and the parameter is
the ID of the first GPU to select:
process. Multiple processes can share a single GPU and in many cases it
will be more efficient to run with multiple processes per GPU. Any GPU
accelerated style requires that "fix gpu"_fix_gpu.html be used in the
input script to select and initialize the GPUs. The format for the fix
is:
pair_style lj/cut/gpu one/node 0 2.5 :pre
fix {name} all gpu {mode} {first} {last} {split} :pre
The ID is the GPU ID reported by the driver for CUDA enabled graphics
cards. For multiple GPU cards on a node, an MPI process should be run
for each graphics card. In this case, each process will grab the GPU
with ID equal to the process rank plus the GPU parameter.
where {name} is the name for the fix. The gpu fix must be the first
fix specified for a given run, otherwise the program will exit
with an error. The gpu fix will not have any effect on runs
that do not use GPU acceleration; there should be no problem
with specifying the fix first in any input script.
For multiple nodes with one GPU per node, the mode is "one/gpu" and
the parameter is the ID of the GPU used on every node:
{mode} can be either "force" or "force/neigh". In the former,
neighbor list calculation is performed on the CPU using the
standard LAMMPS routines. In the latter, the neighbor list
calculation is performed on the GPU. The GPU neighbor list
can be used for better performance, however, it
should not be used with a triclinic box.
pair_style lj/cut/gpu one/gpu 1 2.5 :pre
There are cases when it might be more efficient to select the CPU for neighbor
list builds. If a non-GPU enabled style requires a neighbor list, it will also
be built using CPU routines. Redundant CPU and GPU neighbor list calculations
will typically be less efficient. For "hybrid"_pair_hybrid.html pair
styles, GPU calculated neighbor lists might be less efficient because
no particles will be skipped in a given neighbor list.
In this case, MPI should be run with exactly one process per node.
{first} is the ID (as reported by lammps/lib/gpu/nvc_get_devices)
of the first GPU that will be used on each node. {last} is the
ID of the last GPU that will be used on each node. If you have
only one GPU per node, {first} and {last} will typically both be
0. Selecting a non-sequential set of GPU IDs (e.g. 0,1,3)
is not currently supported.
For multiple nodes with multiple GPUs, the mode is "multi/gpu" and the
parameter is the number of GPUs per node:
{split} is the fraction of particles whose forces, torques,
energies, and/or virials will be calculated on the GPU. This
can be used to perform CPU and GPU force calculations
simultaneously. If {split} is negative, the software will
attempt to calculate the optimal fraction automatically
every 25 timesteps based on CPU and GPU timings. Because the GPU speedups
are dependent on the number of particles, automatic calculation of the
split can be less efficient, but typically results in loop times
within 20% of an optimal fixed split.
pair_style lj/cut/gpu multi/gpu 3 2.5 :pre
If you have two GPUs per node, 8 CPU cores per node, and
would like to run on 4 nodes with dynamic balancing of
force calculation across CPU and GPU cores, the fix
might be
In this case, LAMMPS will attempt to grab 3 GPUs per node and this
requires that the number of processes per node be 3. The first GPU
selected must have ID zero for this mode (in the example, GPUs 0, 1,
and 2 will be selected on every node). An additional constraint is
that the MPI processes must be filled by slot on each node such that
the process ranks on each node are always sequential. This is a option
for the MPI launcher (mpirun/mpiexec) and will be the default on many
clusters.
fix 0 all gpu force/neigh 0 1 -1 :pre
with LAMMPS run on 32 processes. In this case, all
CPU cores and GPU devices on the nodes would be utilized.
Each GPU device would be shared by 4 CPU cores. The
CPU cores would perform force calculations for some
fraction of the particles at the same time the GPUs
performed force calculation for the other particles.
Because of the large number of cores on each GPU
device, it might be more efficient to run on fewer
processes per GPU when the number of particles per process
is small (100's of particles); this can be necessary
to keep the GPU cores busy.
GPU input script :h4
In order to use GPU acceleration in LAMMPS,
"fix_gpu"_fix_gpu.html
should be used in order to initialize and configure the
GPUs for use. Additionally, GPU enabled styles must be
selected in the input script. Currently,
this is limited to a few "pair styles"_pair_style.html.
Some GPU-enabled styles have additional restrictions
listed in their documentation.
GPU asynchronous pair computation :h4
The GPU accelerated pair styles can be used to perform
pair style force calculation on the GPU while other
calculations are
performed on the CPU. One method to do this is to specify
a {split} in the gpu fix as described above. In this case,
force calculation for the pair style will also be performed
on the CPU.
When the CPU work in a GPU pair style has finished,
the next force computation will begin, possibly before the
GPU has finished. If {split} is 1.0 in the gpu fix, the next
force computation will begin almost immediately. This can
be used to run a "hybrid"_pair_hybrid.html GPU pair style at
the same time as a hybrid CPU pair style. In this case, the
GPU pair style should be first in the hybrid command in order to
perform simultaneous calculations. This also
allows "bond"_bond_style.html, "angle"_angle_style.html,
"dihedral"_dihedral_style.html, "improper"_improper_style.html,
and "long-range"_kspace_style.html force
computations to be run simultaneously with the GPU pair style.
Once all CPU force computations have completed, the gpu fix
will block until the GPU has finished all work before continuing
the run.
GPU timing :h4
GPU accelerated pair styles can perform computations asynchronously
with CPU computations. The "Pair" time reported by LAMMPS
will be the maximum of the time required to complete the CPU
pair style computations and the time required to complete the GPU
pair style computations. Any time spent for GPU-enabled pair styles
for computations that run simultaneously with "bond"_bond_style.html,
"angle"_angle_style.html, "dihedral"_dihedral_style.html,
"improper"_improper_style.html, and "long-range"_kspace_style.html calculations
will not be included in the "Pair" time.
When {mode} for the gpu fix is force/neigh,
the time for neighbor list calculations on the GPU will be added
into the "Pair" time, not the "Neigh" time. A breakdown of the
times required for various tasks on the GPU (data copy, neighbor
calculations, force computations, etc.) are output only
with the LAMMPS screen output at the end of each run. These timings represent
total time spent on the GPU for each routine, regardless of asynchronous
CPU calculations.
GPU single vs double precision :h4
See the lammps/lib/gpu/README file for instructions on how to build
the LAMMPS gpu library for single vs double precision. The latter
requires that your GPU card supports double precision. The lj/cut/gpu
pair style does not support double precision.
the LAMMPS gpu library for single, mixed, and double precision. The latter
requires that your GPU card supports double precision.
:line

107
doc/fix_gpu.html Normal file
View File

@ -0,0 +1,107 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID gpu mode first last split
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>gpu = style name of this fix command
<LI>mode = force or force/neigh
<LI>first = ID of first GPU to be used on each node
<LI>last = ID of last GPU to be used on each node
<LI>split = fraction of particles assigned to the GPU
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 0 all gpu force 0 0 1.0
fix 0 all gpu force 0 0 0.75
fix 0 all gpu force/neigh 0 0 1.0
fix 0 all gpu force/neigh 0 1 -1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Select and initialize GPUs to be used for acceleration and configure
GPU acceleration in LAMMPS. This fix is required in order to use
any style with GPU acceleration. The fix must be the first fix
specified for a run or an error will be generated. The fix will not have an
effect on any LAMMPS computations that do not use GPU acceleration, so there
should not be any problems with specifying this fix first in input scripts.
</P>
<P><I>mode</I> specifies where neighbor list calculations will be performed.
If <I>mode</I> is force, neighbor list calculation is performed on the
CPU. If <I>mode</I> is force/neigh, neighbor list calculation is
performed on the GPU. GPU neighbor
list calculation currently cannot be used with a triclinic box.
GPU neighbor lists are not compatible with styles that are not GPU-enabled.
When a non-GPU enabled style requires a neighbor list, it will also be
built using CPU routines. In these cases, it will typically be more efficient
to only use CPU neighbor list builds. For <A HREF = "pair_hybrid.html">hybrid</A> pair
styles, GPU calculated neighbor lists might be less efficient because
no particles will be skipped in a given neighbor list.
</P>
<P><I>first</I> and <I>last</I> specify the GPUs that will be used for simulation.
On each node, the GPU IDs in the inclusive range from <I>first</I> to <I>last</I> will
be used.
</P>
<P><I>split</I> can be used for load balancing force calculation work between
CPU and GPU cores in GPU-enabled pair styles. If 0<<I>split</I><1.0,
a fixed fraction of particles is offloaded to the GPU while force calculation
for the other particles occurs simulataneously on the CPU. If <I>split</I><0,
the optimal fraction (based on CPU and GPU timings) is calculated
every 25 timesteps. If <I>split</I>=1.0, all force calculations for
GPU accelerated pair styles are performed
on the GPU. In this case, <A HREF = "pair_hybrid.html">hybrid</A>,
<A HREF = "bond_style.html">bond</A>, <A HREF = "angle_style.html">angle</A>,
<A HREF = "dihedral_style.html">dihedral</A>, <A HREF = "improper_style.html">improper</A>,
and <A HREF = "kspace_style.html">long-range</A> calculations can be performed on the CPU
while the GPU is performing force calculations for the GPU-enabled pair
style.
</P>
<P>In order to use GPU acceleration, a GPU enabled style must be
selected in the input script in addition to this fix. Currently,
this is limited to a few <A HREF = "pair_style.html">pair styles</A>.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>The fix must be the first fix specified for a given run. The force/neigh
<I>mode</I> should not be used with a triclinic box or GPU-enabled pair styles
that need <A HREF = "special_bonds.html">special_bonds</A> settings.
</P>
<P>Currently, group-ID must be all.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

97
doc/fix_gpu.txt Normal file
View File

@ -0,0 +1,97 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix gpu command :h3
[Syntax:]
fix ID group-ID gpu mode first last split :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
gpu = style name of this fix command :l
mode = force or force/neigh :l
first = ID of first GPU to be used on each node :l
last = ID of last GPU to be used on each node :l
split = fraction of particles assigned to the GPU :l
:ule
[Examples:]
fix 0 all gpu force 0 0 1.0
fix 0 all gpu force 0 0 0.75
fix 0 all gpu force/neigh 0 0 1.0
fix 0 all gpu force/neigh 0 1 -1.0 :pre
[Description:]
Select and initialize GPUs to be used for acceleration and configure
GPU acceleration in LAMMPS. This fix is required in order to use
any style with GPU acceleration. The fix must be the first fix
specified for a run or an error will be generated. The fix will not have an
effect on any LAMMPS computations that do not use GPU acceleration, so there
should not be any problems with specifying this fix first in input scripts.
{mode} specifies where neighbor list calculations will be performed.
If {mode} is force, neighbor list calculation is performed on the
CPU. If {mode} is force/neigh, neighbor list calculation is
performed on the GPU. GPU neighbor
list calculation currently cannot be used with a triclinic box.
GPU neighbor lists are not compatible with styles that are not GPU-enabled.
When a non-GPU enabled style requires a neighbor list, it will also be
built using CPU routines. In these cases, it will typically be more efficient
to only use CPU neighbor list builds. For "hybrid"_pair_hybrid.html pair
styles, GPU calculated neighbor lists might be less efficient because
no particles will be skipped in a given neighbor list.
{first} and {last} specify the GPUs that will be used for simulation.
On each node, the GPU IDs in the inclusive range from {first} to {last} will
be used.
{split} can be used for load balancing force calculation work between
CPU and GPU cores in GPU-enabled pair styles. If 0<{split}<1.0,
a fixed fraction of particles is offloaded to the GPU while force calculation
for the other particles occurs simulataneously on the CPU. If {split}<0,
the optimal fraction (based on CPU and GPU timings) is calculated
every 25 timesteps. If {split}=1.0, all force calculations for
GPU accelerated pair styles are performed
on the GPU. In this case, "hybrid"_pair_hybrid.html,
"bond"_bond_style.html, "angle"_angle_style.html,
"dihedral"_dihedral_style.html, "improper"_improper_style.html,
and "long-range"_kspace_style.html calculations can be performed on the CPU
while the GPU is performing force calculations for the GPU-enabled pair
style.
In order to use GPU acceleration, a GPU enabled style must be
selected in the input script in addition to this fix. Currently,
this is limited to a few "pair styles"_pair_style.html.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
[Restrictions:]
The fix must be the first fix specified for a given run. The force/neigh
{mode} should not be used with a triclinic box or GPU-enabled pair styles
that need "special_bonds"_special_bonds.html settings.
Currently, group-ID must be all.
[Related commands:] none
[Default:] none

39
doc/pair_cmm.html
View File

@ -11,19 +11,25 @@
<H3>pair_style cg/cmm command
</H3>
<H3>pair_style cg/cmm/gpu command
</H3>
<H3>pair_style cg/cmm/coul/cut command
</H3>
<H3>pair_style cg/cmm/coul/long command
</H3>
<H3>pair_style cg/cmm/coul/long/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>cg/cmm</I> or <I>cg/cmm/coul/cut</I> or <I>cg/cmm/coul/long</I>
<UL><LI>style = <I>cg/cmm</I> or <I>cg/cmm/gpu</I> or <I>cg/cmm/coul/cut</I> or <I>cg/cmm/coul/long</I> or <I>cg/cmm/coul/long/gpu</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>cg/cmm</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/gpu</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/coul/cut</I> args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -32,6 +38,10 @@
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<PRE> <I>cg/cmm/coul/long/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style cg/cmm 2.5
@ -55,6 +65,9 @@ given by
<P>as required for the CMM Coarse-grained MD parametrization discussed in
<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
</P>
<P>Style <I>cg/cmm/gpu</I> is a GPU-enabled version of style <I>cg/cmm</I>.
See more details below.
</P>
<P>Style <I>cg/cmm/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
@ -83,6 +96,9 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>cg/cmm/coul/long/gpu</I> is a GPU-enabled version of style <I>cg/cmm/coul/long</I>.
See more details below.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -113,6 +129,27 @@ pair_style command.
</P>
<HR>
<P>The <I>cg/cmm/gpu</I> and <I>cg/cmm/coul/long/gpu</I> styles
are identical to the <I>cg/cmm</I> and <I>cg/cmm/coul/long</I>
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
</P>
<P>Additional requirements in your input script to run with GPU-enabled styles
are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients

36
doc/pair_cmm.txt
View File

@ -7,17 +7,21 @@
:line
pair_style cg/cmm command :h3
pair_style cg/cmm/gpu command :h3
pair_style cg/cmm/coul/cut command :h3
pair_style cg/cmm/coul/long command :h3
pair_style cg/cmm/coul/long/gpu command :h3
[Syntax:]
pair_style style args :pre
style = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long}
style = {cg/cmm} or {cg/cmm/gpu} or {cg/cmm/coul/cut} or {cg/cmm/coul/long} or {cg/cmm/coul/long/gpu}
args = list of arguments for a particular style :ul
{cg/cmm} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{cg/cmm/gpu} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -25,6 +29,9 @@ args = list of arguments for a particular style :ul
{cg/cmm/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
{cg/cmm/coul/long/gpu} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
@ -49,6 +56,9 @@ given by
as required for the CMM Coarse-grained MD parametrization discussed in
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
Style {cg/cmm/gpu} is a GPU-enabled version of style {cg/cmm}.
See more details below.
Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
@ -77,6 +87,9 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {cg/cmm/coul/long/gpu} is a GPU-enabled version of style {cg/cmm/coul/long}.
See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -107,6 +120,27 @@ pair_style command.
:line
The {cg/cmm/gpu} and {cg/cmm/coul/long/gpu} styles
are identical to the {cg/cmm} and {cg/cmm/coul/long}
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
Additional requirements in your input script to run with GPU-enabled styles
are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps.
:line
[Mixing, shift, table, tail correction, restart, and rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients

34
doc/pair_gayberne.html
View File

@ -17,11 +17,9 @@
</P>
<PRE>pair_style gayberne gamma upsilon mu cutoff
</PRE>
<PRE>pair_style gayberne/gpu gpuflag gpunum gamma upsilon mu cutoff
<PRE>pair_style gayberne/gpu gamma upsilon mu cutoff
</PRE>
<UL><LI>style = <I>gayberne</I> or <I>gayberne/gpu</I>
<LI>gpumode = <I>one/node</I> or <I>one/gpu</I> or <I>multi/gpu</I>, only used with gayberne/gpu
<LI>gpuID = ID or number of GPUs, only used with gayberne/gpu
<LI>gamma = shift for potential minimum (typically 1)
<LI>upsilon = exponent for eta orientation-dependent energy function
<LI>mu = exponent for chi orientation-dependent energy function
@ -30,7 +28,7 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
pair_style gayberne/gpu one/node 0 1.0 1.0 1.0 10.0
pair_style gayberne/gpu 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</PRE>
<P><B>Description:</B>
@ -50,10 +48,8 @@ both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical").
</P>
<P>Style <I>gayberne/gpu</I> is a GPU-enabled version of style <I>gayberne</I> that
should give identical answers. Depending on system size and the GPU
processor you have on your system, it may be 100x faster (for the
pairwise portion of the run time). See more details below.
<P>Style <I>gayberne/gpu</I> is a GPU-enabled version of style <I>gayberne</I>.
See more details below.
</P>
<P>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
@ -141,27 +137,11 @@ to specify its interaction with other spherical particles.
<P>The <I>gayberne/gpu</I> style is identical to the <I>gayberne</I> style, except
that each processor off-loads its pairwise calculations to a GPU chip.
Depending on the hardware available on your system this can provide a
significant speed-up, espcially for the relatively expensive
significant speed-up, especially for the relatively expensive
computations inherent in Gay-Berne interactions. See the <A HREF = "Section_start.html#2_8">Running on
GPUs</A> section of the manual for more details
about hardware and software requirements for using GPUs.
</P>
<P>The <I>gpumode</I> and <I>gpuID</I> settings in the pair_style command refer to
how the GPUs on your system are configured.
</P>
<P>Set <I>gpumode</I> to <I>one/node</I> if you have a single compute "node" on
your system, which may have multiple cores and/or GPUs. <I>GpuID</I>
should be set to the ID of the (first) GPU you wish to use with LAMMPS
(another GPU might be driving your display).
</P>
<P>Set <I>gpumode</I> to <I>one/gpu</I> if you have multiple compute "nodes" on
your system, with one GPU per node. <I>GpuID</I> should be set to the ID
of the GPU.
</P>
<P>Set <I>gpumode</I> to <I>multi/gpu</I> if you have multiple compute "nodes" on
your system, each with multiple GPUs. <I>GpuID</I> should be set to the
number of GPUs per node.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
@ -169,7 +149,9 @@ manual.
<P>Additional requirements in your input script to run with style
<I>gayberne/gpu</I> are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I>.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps.
</P>
<HR>

34
doc/pair_gayberne.txt
View File

@ -12,11 +12,9 @@ pair_style gayberne/gpu command :h3
[Syntax:]
pair_style gayberne gamma upsilon mu cutoff :pre
pair_style gayberne/gpu gpuflag gpunum gamma upsilon mu cutoff :pre
pair_style gayberne/gpu gamma upsilon mu cutoff :pre
style = {gayberne} or {gayberne/gpu}
gpumode = {one/node} or {one/gpu} or {multi/gpu}, only used with gayberne/gpu
gpuID = ID or number of GPUs, only used with gayberne/gpu
gamma = shift for potential minimum (typically 1)
upsilon = exponent for eta orientation-dependent energy function
mu = exponent for chi orientation-dependent energy function
@ -25,7 +23,7 @@ cutoff = global cutoff for interactions (distance units) :ul
[Examples:]
pair_style gayberne 1.0 1.0 1.0 10.0
pair_style gayberne/gpu one/node 0 1.0 1.0 1.0 10.0
pair_style gayberne/gpu 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:]
@ -45,10 +43,8 @@ both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical").
Style {gayberne/gpu} is a GPU-enabled version of style {gayberne} that
should give identical answers. Depending on system size and the GPU
processor you have on your system, it may be 100x faster (for the
pairwise portion of the run time). See more details below.
Style {gayberne/gpu} is a GPU-enabled version of style {gayberne}.
See more details below.
For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
@ -136,27 +132,11 @@ to specify its interaction with other spherical particles.
The {gayberne/gpu} style is identical to the {gayberne} style, except
that each processor off-loads its pairwise calculations to a GPU chip.
Depending on the hardware available on your system this can provide a
significant speed-up, espcially for the relatively expensive
significant speed-up, especially for the relatively expensive
computations inherent in Gay-Berne interactions. See the "Running on
GPUs"_Section_start.html#2_8 section of the manual for more details
about hardware and software requirements for using GPUs.
The {gpumode} and {gpuID} settings in the pair_style command refer to
how the GPUs on your system are configured.
Set {gpumode} to {one/node} if you have a single compute "node" on
your system, which may have multiple cores and/or GPUs. {GpuID}
should be set to the ID of the (first) GPU you wish to use with LAMMPS
(another GPU might be driving your display).
Set {gpumode} to {one/gpu} if you have multiple compute "nodes" on
your system, with one GPU per node. {GpuID} should be set to the ID
of the GPU.
Set {gpumode} to {multi/gpu} if you have multiple compute "nodes" on
your system, each with multiple GPUs. {GpuID} should be set to the
number of GPUs per node.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
@ -164,7 +144,9 @@ manual.
Additional requirements in your input script to run with style
{gayberne/gpu} are as follows:
The "newton pair"_newton.html setting must be {off}.
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps.
:line

50
doc/pair_lj.html
View File

@ -17,30 +17,35 @@
</H3>
<H3>pair_style lj/cut/coul/cut command
</H3>
<H3>pair_style lj/cut/coul/cut/gpu command
</H3>
<H3>pair_style lj/cut/coul/debye command
</H3>
<H3>pair_style lj/cut/coul/long command
</H3>
<H3>pair_style lj/cut/coul/long/gpu command
</H3>
<H3>pair_style lj/cut/coul/long/tip4p command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/gpu</I> or <I>lj/cut/opt</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/tip4p</I>
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/gpu</I> or <I>lj/cut/opt</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/tip4p</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/cut</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/gpu</I> args = gpumode gpuID cutoff
gpumode = <I>one/node</I> or <I>one/gpu</I> or <I>multi/gpu</I>
gpuID = ID or number of GPUs
<I>lj/cut/gpu</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/opt</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/cut/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/debye</I> args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
@ -48,6 +53,9 @@
<I>lj/cut/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long/gpu</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long/tip4p</I> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -58,12 +66,13 @@
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut 2.5
pair_style lj/cut/gpu one/node 0 2.5
pair_style lj/cut/gpu 2.5
pair_style lj/cut/opt 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
</PRE>
<PRE>pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut/gpu 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -76,6 +85,7 @@ pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
</PRE>
<PRE>pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/gpu 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -94,10 +104,8 @@ given by
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut</I> that
should give identical answers. Depending on system size and the GPU
processor you have on your system, it may be 4x faster (for the
pairwise portion of the run time). See more details below.
<P>Style <I>lj/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut</I>.
See more details below.
</P>
<P>Style <I>lj/cut/opt</I> is an optimized version of style <I>lj/cut</I> that
should give identical answers. Depending on system size and the
@ -115,6 +123,9 @@ specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>Style <I>lj/cut/coul/cut/gpu</I> is a GPU-enabled version of style <I>lj/cut/coul/cut</I>.
See more details below.
</P>
<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
to the Coulombic term, given by
</P>
@ -131,6 +142,9 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>lj/cut/coul/long/gpu</I> is a GPU-enabled version of style <I>lj/cut/coul/long</I>.
See more details below.
</P>
<P>Style <I>lj/cut/coul/long/tip4p</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
@ -177,9 +191,10 @@ Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P>The <I>lj/cut/gpu</I> style is identical to the <I>lj/cut</I> style, except that
each processor off-loads its pairwise calculations to a GPU chip.
Depending on the hardware available on your system this can provide a
<P>The <I>lj/cut/gpu</I>, <I>lj/cut/coul/cut/gpu</I>, and <I>lj/cut/coul/long/gpu</I> styles
are identical to the <I>lj/cut</I>, <I>lj/cut/coul/cut</I>, and <I>lj/cut/coul/long</I>
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
@ -204,10 +219,12 @@ number of GPUs per node.
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
</P>
<P>Additional requirements in your input script to run with style
<I>lj/cut/gpu</I> are as follows:
<P>Additional requirements in your input script to run with GPU-enabled styles
are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I>.
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls
the essential GPU selection and initialization steps.
</P>
<HR>
@ -248,7 +265,8 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> styles are part of
the "kspace" package. The <I>lj/cut/gpu</I> style is part of the "gpu"
the "kspace" package. The <I>lj/cut/gpu</I>, <I>lj/cut/coul/cut/gpu</I>, and
<I>lj/cut/coul/long/gpu</I> styles are part of the "gpu"
package. The <I>lj/cut/opt</I> style is part of the "opt" package. They
are only enabled if LAMMPS was built with those packages. See the
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info. Note

50
doc/pair_lj.txt
View File

@ -10,28 +10,31 @@ pair_style lj/cut command :h3
pair_style lj/cut/gpu command :h3
pair_style lj/cut/opt command :h3
pair_style lj/cut/coul/cut command :h3
pair_style lj/cut/coul/cut/gpu command :h3
pair_style lj/cut/coul/debye command :h3
pair_style lj/cut/coul/long command :h3
pair_style lj/cut/coul/long/gpu command :h3
pair_style lj/cut/coul/long/tip4p command :h3
[Syntax:]
pair_style style args :pre
style = {lj/cut} or {lj/cut/gpu} or {lj/cut/opt} or {lj/cut/coul/cut} or {lj/cut/coul/debye} \
or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
style = {lj/cut} or {lj/cut/gpu} or {lj/cut/opt} or {lj/cut/coul/cut} \
or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
args = list of arguments for a particular style :ul
{lj/cut} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/gpu} args = gpumode gpuID cutoff
gpumode = {one/node} or {one/gpu} or {multi/gpu}
gpuID = ID or number of GPUs
{lj/cut/gpu} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/opt} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/cut/gpu} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/debye} args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
@ -39,6 +42,9 @@ args = list of arguments for a particular style :ul
{lj/cut/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long/gpu} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long/tip4p} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -49,12 +55,13 @@ args = list of arguments for a particular style :ul
[Examples:]
pair_style lj/cut 2.5
pair_style lj/cut/gpu one/node 0 2.5
pair_style lj/cut/gpu 2.5
pair_style lj/cut/opt 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 :pre
pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut/gpu 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
@ -67,6 +74,7 @@ pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0 :pre
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long/gpu 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
@ -85,10 +93,8 @@ given by
Rc is the cutoff.
Style {lj/cut/gpu} is a GPU-enabled version of style {lj/cut} that
should give identical answers. Depending on system size and the GPU
processor you have on your system, it may be 4x faster (for the
pairwise portion of the run time). See more details below.
Style {lj/cut/gpu} is a GPU-enabled version of style {lj/cut}.
See more details below.
Style {lj/cut/opt} is an optimized version of style {lj/cut} that
should give identical answers. Depending on system size and the
@ -106,6 +112,9 @@ specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
Style {lj/cut/coul/cut/gpu} is a GPU-enabled version of style {lj/cut/coul/cut}.
See more details below.
Style {lj/cut/coul/debye} adds an additional exp() damping factor
to the Coulombic term, given by
@ -122,6 +131,9 @@ option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {lj/cut/coul/long/gpu} is a GPU-enabled version of style {lj/cut/coul/long}.
See more details below.
Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
@ -168,9 +180,10 @@ Coulombic cutoff specified in the pair_style command.
:line
The {lj/cut/gpu} style is identical to the {lj/cut} style, except that
each processor off-loads its pairwise calculations to a GPU chip.
Depending on the hardware available on your system this can provide a
The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and {lj/cut/coul/long/gpu} styles
are identical to the {lj/cut}, {lj/cut/coul/cut}, and {lj/cut/coul/long}
styles, except that each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
@ -195,10 +208,12 @@ More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
Additional requirements in your input script to run with style
{lj/cut/gpu} are as follows:
Additional requirements in your input script to run with GPU-enabled styles
are as follows:
The "newton pair"_newton.html setting must be {off}.
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls
the essential GPU selection and initialization steps.
:line
@ -239,7 +254,8 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
the "kspace" package. The {lj/cut/gpu} style is part of the "gpu"
the "kspace" package. The {lj/cut/gpu}, {lj/cut/coul/cut/gpu}, and
{lj/cut/coul/long/gpu} styles are part of the "gpu"
package. The {lj/cut/opt} style is part of the "opt" package. They
are only enabled if LAMMPS was built with those packages. See the
"Making LAMMPS"_Section_start.html#2_3 section for more info. Note

37
doc/pair_lj96_cut.html
View File

@ -11,15 +11,19 @@
<H3>pair_style lj96/cut command
</H3>
<H3>pair_style lj96/cut/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj96/cut cutoff
<PRE>pair_style style cutoff
</PRE>
<UL><LI>cutoff = global cutoff for lj96/cut interactions (distance units)
<UL><LI>style = <I>lj96/cut</I> or <I>lj96/cut/gpu</I>
<LI>cutoff = global cutoff for lj96/cut interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj96/cut 2.5
pair_style lj96/cut/gpu 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0
</PRE>
@ -32,6 +36,9 @@ of the standard 12/6 potential, given by
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj96/cut/gpu</I> is a GPU-enabled version of style <I>lj96/cut</I>.
See more details below.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
@ -47,6 +54,26 @@ cutoff specified in the pair_style command is used.
</P>
<HR>
<P>The <I>lj96/cut/gpu</I> style is identical to the <I>lj96/cut</I> style, except that
each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the <A HREF = "Section_start.html#2_8">Running on GPUs</A> section of
the manual for more details about hardware and software requirements
for using GPUs.
</P>
<P>More details about these settings and various possible hardware
configuration are in <A HREF = "Section_start.html#2_8">this section</A> of the
manual.
</P>
<P>Additional requirements in your input script to run with the <I>lj96/cut/gpu</I>
style are as follows:
</P>
<P>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I> and
<A HREF = "fix_gpu.html">fix gpu</A> must be used. The fix controls the
essential GPU selection and initialization steps
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
@ -76,7 +103,11 @@ details.
</P>
<HR>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>The <I>lj96/cut/gpu</I> style is part of the "gpu" package. It
is only enabled if LAMMPS is built with this packages. See the
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

34
doc/pair_lj96_cut.txt
View File

@ -7,16 +7,19 @@
:line
pair_style lj96/cut command :h3
pair_style lj96/cut/gpu command :h3
[Syntax:]
pair_style lj96/cut cutoff :pre
pair_style style cutoff :pre
style = {lj96/cut} or {lj96/cut/gpu}
cutoff = global cutoff for lj96/cut interactions (distance units) :ul
[Examples:]
pair_style lj96/cut 2.5
pair_style lj96/cut/gpu 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 :pre
@ -29,6 +32,9 @@ of the standard 12/6 potential, given by
Rc is the cutoff.
Style {lj96/cut/gpu} is a GPU-enabled version of style {lj96/cut}.
See more details below.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
@ -44,6 +50,26 @@ cutoff specified in the pair_style command is used.
:line
The {lj96/cut/gpu} style is identical to the {lj96/cut} style, except that
each processor off-loads its pairwise calculations to a
GPU chip. Depending on the hardware available on your system this can provide a
speed-up. See the "Running on GPUs"_Section_start.html#2_8 section of
the manual for more details about hardware and software requirements
for using GPUs.
More details about these settings and various possible hardware
configuration are in "this section"_Section_start.html#2_8 of the
manual.
Additional requirements in your input script to run with the {lj96/cut/gpu}
style are as follows:
The "newton pair"_newton.html setting must be {off} and
"fix gpu"_fix_gpu.html must be used. The fix controls the
essential GPU selection and initialization steps
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
@ -73,7 +99,11 @@ details.
:line
[Restrictions:] none
[Restrictions:]
The {lj96/cut/gpu} style is part of the "gpu" package. It
is only enabled if LAMMPS is built with this packages. See the
"Making LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]