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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@281 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-02-09 21:37:30 +00:00
parent 6e94c3652b
commit 47b87458b0
78 changed files with 3062 additions and 2395 deletions
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16
doc/Manual.html
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@ -59,13 +59,17 @@ we can improve the LAMMPS documentation.
<BR>
2.2 <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#2_3">Running LAMMPS</A>
2.3 <A HREF = "#2_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#2_4">Command-line options</A>
2.4 <A HREF = "#2_4">Building LAMMPS as a library</A>
<BR>
2.5 <A HREF = "Section_start.html#2_5">Screen output</A>
2.5 <A HREF = "Section_start.html#2_5">Running LAMMPS</A>
<BR>
2.6 <A HREF = "Section_start.html#2_6">Tips for users of previous versions</A>
2.6 <A HREF = "Section_start.html#2_6">Command-line options</A>
<BR>
2.7 <A HREF = "Section_start.html#2_7">Screen output</A>
<BR>
2.8 <A HREF = "Section_start.html#2_8">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
@ -182,6 +186,10 @@ we can improve the LAMMPS documentation.

12
doc/Manual.txt
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@ -47,10 +47,12 @@ we can improve the LAMMPS documentation.
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_2_1 :ulb,b
2.2 "Making LAMMPS"_2_2 :b
2.3 "Running LAMMPS"_2_3 :b
2.4 "Command-line options"_2_4 :b
2.5 "Screen output"_2_5 :b
2.6 "Tips for users of previous versions"_2_6 :ule,b
2.3 "Making LAMMPS with optional packages"_#2_3 :b
2.4 "Building LAMMPS as a library"_#2_4 :b
2.5 "Running LAMMPS"_2_5 :b
2.6 "Command-line options"_2_6 :b
2.7 "Screen output"_2_7 :b
2.8 "Tips for users of previous versions"_2_8 :ule,b
"Commands"_Section_commands.html :l
3.1 "LAMMPS input script"_3_1 :ulb,b
3.2 "Parsing rules"_3_2 :b
@ -93,6 +95,8 @@ we can improve the LAMMPS documentation.
:link(2_4,Section_start.html#2_4)
:link(2_5,Section_start.html#2_5)
:link(2_6,Section_start.html#2_6)
:link(2_7,Section_start.html#2_7)
:link(2_8,Section_start.html#2_8)
:link(3_1,Section_commands.html#3_1)
:link(3_2,Section_commands.html#3_2)

155
doc/Section_commands.html
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@ -181,7 +181,6 @@ set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "special_bonds.html">special_bonds</A>.
</P>
<P>Various simulation parameters are set by these commands:
<A HREF = "temperature.html">temperature</A>, <A HREF = "temp_modify.html">temp_modify</A>,
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
@ -190,8 +189,13 @@ set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
<P>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
</P>
<P>Output options are set by these commands: <A HREF = "thermo.html">thermo</A>,
<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A>.
<P>Various computations can be specified for execution during a
simulation using the <A HREF = "compute.html">compute</A>,
<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
commands.
</P>
<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
and <A HREF = "restart.html">restart</A> commands.
</P>
<P>(4) Run a simulation
</P>
@ -245,14 +249,17 @@ in the command's documentation.
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "set.html">set</A>, <A HREF = "temp_modify.html">temp_modify</A>,
<A HREF = "temperature.html">temperature</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "velocity.html">velocity</A>
<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
</P>
<P>Computes:
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
<A HREF = "uncompute.html">uncompute</A>
</P>
<P>Output:
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_modify.html">dump_modify</A>,
@ -288,83 +295,109 @@ in the command's documentation.
</P>
<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 = "clear.html">clear</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temp_modify.html">temp_modify</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "temperature.html">temperature</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "undump.html">undump</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<P>Fix styles. See the <A HREF = "fix.html">fix</A> command for one-line descriptions
or click on the command itself for a full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">fix addforce</A></TD><TD ><A HREF = "fix_aveforce.html">fix aveforce</A></TD><TD ><A HREF = "fix_com.html">fix com</A></TD><TD ><A HREF = "fix_deposit.html">fix deposit</A></TD><TD ><A HREF = "fix_drag.html">fix drag</A></TD><TD ><A HREF = "fix_efield.html">fix efield</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">fix enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">fix freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">fix gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">fix gravity</A></TD><TD ><A HREF = "fix_gyration.html">fix gyration</A></TD><TD ><A HREF = "fix_indent.html">fix indent</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">fix langevin</A></TD><TD ><A HREF = "fix_lineforce.html">fix lineforce</A></TD><TD ><A HREF = "fix_msd.html">fix msd</A></TD><TD ><A HREF = "fix_momentum.html">fix momentum</A></TD><TD ><A HREF = "fix_nph.html">fix nph</A></TD><TD ><A HREF = "fix_npt.html">fix npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">fix nve</A></TD><TD ><A HREF = "fix_nve_gran.html">fix nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">fix nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">fix orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">fix planeforce</A></TD><TD ><A HREF = "fix_poems.html">fix poems</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">fix pour</A></TD><TD ><A HREF = "fix_print.html">fix print</A></TD><TD ><A HREF = "fix_rdf.html">fix rdf</A></TD><TD ><A HREF = "fix_recenter.html">fix recenter</A></TD><TD ><A HREF = "fix_rigid.html">fix rigid</A></TD><TD ><A HREF = "fix_setforce.html">fix setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">fix shake</A></TD><TD ><A HREF = "fix_spring.html">fix spring</A></TD><TD ><A HREF = "fix_spring_rg.html">fix spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">fix spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">fix temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">fix tmd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_uniaxial.html">fix uniaxial</A></TD><TD ><A HREF = "fix_vcm.html">fix vcm</A></TD><TD ><A HREF = "fix_viscous.html">fix viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">fix volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">fix wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">fix wall/lj93</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj126.html">fix wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">fix wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
<P>Pair styles. 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
<P>Fix commands. 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 WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_style_none.html">none</A></TD><TD ><A HREF = "pair_style_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_style_buck.html">buck</A></TD><TD ><A HREF = "pair_style_buck.html">buck/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_style_dpd.html">dpd</A></TD><TD ><A HREF = "pair_style_eam.html">eam</A></TD><TD ><A HREF = "pair_style_eam.html">eam/alloy</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_style_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_style_gran.html">gran/history</A></TD><TD ><A HREF = "pair_style_gran.html">gran/no_history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_style_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_style_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_style_class2.html">lj/class2</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_style_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_style_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_style_lj_expand.html">lj/expand</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_style_meam.html">meam</A></TD><TD ><A HREF = "pair_style_morse.html">morse</A></TD><TD ><A HREF = "pair_style_soft.html">soft</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style_sw.html">sw</A></TD><TD ><A HREF = "pair_style_table.html">table</A></TD><TD ><A HREF = "pair_style_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_style_yukawa.html">yukawa</A>
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD><TD ><A HREF = "fix_vcm.html">vcm</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<P>Bond styles. 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
<HR>
<P>Compute commands. 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 WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_style_fene.html">fene</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_style_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_style_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_style_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_style_nonlinear.html">nonlinear</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_style_quartic.html">quartic</A>
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_etotal_atom.html">etotal/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A>
</TD></TR></TABLE></DIV>
<P>Angle styles. 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
<HR>
<P>Pair_style potentials. 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 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_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_dpd.html">dpd</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_gran.html">gran/history</A></TD><TD ><A HREF = "pair_gran.html">gran/no_history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</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/tip4p</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
</TD></TR></TABLE></DIV>
<HR>
<P>Bond_style potentials. 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 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></TR></TABLE></DIV>
<HR>
<P>Angle_style potentials. 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 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_squared.html">cosine/squared</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A>
</TD></TR></TABLE></DIV>
<HR>
<P>Dihedral_style potentials. See the
<A HREF = "dihedral_style.html">dihedral_style</A> command for an overview of
dihedral potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_style_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "angle_style_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_style_cosine_squared.html">cosine/squared</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_style_harmonic.html">harmonic</A>
<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>
<P>Dihedral styles. See the <A HREF = "dihedral_style.html">dihedral_style</A> command
for an overview of dihedral potentials. Click on the style itself for
a full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_style_multi_harmonic.html">multi/harmonic</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_style_opls.html">opls</A>
</TD></TR></TABLE></DIV>
<HR>
<P>Improper styles. See the <A HREF = "improper_style.html">improper_style</A> command for an
overview of improper potentials. Click on the style itself for a full
<P>Improper_style potentials. See the
<A HREF = "improper_style.html">improper_style</A> command for an overview of
improper potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_style_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_style_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_style_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_style_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_style_harmonic.html">harmonic</A>
<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></TR></TABLE></DIV>
</HTML>

306
doc/Section_commands.txt
View File

@ -178,7 +178,6 @@ set in the read-in files): "pair_coeff"_pair_coeff.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"temperature"_temperature.html, "temp_modify"_temp_modify.html,
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
@ -187,8 +186,13 @@ Various simulation parameters are set by these commands:
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Output options are set by these commands: "thermo"_thermo.html,
"dump"_dump.html, "restart"_restart.html.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
@ -242,14 +246,17 @@ Settings:
"min_modify"_min_modify.html, "min_style"_min_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"set"_set.html, "temp_modify"_temp_modify.html,
"temperature"_temperature.html, "timestep"_timestep.html,
"velocity"_velocity.html
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
Fixes:
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
Computes:
"compute"_compute.html, "compute_modify"_compute_modify.html,
"uncompute"_uncompute.html
Output:
"dump"_dump.html, "dump_modify"_dump_modify.html,
@ -291,6 +298,8 @@ in the command's documentation.
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"clear"_clear.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
@ -341,13 +350,12 @@ in the command's documentation.
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"temp_modify"_temp_modify.html,
"temper"_temper.html,
"temperature"_temperature.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
@ -355,137 +363,177 @@ in the command's documentation.
"velocity"_velocity.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
Fix styles. See the "fix"_fix.html command for one-line descriptions
or click on the command itself for a full description:
:line
"fix addforce"_fix_addforce.html,
"fix aveforce"_fix_aveforce.html,
"fix com"_fix_com.html,
"fix deposit"_fix_deposit.html,
"fix drag"_fix_drag.html,
"fix efield"_fix_efield.html,
"fix enforce2d"_fix_enforce2d.html,
"fix freeze"_fix_freeze.html,
"fix gran/diag"_fix_gran_diag.html,
"fix gravity"_fix_gravity.html,
"fix gyration"_fix_gyration.html,
"fix indent"_fix_indent.html,
"fix langevin"_fix_langevin.html,
"fix lineforce"_fix_lineforce.html,
"fix msd"_fix_msd.html,
"fix momentum"_fix_momentum.html,
"fix nph"_fix_nph.html,
"fix npt"_fix_npt.html,
"fix nve"_fix_nve.html,
"fix nve/gran"_fix_nve_gran.html,
"fix nvt"_fix_nvt.html,
"fix orient/fcc"_fix_orient_fcc.html,
"fix planeforce"_fix_planeforce.html,
"fix poems"_fix_poems.html,
"fix pour"_fix_pour.html,
"fix print"_fix_print.html,
"fix rdf"_fix_rdf.html,
"fix recenter"_fix_recenter.html,
"fix rigid"_fix_rigid.html,
"fix setforce"_fix_setforce.html,
"fix shake"_fix_shake.html,
"fix spring"_fix_spring.html,
"fix spring/rg"_fix_spring_rg.html,
"fix spring/self"_fix_spring_self.html,
"fix temp/rescale"_fix_temp_rescale.html,
"fix tmd"_fix_tmd.html,
"fix uniaxial"_fix_uniaxial.html,
"fix vcm"_fix_vcm.html,
"fix viscous"_fix_viscous.html,
"fix volume/rescale"_fix_volume_rescale.html,
"fix wall/gran"_fix_wall_gran.html,
"fix wall/lj93"_fix_wall_lj93.html,
"fix wall/lj126"_fix_wall_lj126.html,
"fix wall/reflect"_fix_wall_reflect.html,
"fix wiggle"_fix_wiggle.html :tb(c=6,ea=c)
Pair styles. See the "pair_style"_pair_style.html command for an
overview of pair potentials. Click on the style itself for a full
Fix commands. See the "fix"_fix.html command for one-line
descriptions of each style or click on the style itself for a full
description:
"none"_pair_style_none.html,
"hybrid"_pair_style_hybrid.html,
"buck"_pair_style_buck.html,
"buck/coul/cut"_pair_style_buck.html,
"buck/coul/long"_pair_style_buck.html,
"dpd"_pair_style_dpd.html,
"eam"_pair_style_eam.html,
"eam/alloy"_pair_style_eam.html,
"eam/fs"_pair_style_eam.html,
"gran/hertzian"_pair_style_gran.html,
"gran/history"_pair_style_gran.html,
"gran/no_history"_pair_style_gran.html,
"lj/charmm/coul/charmm"_pair_style_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_style_charmm.html,
"lj/charmm/coul/long"_pair_style_charmm.html,
"lj/class2"_pair_style_class2.html,
"lj/class2/coul/cut"_pair_style_class2.html,
"lj/class2/coul/long"_pair_style_class2.html,
"lj/cut"_pair_style_lj.html,
"lj/cut/coul/cut"_pair_style_lj.html,
"lj/cut/coul/debye"_pair_style_lj.html,
"lj/cut/coul/long"_pair_style_lj.html,
"lj/cut/coul/long/tip4p"_pair_style_lj.html,
"lj/expand"_pair_style_lj_expand.html,
"lj/smooth"_pair_style_lj_smooth.html,
"meam"_pair_style_meam.html,
"morse"_pair_style_morse.html,
"soft"_pair_style_soft.html,
"sw"_pair_style_sw.html,
"table"_pair_style_table.html,
"tersoff"_pair_style_tersoff.html,
"yukawa"_pair_style_yukawa.html :tb(c=4,ea=c)
"addforce"_fix_addforce.html,
"aveforce"_fix_aveforce.html,
"com"_fix_com.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"efield"_fix_efield.html,
"enforce2d"_fix_enforce2d.html,
"freeze"_fix_freeze.html,
"gran/diag"_fix_gran_diag.html,
"gravity"_fix_gravity.html,
"gyration"_fix_gyration.html,
"indent"_fix_indent.html,
"langevin"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"msd"_fix_msd.html,
"momentum"_fix_momentum.html,
"nph"_fix_nph.html,
"npt"_fix_npt.html,
"nve"_fix_nve.html,
"nve/gran"_fix_nve_gran.html,
"nvt"_fix_nvt.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"print"_fix_print.html,
"rdf"_fix_rdf.html,
"recenter"_fix_recenter.html,
"rigid"_fix_rigid.html,
"setforce"_fix_setforce.html,
"shake"_fix_shake.html,
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"temp/rescale"_fix_temp_rescale.html,
"tmd"_fix_tmd.html,
"uniaxial"_fix_uniaxial.html,
"vcm"_fix_vcm.html,
"viscous"_fix_viscous.html,
"volume/rescale"_fix_volume_rescale.html,
"wall/gran"_fix_wall_gran.html,
"wall/lj93"_fix_wall_lj93.html,
"wall/lj126"_fix_wall_lj126.html,
"wall/reflect"_fix_wall_reflect.html,
"wiggle"_fix_wiggle.html :tb(c=8,ea=c)
Bond styles. See the "bond_style"_bond_style.html command for an
overview of bond potentials. Click on the style itself for a full
:line
Compute commands. See the "compute"_compute.html command for one-line
descriptions of each style or click on the style itself for a full
description:
"none"_bond_style_none.html,
"hybrid"_bond_style_hybrid.html,
"class2"_bond_style_class2.html,
"fene"_bond_style_fene.html,
"fene/expand"_bond_style_fene_expand.html,
"harmonic"_bond_style_harmonic.html,
"morse"_bond_style_morse.html,
"nonlinear"_bond_style_nonlinear.html,
"quartic"_bond_style_quartic.html :tb(c=4,ea=c,w=100)
"centro/atom"_compute_centro_atom.html,
"epair/atom"_compute_epair_atom.html,
"etotal/atom"_compute_etotal_atom.html,
"ke/atom"_compute_ke_atom.html,
"pressure"_compute_pressure.html,
"rotate/dipole"_compute_rotate_dipole.html,
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/partial"_compute_temp_partial.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html :tb(c=6,ea=c)
Angle styles. See the "angle_style"_angle_style.html command for an
overview of angle potentials. Click on the style itself for a full
:line
Pair_style potentials. See the "pair_style"_pair_style.html command
for an overview of pair potentials. Click on the style itself for a
full description:
"none"_pair_none.html,
"hybrid"_pair_hybrid.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
"dpd"_pair_dpd.html,
"eam"_pair_eam.html,
"eam/opt"_pair_eam.html,
"eam/alloy"_pair_eam.html,
"eam/alloy/opt"_pair_eam.html,
"eam/fs"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"gran/hertzian"_pair_gran.html,
"gran/history"_pair_gran.html,
"gran/no_history"_pair_gran.html,
"lj/charmm/coul/charmm"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
"lj/charmm/coul/long"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/class2"_pair_class2.html,
"lj/class2/coul/cut"_pair_class2.html,
"lj/class2/coul/long"_pair_class2.html,
"lj/cut"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/cut/coul/cut"_pair_lj.html,
"lj/cut/coul/debye"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/long/tip4p"_pair_lj.html,
"lj/expand"_pair_lj_expand.html,
"lj/smooth"_pair_lj_smooth.html,
"meam"_pair_meam.html,
"morse"_pair_morse.html,
"morse/opt"_pair_morse.html,
"soft"_pair_soft.html,
"sw"_pair_sw.html,
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"yukawa"_pair_yukawa.html :tb(c=4,ea=c)
:line
Bond_style potentials. See the "bond_style"_bond_style.html command
for an overview of bond potentials. Click on the style itself for a
full description:
"none"_bond_none.html,
"hybrid"_bond_hybrid.html,
"class2"_bond_class2.html,
"fene"_bond_fene.html,
"fene/expand"_bond_fene_expand.html,
"harmonic"_bond_harmonic.html,
"morse"_bond_morse.html,
"nonlinear"_bond_nonlinear.html,
"quartic"_bond_quartic.html :tb(c=4,ea=c,w=100)
:line
Angle_style potentials. See the "angle_style"_angle_style.html
command for an overview of angle potentials. Click on the style
itself for a full description:
"none"_angle_none.html,
"hybrid"_angle_hybrid.html,
"charmm"_angle_charmm.html,
"class2"_angle_class2.html,
"cosine"_angle_cosine.html,
"cosine/squared"_angle_cosine_squared.html,
"harmonic"_angle_harmonic.html :tb(c=4,ea=c,w=100)
:line
Dihedral_style potentials. See the
"dihedral_style"_dihedral_style.html command for an overview of
dihedral potentials. Click on the style itself for a full
description:
"none"_angle_style_none.html,
"hybrid"_angle_style_hybrid.html,
"charmm"_angle_style_charmm.html,
"class2"_angle_style_class2.html,
"cosine"_angle_style_cosine.html,
"cosine/squared"_angle_style_cosine_squared.html,
"harmonic"_angle_style_harmonic.html :tb(c=6,ea=c,w=100)
"none"_dihedral_none.html,
"hybrid"_dihedral_hybrid.html,
"charmm"_dihedral_charmm.html,
"class2"_dihedral_class2.html,
"harmonic"_dihedral_harmonic.html,
"helix"_dihedral_helix.html,
"multi/harmonic"_dihedral_multi_harmonic.html,
"opls"_dihedral_opls.html :tb(c=4,ea=c,w=100)
Dihedral styles. See the "dihedral_style"_dihedral_style.html command
for an overview of dihedral potentials. Click on the style itself for
a full description:
:line
"none"_dihedral_style_none.html,
"hybrid"_dihedral_style_hybrid.html,
"charmm"_dihedral_style_charmm.html,
"class2"_dihedral_style_class2.html,
"harmonic"_dihedral_style_harmonic.html,
"helix"_dihedral_style_helix.html,
"multi/harmonic"_dihedral_style_multi_harmonic.html,
"opls"_dihedral_style_opls.html :tb(c=7,ea=c,w=100)
Improper styles. See the "improper_style"_improper_style.html command for an
overview of improper potentials. Click on the style itself for a full
Improper_style potentials. See the
"improper_style"_improper_style.html command for an overview of
improper potentials. Click on the style itself for a full
description:
"none"_improper_style_none.html,
"hybrid"_improper_style_hybrid.html,
"class2"_improper_style_class2.html,
"cvff"_improper_style_cvff.html,
"harmonic"_improper_style_harmonic.html :tb(c=4,ea=c,w=100)
"none"_improper_none.html,
"hybrid"_improper_hybrid.html,
"class2"_improper_class2.html,
"cvff"_improper_cvff.html,
"harmonic"_improper_harmonic.html :tb(c=4,ea=c,w=100)

4
doc/Section_errors.html
View File

@ -1,5 +1,7 @@
<HTML>
<CENTER><A HREF = "Section_modify.html">Previous Section</A> - <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> - <A HREF = "Section_history.html">Next Section</A>
<CENTER><A HREF = "Section_modify.html">Previous Section</A> - <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> - <A HREF = "Section_history.html">Next
Section</A>
</CENTER>

4
doc/Section_errors.txt
View File

@ -1,4 +1,6 @@
"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_history.html :c
"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_history.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)

94
doc/Section_howto.html
View File

@ -263,7 +263,7 @@ jump in.polymer
<P>All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in <A HREF = "Section_start.html#2_4">this
the "-partition" command-line switch as described in <A HREF = "Section_start.html#2_6">this
section</A> of the manual.
</P>
<P>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
@ -287,7 +287,7 @@ simulation are run at different temperatures on different sets of
processors, and Monte Carlo temperature swaps are performed between
pairs of copies.
</P>
<P>Use the -procs and -in <A HREF = "Section_start.html#2_4">command-line switches</A>
<P>Use the -procs and -in <A HREF = "Section_start.html#2_6">command-line switches</A>
to launch LAMMPS on multiple partitions.
</P>
<P>In your input script, define a set of temperatures, one for each
@ -409,10 +409,12 @@ This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of <I>harmonic</I> and an
angle style of <I>harmonic</I> or <I>charmm</I> should also be used.
</P>
<P>Two different four-point models (cutoff and long-range Coulombics) can
be implemented using LAMMPS pair styles with <I>tip4p</I> in their style
name. For both models, the bond lengths and bond angles should be
held fixed using the <A HREF = "fix_shake.html">fix shake</A> command.
<P>Currently, only a four-point model for long-range Coulombics is
implemented via the LAMMPS <A HREF = "pair_lj.html">pair style
lj/cut/coul/long/tip4p</A>. We plan to add a cutoff
version in the future. For both models, the bond lengths and bond
angles should be held fixed using the <A HREF = "fix_shake.html">fix shake</A>
command.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
@ -510,16 +512,16 @@ a new fix to LAMMPS.
<P>(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other
code is not called during the timesteps of a LAMMPS run, but between
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
<A HREF = "run.html">run</A> command facilitates this with its <I>every</I> option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
</P>
<P>In this scenario, the other code can be a library, called by the
command, or it could be a stand-alone code, invoked by a system() call
<P>In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
@ -535,49 +537,55 @@ Again, the <A HREF = "run.html">run</A> command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.
</P>
<P><A HREF = "Section_start.html#2_2">This section</A> of the documentation describes
how to build LAMMPS as a library. Once this is done, you can interface
with LAMMPS either via C++, C, or Fortran (or any other language that
supports a vanilla C-like interface, e.g. a scripting language). For
example, from C++ you could create an "instance" of LAMMPS, and
initialize it, pass it an input script to process, or execute
<P><A HREF = "Section_start.html#2_4">This section</A> of the documentation describes
how to build LAMMPS as a library. Once this is done, you can
interface with LAMMPS either via C++, C, or Fortran (or any other
language that supports a vanilla C-like interface, e.g. a scripting
language). For example, from C++ you could create one (or more)
"instances" of LAMMPS, pass it an input script to process, or execute
individual commands, all by invoking the correct class methods in
LAMMPS. From C or Fortran you would make function calls to do the
same things. Library.cpp and library.h contain such a C interface
that illustrates this with the functions:
LAMMPS. From C or Fortran you can make function calls to do the same
things. Library.cpp and library.h contain such a C interface with the
functions:
</P>
<PRE>void lammps_open(int, char **, MPI_Comm);
void lammps_close();
void lammps_file(char *);
char *lammps_command(char *);
<PRE>void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *);
void lammps_file(void *, char *);
char *lammps_command(doivd *, char *);
</PRE>
<P>The functions contain the C++ code you would need to put in a C++
application that was invoking LAMMPS directly.
<P>The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are
defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application.
</P>
<P>Two of the routines in library.cpp are of particular note. The
lammps_open() function initiates LAMMPS and takes an MPI communicator
as an argument. LAMMPS will run on the set of processors in the
communicator. This means the calling code can run LAMMPS on all or a
subset of processors. For example, a wrapper script might decide to
alternate between LAMMPS and another code, allowing them both to run
on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically.
as an argument. It returns a pointer to a LAMMPS "object". As with
C++, the lammps_open() function can be called mutliple times, to
create multiple instances of LAMMPS.
</P>
<P>Library.cpp also contains a lammps_command() function to which the
caller passes a single LAMMPS command (a string). Thus the calling
code can read or generate a series of LAMMPS commands (e.g. an input
script) one line at a time and pass it thru the library interface to
setup a problem and then run it.
<P>LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically.
</P>
<P>A few other sample routines are included in library.cpp, but the key
idea is that you can write any routines you wish to define an
<P>Library.cpp contains a lammps_command() function to which the caller
passes a single LAMMPS command (a string). Thus the calling code can
read or generate a series of LAMMPS commands (e.g. an input script)
one line at a time and pass it thru the library interface to setup a
problem and then run it.
</P>
<P>A few other sample functions are included in library.cpp, but the key
idea is that you can write any functions you wish to define an
interface for how your code talks to LAMMPS and add them to
library.cpp and library.h. The routines you add can access any LAMMPS
data. The umbrella.cpp code in examples/couple is a simple example of
how a stand-alone code can link LAMMPS as a library, run LAMMPS on a
subset of processors, grab data from LAMMPS, change it, and put it
back into LAMMPS.
data. The examples/couple directory has example C++ and C codes which
show how a stand-alone code can link LAMMPS as a library, run LAMMPS
on a subset of processors, grab data from LAMMPS, change it, and put
it back into LAMMPS.
</P>
<HR>

94
doc/Section_howto.txt
View File

@ -260,7 +260,7 @@ All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
the "-partition" command-line switch as described in "this
section"_Section_start.html#2_4 of the manual.
section"_Section_start.html#2_6 of the manual.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
@ -283,7 +283,7 @@ simulation are run at different temperatures on different sets of
processors, and Monte Carlo temperature swaps are performed between
pairs of copies.
Use the -procs and -in "command-line switches"_Section_start.html#2_4
Use the -procs and -in "command-line switches"_Section_start.html#2_6
to launch LAMMPS on multiple partitions.
In your input script, define a set of temperatures, one for each
@ -405,10 +405,12 @@ This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of {harmonic} and an
angle style of {harmonic} or {charmm} should also be used.
Two different four-point models (cutoff and long-range Coulombics) can
be implemented using LAMMPS pair styles with {tip4p} in their style
name. For both models, the bond lengths and bond angles should be
held fixed using the "fix shake"_fix_shake.html command.
Currently, only a four-point model for long-range Coulombics is
implemented via the LAMMPS "pair style
lj/cut/coul/long/tip4p"_pair_lj.html. We plan to add a cutoff
version in the future. For both models, the bond lengths and bond
angles should be held fixed using the "fix shake"_fix_shake.html
command.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
@ -506,16 +508,16 @@ a new fix to LAMMPS.
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other
code is not called during the timesteps of a LAMMPS run, but between
other code are on a more equal footing. Note that now the other code
is not called during the timestepping of a LAMMPS run, but between
runs. The LAMMPS input script can be used to alternate LAMMPS runs
with calls to the other code, invoked via the new command. The
"run"_run.html command facilitates this with its {every} option, which
makes it easy to run a few steps, invoke the command, run a few steps,
invoke the command, etc.
In this scenario, the other code can be a library, called by the
command, or it could be a stand-alone code, invoked by a system() call
In this scenario, the other code can be called as a library, as in
(1), or it could be a stand-alone code, invoked by a system() call
made by the command (assuming your parallel machine allows one or more
processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
@ -531,49 +533,55 @@ Again, the "run"_run.html command has options that allow it to be
invoked with minimal overhead (no setup or clean-up) if you wish to do
multiple short runs, driven by another program.
"This section"_Section_start.html#2_2 of the documentation describes
how to build LAMMPS as a library. Once this is done, you can interface
with LAMMPS either via C++, C, or Fortran (or any other language that
supports a vanilla C-like interface, e.g. a scripting language). For
example, from C++ you could create an "instance" of LAMMPS, and
initialize it, pass it an input script to process, or execute
"This section"_Section_start.html#2_4 of the documentation describes
how to build LAMMPS as a library. Once this is done, you can
interface with LAMMPS either via C++, C, or Fortran (or any other
language that supports a vanilla C-like interface, e.g. a scripting
language). For example, from C++ you could create one (or more)
"instances" of LAMMPS, pass it an input script to process, or execute
individual commands, all by invoking the correct class methods in
LAMMPS. From C or Fortran you would make function calls to do the
same things. Library.cpp and library.h contain such a C interface
that illustrates this with the functions:
LAMMPS. From C or Fortran you can make function calls to do the same
things. Library.cpp and library.h contain such a C interface with the
functions:
void lammps_open(int, char **, MPI_Comm);
void lammps_close();
void lammps_file(char *);
char *lammps_command(char *); :pre
void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *);
void lammps_file(void *, char *);
char *lammps_command(doivd *, char *); :pre
The functions contain the C++ code you would need to put in a C++
application that was invoking LAMMPS directly.
The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are
defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application.
Two of the routines in library.cpp are of particular note. The
lammps_open() function initiates LAMMPS and takes an MPI communicator
as an argument. LAMMPS will run on the set of processors in the
communicator. This means the calling code can run LAMMPS on all or a
subset of processors. For example, a wrapper script might decide to
alternate between LAMMPS and another code, allowing them both to run
on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically.
as an argument. It returns a pointer to a LAMMPS "object". As with
C++, the lammps_open() function can be called mutliple times, to
create multiple instances of LAMMPS.
Library.cpp also contains a lammps_command() function to which the
caller passes a single LAMMPS command (a string). Thus the calling
code can read or generate a series of LAMMPS commands (e.g. an input
script) one line at a time and pass it thru the library interface to
setup a problem and then run it.
LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
processors. For example, a wrapper script might decide to alternate
between LAMMPS and another code, allowing them both to run on all the
processors. Or it might allocate half the processors to LAMMPS and
half to the other code and run both codes simultaneously before
syncing them up periodically.
A few other sample routines are included in library.cpp, but the key
idea is that you can write any routines you wish to define an
Library.cpp contains a lammps_command() function to which the caller
passes a single LAMMPS command (a string). Thus the calling code can
read or generate a series of LAMMPS commands (e.g. an input script)
one line at a time and pass it thru the library interface to setup a
problem and then run it.
A few other sample functions are included in library.cpp, but the key
idea is that you can write any functions you wish to define an
interface for how your code talks to LAMMPS and add them to
library.cpp and library.h. The routines you add can access any LAMMPS
data. The umbrella.cpp code in examples/couple is a simple example of
how a stand-alone code can link LAMMPS as a library, run LAMMPS on a
subset of processors, grab data from LAMMPS, change it, and put it
back into LAMMPS.
data. The examples/couple directory has example C++ and C codes which
show how a stand-alone code can link LAMMPS as a library, run LAMMPS
on a subset of processors, grab data from LAMMPS, change it, and put
it back into LAMMPS.
:line

678
doc/Section_modify.html
View File

@ -14,29 +14,34 @@ Section</A>
<H3>8. Modifying & extending LAMMPS
</H3>
<P>LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In this section, changes and additions
users can make are listed along with some minimal instructions.
Realistically, the best way to add a new feature is to find a similar
feature in LAMMPS and look at the corresponding source and header
files to figure out what it does. You will need some knowledge of C++
to be able to understand the hi-level structure of LAMMPS and its
class organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
extend with new functionality. In fact, about 75% if its source code
is files added in this fashion.
</P>
<P>In this section, changes and additions users can make are listed along
with minimal instructions. The best way to add a new feature is to
find a similar feature in LAMMPS and look at the corresponding source
and header files to figure out what it does. You will need some
knowledge of C++ to be able to understand the hi-level structure of
LAMMPS and its class organization, but functions (class methods) that
do actual computations are written in vanilla C-style code and operate
on simple C-style data structures (vectors and arrays).
</P>
<P>Most of the new features described in this section require you to
write a new C++ class (except for dump, thermo, and variable options,
described below, where you can make small edits to existing files).
Creating a new class requires 2 files, a source code file (*.cpp) and
a header file (*.h). Their contents are briefly discussed below.
Enabling LAMMPS to invoke the new class is as simple as adding two
definition lines to the style_user.h file, in the same syntax as the
existing LAMMPS classes are defined in the style.h file.
write a new C++ derived class (except for exceptions described below,
where you can make small edits to existing files). Creating a new
class requires 2 files, a source code file (*.cpp) and a header file
(*.h). The derived class must provide certain methods to work as a
new option. Depending on how different your new feature is compared
to existing features, you can either derive from the base class
itself, or from a derived class that already exists. Enabling LAMMPS
to invoke the new class is as simple as adding two lines to the
style_user.h file, in the same syntax as other LAMMPS classes are
specified in the style.h file.
</P>
<P>The power of C++ and its object-orientation is that usually, all the
code and variables needed to define the new feature are contained in
the 2 files you write, and thus shouldn't make the rest of the code
more complex or cause side-effect bugs.
<P>The advantage of C++ and its object-orientation is that all the code
and variables needed to define the new feature are in the 2 files you
write, and thus shouldn't make the rest of LAMMPS more complex or
cause side-effect bugs.
</P>
<P>Here is a concrete example. Suppose you write 2 files pair_foo.cpp
and pair_foo.h that define a new class PairFoo that computes pairwise
@ -46,8 +51,8 @@ command like
</P>
<PRE>pair_style foo 0.1 3.5
</PRE>
<P>you simply need to put your 2 files in the LAMMPS src directory, add 2
lines to the style_user.h file, and re-make the code.
<P>you put your 2 files in the LAMMPS src directory, add 2 lines to the
style_user.h file, and re-make the code.
</P>
<P>The first line added to style_user.h would be
</P>
@ -69,108 +74,121 @@ the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
</P>
<P>Note that if you are using Makefile.list instead of Makefile to build
LAMMPS, you will need to explicitly add the names of your new .cpp and
.h file to Makefile.list.
<P>Here is a list of the new features that can be added in this way:
</P>
<P>Here is a list of the kinds of new features that can be added in this
way. The dump and thermo options do not typically require new styles;
LAMMPS can simply be recompiled after new code is added to
dump_custom.cpp or thermo_custom.cpp.
</P>
<UL><LI><A HREF = "#pair">Pairwise potentials</A>
<UL><LI><A HREF = "#atom">Atom styles</A>
<LI><A HREF = "#bond">Bond, angle, dihedral, improper potentials</A>
<LI><A HREF = "#dump">Dump options</A>
<LI><A HREF = "#thermo">Thermodynamic output options</A>
<LI><A HREF = "#temp">Temperature computation options</A>
<LI><A HREF = "#region">Region geometry options</A>
<LI><A HREF = "#fix">Fix options</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
<LI><A HREF = "#atom">Atom options</A>
<LI><A HREF = "#variable">Variable options</A>
<LI><A HREF = "#command">New top-level commands</A>
<LI><A HREF = "#compute">Compute styles</A>
<LI><A HREF = "#dump">Dump styles</A>
<LI><A HREF = "#fix">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
<LI><A HREF = "#command">Input script commands</A>
<LI><A HREF = "#kspace">Kspace computations</A>
<LI><A HREF = "#min">Minimization solvers</A>
<LI><A HREF = "#pair">Pairwise potentials</A>
<LI><A HREF = "#region">Region styles</A>
</UL>
<P>As illustrated by the pairwise example, these options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
<P>As illustrated by the pairwise example, these options are referred to
in the LAMMPS documentation as the "style" of a particular command.
</P>
<P>The instructions below for each category will list the header file for
the parent class that these styles are sub-classes of. Public
variables in that file are ones used and set by the sub-classes which
are also used by the parent class. Sometimes they are also used by
the rest of LAMMPS. Virtual functions in the header file which are
set = 0 are ones you must define in your new class to give it the
functionality LAMMPS expects. Virtual functions that are not set to 0
are functions you can optionally define.
<P>The instructions below give the header file for the base class that
these styles are derived from. Public variables in that file are ones
used and set by the derived classes which are also used by the base
class. Sometimes they are also used by the rest of LAMMPS. Virtual
functions in the base class header file which are set = 0 are ones you
must define in your new derived class to give it the functionality
LAMMPS expects. Virtual functions that are not set to 0 are functions
you can optionally define.
</P>
<P>Here are some additional guidelines for modifying LAMMPS and adding
new functionality:
</P>
<P>Think about whether what you want to do would be better as a pre- or
post-processing step. Many computations are more easily and more
quickly done that way.
</P>
<P>Don't do anything within the timestepping of a run that isn't
parallel. E.g. don't accumulate a bunch of data on a single processor
and analyze it. You run the risk of seriously degrading the parallel
efficiency.
</P>
<P>If your new feature reads arguments or writes output, make sure you
follow the unit conventions discussed by the <A HREF = "units.html">units</A>
command.
</P>
<P>If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. We might be
interested in adding it to the LAMMPS distribution.
<P>Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained in
these sections:
</P>
<UL><LI><A HREF = "#dump_custom">Dump custom output options</A>
<LI><A HREF = "#thermo">Thermodynamic output options</A>
<LI><A HREF = "#variable">Variable options</A>
</UL>
<HR>
<A NAME = "pair"></A><H4>Pairwise potentials
<P>Here are additional guidelines for modifying LAMMPS and adding new
functionality:
</P>
<UL><LI>Think about whether what you want to do would be better as a pre- or
post-processing step. Many computations are more easily and more
quickly done that way.
<LI>Don't do anything within the timestepping of a run that isn't
parallel. E.g. don't accumulate a bunch of data on a single processor
and analyze it. You run the risk of seriously degrading the parallel
efficiency.
<LI>If your new feature reads arguments or writes output, make sure you
follow the unit conventions discussed by the <A HREF = "units.html">units</A>
command.
<LI>If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. We might be
interested in adding it to the LAMMPS distribution.
</UL>
<HR>
<HR>
<A NAME = "atom"></A><H4>Atom styles
</H4>
<P>All classes that compute pairwise interactions are sub-classes of the
Pair class. See the pair.h file for a list of methods this class
defines.
<P>Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
A new atom style can be created if one of the existing atom styles
does not define all the arrays you need to store and communicate with
atoms.
</P>
<P>Pair_lj_cut.cpp and pair_lj_cut.h are the simplest example of a Pair
class. They implement the <I>lj/cut</I> style of the
<A HREF = "pair_style.html">pair_style</A> command.
<P>Atom_vec_atomic.cpp is a simple example of an atom style.
</P>
<P>Here is a brief description of the class methods in pair.h:
<P>Here is a brief description of methods you define in your new derived
class. See atom.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >compute</TD><TD > the workhorse routine that computes the pairwise interactions</TD></TR>
<TR><TD >settings</TD><TD > reads the input script line with any arguments you define</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one i,j type pair</TD></TR>
<TR><TD >init_one</TD><TD > perform initialization for one i,j type pair</TD></TR>
<TR><TD >write & read_restart</TD><TD > write/read i,j pair coeffs to restart files</TD></TR>
<TR><TD >write & read_restart_settings</TD><TD > write/read global settings to restart files</TD></TR>
<TR><TD >single</TD><TD > force and energy of a single pairwise interaction between 2 atoms</TD></TR>
<TR><TD >compute_inner/middle/outer</TD><TD > versions of compute used by rRESPA
<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths</TD></TR>
<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations</TD></TR>
<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep</TD></TR>
<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces</TD></TR>
<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds</TD></TR>
<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms</TD></TR>
<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer</TD></TR>
<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer</TD></TR>
<TR><TD >create_atom</TD><TD > create an individual atom of this style</TD></TR>
<TR><TD >data_atom</TD><TD > parse an atom line from the data file</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays
</TD></TR></TABLE></DIV>
<P>The inner/middle/outer routines are optional. Only a few of the
pairwise potentials use these in conjunction with rRESPA as set by the
<A HREF = "run_style.html">run_style</A> command.
<P>The constructor of the derived class sets values for several variables
that you must set when defining a new atom style. The atom arrays
themselves are defined in atom.cpp. Search for the word "customize"
and you will find locations you will need to modify.
</P>
<HR>
<A NAME = "bond"></A><H4>Bond, angle, dihedral, improper potentials
</H4>
<P>All classes that compute molecular interactions are sub-classes of the
Bond, Angle, Dihedral, and Improper classes. See the bond.h, angle.h,
dihedral.h, and improper.h file for a list of methods these classes
defines.
<P>Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.
</P>
<P>Bond_harmonic.cpp and bond_harmonic.h are the simplest example of a
Bond class. Ditto for the harmonic forms of the angle, dihedral, and
improper style commands. The bond_harmonic files implement the
<I>harmonic</I> style of the <A HREF = "bond_style.html">bond_style</A> command.
<P>Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
</P>
<P>Here is a brief description of the class methods in bond.h, angle.h,
etc:
<P>Here is a brief description of methods you define in your new derived
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >compute</TD><TD > the workhorse routine that computes the molecular interactions</TD></TR>
<TR><TD >compute</TD><TD > compute the molecular interactions</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one bond type</TD></TR>
<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE</TD></TR>
<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files</TD></TR>
@ -179,145 +197,85 @@ etc:
<HR>
<A NAME = "dump"></A><H4>Dump options
<A NAME = "compute"></A><H4>Compute styles
</H4>
<P>There are several classes that print dump files (snapshots of atoms)
that are sub-classes of the Dump class. These include the
dump_atom.cpp, dump_bond.cpp, and dump_custom.cpp files.
<P>Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
</P>
<P>New dump classes can be added, but it is typically simpler to modify
the DumpCustom class contained in the dump_custom.cpp file. See the
<A HREF = "dump.html">dump</A> command and its <I>custom</I> style for a list of what
atom information can already be dumped by DumpCustom. If the
attribute you want to dump is not in the list, or if you define a <A HREF = "#atom">new
atom style</A> with new attributes (e.g. atoms that store their own
magnetic moment), here is how to dump it out in a snapshot file:
<P>Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
</P>
<P>Search the dump_custom.cpp and dump_custom.h files for the word
"customize". It appears in roughly half a dozen locations. In each
of the locations you can add a bit of code that will extend the
DumpCustom class to enable it to dump a new quantity. E.g. you will
add a keyword, add an if test, add a new small method that packs the
requested data into a buffer, etc. For the latter, you can perform a
modest amount of computation in this method; see the pack_xs()
function for an example.
</P>
<P>If desired, a dump custom option can also compute more complicated
quantities by invoking a fix that computed quantities at the end of a
timestep (should be the same timestep the dump is invoked on). See
the ENERGY, CENTRO, and stress options (SXX, SYY, etc) in
dump_custom.cpp for examples.
</P>
<P>When you re-make LAMMPS, your new option should now be useable via the
dump custom command.
</P>
<HR>
<A NAME = "thermo"></A><H4>Thermodynamic output options
</H4>
<P>There is only one class that computes and prints thermodynamic
information to the screen and log file, although the
<A HREF = "thermo_style.html">thermo_style</A> command treats its options as styles.
</P>
<P>There are several styles defined in thermo.cpp: "one", "multi", and
"granular". There is also a flexible "custom" style which allows you
to specify what quantities will be printed each timestep where
thermodynamics is computed. See the <A HREF = "thermo_style.html">thermo_style</A>
command for a list of pre-defined quantities.
</P>
<P>Here is how you can extend the thermo output capabilities. Search the
thermo.cpp and thermo.h files for the word "customize" which will tell
you where to make these additions. Note that fixes can also print-out
thermodynamic quantities via the <A HREF = "fix_modify.html">fix_modify</A> command,
so you do not need to modify thermo.cpp to print fix information.
</P>
<P>If you want to create a new style (like "one" or "granular") that
prints a collection of pre-defined quantities, you add a few lines
that define the new style to thermo.cpp. First, add a #DEFINE line at
the top of the file which lists the quantities to print. Then add the
style name you have chosen to the if test in the constructor to copy
the defined string to the line<B></B> variable.
</P>
<P>You can also add new quantities to the custom list. Add your new
keyword to the if test in the parse_fields() function where the call
to addfield() specifies the text string (8 character max) that will be
printed with the quantity, the function that will compute it, and the
data type (INT,FLOAT) of the quantity. Then at the bottom of the
file, add a function compute_*() which computes the quantity you wish
to print. The function assigns the quantity to the variable "dvalue"
if it is a floating-point quantity, or to "ivalue" if it is an
integer. See the other compute_*() functions for examples of how
various quantities can be accessed, computed, summed across
processors, normalized as per-atom values, etc. Also, if it makes
sense to allow the quantity to be stored in a variable in the input
script, add a couple of lines to the compute_value() function that is
called when a variable is evaluated. Finally, add a prototype for
your new compute method to thermo.h.
</P>
<HR>
<A NAME = "temp"></A><H4>Temperature computation options
</H4>
<P>All classes that compute the temperature of the system are sub-classes
of the Temperature class. See the temperature.h file for a list of
methods these classes defines. Temperatures are computed by LAMMPS
when velocities are set, when thermodynamics are computed, and when
temperature is controlled by various thermostats like the <A HREF = "fix_nvt.html">fix
nvt</A> of <A HREF = "fix_langevin.html">fix langevin</A> commands.
</P>
<P>Temp_full.cpp and temp_full.h are the simplest example of a
Temperature class. They implement the <I>full</I> style of the
<A HREF = "temperature.html">temperature</A> command.
</P>
<P>Here is a brief description of the class methods in temperature.h:
<P>Here is a brief description of methods you define in your new derived
class. See compute.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >init</TD><TD > setup the temperature computation</TD></TR>
<TR><TD >compute</TD><TD > compute and return temperature
<TR><TD >compute_scalar</TD><TD > compute a scalar quantity</TD></TR>
<TR><TD >compute_vector</TD><TD > compute a vector of quantities</TD></TR>
<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom</TD></TR>
<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate</TD></TR>
<TR><TD >unpack_comm</TD><TD > unpack the buffer</TD></TR>
<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate</TD></TR>
<TR><TD >unpack_reverse</TD><TD > unpack the buffer</TD></TR>
<TR><TD >memory_usage</TD><TD > tally memory usage
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "region"></A><H4>Region geometry options
<A NAME = "dump"></A><H4>Dump styles
</H4>
<P>All classes that define geometric regions are sub-classes of the
Region class. See the region.h file for a list of methods these
classes defines. Regions are used elsewhere in LAMMPS to group atoms,
delete atoms to create a void, insert atoms in a specified region,
etc.
<A NAME = "dump_custom"></A><H4>Dump custom output options
</H4>
<P>Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
DumpCustom class contained in the dump_custom.cpp file.
</P>
<P>Region_sphere.cpp and region_sphere.h are the simplest example of a
Region class. They implement the <I>sphere</I> style of the
<A HREF = "region.html">region</A> command.
<P>Dump_atom.cpp is a simple example of a derived dump class.
</P>
<P>Here is a brief description of the single class method required:
<P>Here is a brief description of methods you define in your new derived
class. See dump.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >match</TD><TD > determine whether a point is in the region
<TR><TD >write_header</TD><TD > write the header section of a snapshot of atoms</TD></TR>
<TR><TD >count</TD><TD > count the number of lines a processor will output</TD></TR>
<TR><TD >pack</TD><TD > pack a proc's output data into a buffer</TD></TR>
<TR><TD >write_data</TD><TD > write a proc's data to a file
</TD></TR></TABLE></DIV>
<P>See the <A HREF = "dump.html">dump</A> command and its <I>custom</I> style for a list of
keywords for atom information that can already be dumped by
DumpCustom. It includes options to dump per-atom info from Compute
classes, so adding a new derived Compute class is one way to calculate
new quantities to dump.
</P>
<P>Alternatively, you can add new keywords to the dump custom command.
Search for the word "customize" in dump_custom.cpp to see the
half-dozen or so locations where code will need to be added.
</P>
<HR>
<A NAME = "fix"></A><H4>Fix options
<A NAME = "fix"></A><H4>Fix styles
</H4>
<P>In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
neighbor list manipulation, and output, is a "fix". This includes
time integration (update of velocity and coordinates), force
constraints (SHAKE or walls), and diagnostics (compute a diffusion
coefficient). See the fix.h file for a list of methods these classes
defines.
neighbor list construction, and output, is a "fix". This includes
time integration (update of coordinates and velocities), force
constraints or boundary conditions (SHAKE or walls), and diagnostics
(compute a diffusion coefficient). New styles can be created to add
new options to LAMMPS.
</P>
<P>There are dozens of fix options in LAMMPS; choose one as a template
that is similar to what you want to implement. They can be as simple
as zeroing out forces (see <A HREF = "fix_enforce2d.html">fix enforce2d</A> which
corresponds to the <I>enforce2d</I> style) or as complicated as applying
SHAKE constraints on bonds and angles (see <A HREF = "fix_shake.html">fix shake</A>
which corresponds to the <I>shake</I> style) which involves many extra
computations.
<P>Fix_setforce.cpp is a simple example of setting forces on atoms to
prescribed values. There are dozens of fix options already in LAMMPS;
choose one as a template that is similar to what you want to
implement.
</P>
<P>Here is a brief description of the class methods in fix.h:
<P>Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep</TD></TR>
@ -347,8 +305,7 @@ computations.
<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity</TD></TR>
<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity</TD></TR>
<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity</TD></TR>
<TR><TD >thermo_fields</TD><TD > define quantities for thermodynamic output</TD></TR>
<TR><TD >thermo_compute</TD><TD > compute thermodynamic quantities
<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output
</TD></TR></TABLE></DIV>
<P>Typically, only a small fraction of these methods are defined for a
@ -363,130 +320,201 @@ when to call the fix. By convention, this is the first argument the
fix defines (after the ID, group-ID, style).
</P>
<P>If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate it with
the atoms as they move from processors to processor by implementing
the grow_arrays, copy_arrays, pack_exchange, and unpack_exchange
methods. Similarly, the pack_restart and unpack_restart methods can be
implemented to store information about the fix in restart files. If
you wish an integrator or force constraint fix to work with rRESPA (see
the <A HREF = "run_style.html">run_style</A> command), the initial_integrate,
post_force_integrate, and final_integrate_respa methods can be
implemented. The thermo_fields and thermo_compute methods enable a
fix to contribute values to thermodynamic output, as printed
timestep to timestep, it can manage that memory and migrate the info
with the atoms as they move from processors to processor by
implementing the grow_arrays, copy_arrays, pack_exchange, and
unpack_exchange methods. Similarly, the pack_restart and
unpack_restart methods can be implemented to store information about
the fix in restart files. If you wish an integrator or force
constraint fix to work with rRESPA (see the <A HREF = "run_style.html">run_style</A>
command), the initial_integrate, post_force_integrate, and
final_integrate_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.
</P>
<HR>
<A NAME = "atom"></A><H4>Atom options
<A NAME = "command"></A><H4>Input script commands
</H4>
<P>All classes that define an atom style are sub-classes of the Atom
class. See the atom.h file for a list of methods these classes
defines. The atom style determines what quantities are associated
with an atom in a LAMMPS simulation. If one of the existing atom
styles does not define all the arrays you need to store with an atom,
then a new atom class can be created.
</P>
<P>Atom_atomic.cpp and atom_atomic.h are the simplest example of an Atom
class. They implement the <I>atomic</I> style of the
<A HREF = "atom_style.html">atom_style</A> command.
</P>
<P>Here is a brief description of the class methods in atom.h:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >copy</TD><TD > copy info for one atom to another atom's array location</TD></TR>
<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep</TD></TR>
<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces</TD></TR>
<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds</TD></TR>
<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor</TD></TR>
<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer</TD></TR>
<TR><TD >
</TD></TR></TABLE></DIV>
<P>There are also several methods in atom.cpp you will need to augment
with information about your new atom class, following the patterns of
the other atom styles. These routines are so similar for all classes,
that it was simpler to just have one master routine for all classes.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >constructor</TD><TD > create style variable and atom array ptrs to NULL</TD></TR>
<TR><TD >destructor</TD><TD > free memory for atom arrays</TD></TR>
<TR><TD >set_style</TD><TD > set style variable</TD></TR>
<TR><TD >check_style</TD><TD > check for pure style vs hybrid style</TD></TR>
<TR><TD >style2arg</TD><TD > convert style variables to keywords</TD></TR>
<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths</TD></TR>
<TR><TD >unpack_data</TD><TD > parse atom lines from data file</TD></TR>
<TR><TD >create_one</TD><TD > create an individual atom of this style</TD></TR>
<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms</TD></TR>
<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer</TD></TR>
<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer</TD></TR>
<TR><TD >memory_usage</TD><TD > memory allocated by atom arrays</TD></TR>
<TR><TD >
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "variable"></A><H4>Variable options
</H4>
<P>The variable class stores and evaluates input script variables $a, $b,
... $z, as described in <A HREF = "Section_commands.html#3_2">this section</A>.
<I>Equal</I>-style variables are defined by an equation that is evaluated
each time the variable is used. The equation can include functions,
vectors, keywords, and numbers as described in the
<A HREF = "variable.html">variable</A> command. The list of valid functions,
vectors, and keywords, can be extended by adding a few lines of code
to the evaluate() method at the end of the variable.cpp file. Search
for the word "customize" to find the correct locations for adding
code.
</P>
<P>A new function (e.g. foo(arg1,arg2,...)) can be added in the section
that starts with the comment
</P>
<PRE>// customize by adding function to this list and to if statement
</PRE>
<P>A new vector (e.g. q<B></B>) can be added in the section that starts with
the comment
</P>
<PRE>// customize by adding vector to this list and to if statement
</PRE>
<P>A new keyword (e.g. mysum) can be added in the section that starts with
the comment
</P>
<PRE>// customize by adding keyword to this list and to if statement
</PRE>
<P>Note that keywords supported by the <A HREF = "themo_style.html">thermo_style
custom</A> command are evaluated by the thermo routines,
so do not need to be added to variable.cpp.
</P>
<HR>
<A NAME = "command"></A><H4>New top-level commands
</H4>
<P>It is possible to add a new command to a LAMMPS input script as
opposed to adding a new style to an existing command (atom_style,
pair_style, fix, etc). For example the create_atoms, read_data,
velocity, and run commands are all top-level LAMMPS commands that are
listed in the Command section of style.h. When such a command is
encountered in the LAMMPS input script, the topmost level of LAMMPS
(lammps.cpp) simply creates a class with the corresponding name,
<P>New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method and are listed in the Command
sections of style.h (or style_user.h). For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on the LAMMPS data structures.
operations it wishes on LAMMPS data structures.
</P>
<P>Thus to add a new command, you simply need to add a *.cpp and *.h file
containing a single class:
<P>The single method your new class must define is as follows:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >command</TD><TD > operations performed by the new command
</TD></TR></TABLE></DIV>
<P>Of course, the new class can define other methods and variables that
it uses internally.
<P>Of course, the new class can define other methods and variables as
needed.
</P>
<HR>
<A NAME = "kspace"></A><H4>Kspace computations
</H4>
<P>Classes that compute long-range Coulombic interactions via K-space
represenations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.
</P>
<P>Ewald.cpp is an example of computing K-space interactions.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >init</TD><TD > initialize the calculation before a run</TD></TR>
<TR><TD >setup</TD><TD > computation before the 1st timestep of a run</TD></TR>
<TR><TD >compute</TD><TD > every-timestep computation</TD></TR>
<TR><TD >memory_usage</TD><TD > tally of memory usage
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "min"></A><H4>Minimization solvers
</H4>
<P>Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.
</P>
<P>Min_cg.cpp is an example of conjugate gradient minimization.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See min.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >init</TD><TD > initialize the minimization before a run</TD></TR>
<TR><TD >run</TD><TD > perform the minimization</TD></TR>
<TR><TD >memory_usage</TD><TD > tally of memory usage
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "pair"></A><H4>Pairwise potentials
</H4>
<P>Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
</P>
<P>Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
</P>
<P>Here is a brief description of the class methods in pair.h:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >compute</TD><TD > workhorse routine that computes pairwise interactions</TD></TR>
<TR><TD >settings</TD><TD > reads the input script line with arguments you define</TD></TR>
<TR><TD >coeff</TD><TD > set coefficients for one i,j type pair</TD></TR>
<TR><TD >init_one</TD><TD > perform initialization for one i,j type pair</TD></TR>
<TR><TD >init_style</TD><TD > initialization specific to this pair style</TD></TR>
<TR><TD >write & read_restart</TD><TD > write/read i,j pair coeffs to restart files</TD></TR>
<TR><TD >write & read_restart_settings</TD><TD > write/read global settings to restart files</TD></TR>
<TR><TD >single</TD><TD > force and energy of a single pairwise interaction between 2 atoms</TD></TR>
<TR><TD >compute_inner/middle/outer</TD><TD > versions of compute used by rRESPA
</TD></TR></TABLE></DIV>
<P>The inner/middle/outer routines are optional.
</P>
<HR>
<A NAME = "region"></A><H4>Region styles
</H4>
<P>Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
styles can be created to add new region shapes to LAMMPS.
</P>
<P>Region_sphere.cpp is an example of a spherical region.
</P>
<P>Here is a brief description of methods you define in your new derived
class. See region.h for details.
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >match</TD><TD > determine whether a point is in the region
</TD></TR></TABLE></DIV>
<HR>
<A NAME = "thermo"></A><H4>Thermodynamic output options
</H4>
<P>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
</P>
<P>There are several styles defined in thermo.cpp: "one", "multi",
"granular", etc. There is also a flexible "custom" style which allows
the user to explicitly list keywords for quantities to print when
thermodynamic info is output. See the
<A HREF = "thermo_style.html">thermo_style</A> command for a list of defined
quantities.
</P>
<P>The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requies defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
</P>
<P>New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
</P>
<P>Note that the <A HREF = "thermo.html">thermo_style custom</A> command already allows
for thermo output of quantities calculated by <A HREF = "fix.html">fixes</A>,
<A HREF = "compute.html">computes</A>, and <A HREF = "variable.html">variables</A>. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
</P>
<HR>
<A NAME = "variable"></A><H4>Variable options
</H4>
<P>There is one class that computes and stores <A HREF = "variable.html">variable</A>
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
via the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix print</A>, or
<A HREF = "thermo_style.html">thermo_style custom</A> commands. Variables of style
"equal" can compute complex equations that involve the following types
of arguments:
</P>
<P>thermo keywords = ke, vol, atoms, ...
other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ...
compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ...
</P>
<P>Adding keywords for the <A HREF = "themo_style.html">thermo_style custom</A> command
(which can then be accessed by variables) was discussed
<A HREF = "Section_modify.html#thermo">here</A> on this page.
</P>
<P>Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaulate() method. Search for
the word "customize" to find the appropriate location.
</P>
<P>Adding a new group function can be done by editing one section of the
Variable::evaulate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
</P>
<P>Accessing a new atom-based vector can be done by editing one section
of the Variable::evaulate() method. Search for the word "customize"
to find the appropriate location.
</P>
<P>Adding new <A HREF = "compute.html">compute styles</A> (whose calculated values can
then be accessed by variables) was discussed
<A HREF = "Section_modify.html#compute">here</A> on this page.
</P>
<HR>
<HR>
<A NAME = "Foo"></A>
<P><B>(Foo)</B> Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).

611
doc/Section_modify.txt
View File

@ -11,29 +11,34 @@ Section"_Section_errors.html :c
8. Modifying & extending LAMMPS :h3
LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In this section, changes and additions
users can make are listed along with some minimal instructions.
Realistically, the best way to add a new feature is to find a similar
feature in LAMMPS and look at the corresponding source and header
files to figure out what it does. You will need some knowledge of C++
to be able to understand the hi-level structure of LAMMPS and its
class organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
extend with new functionality. In fact, about 75% if its source code
is files added in this fashion.
In this section, changes and additions users can make are listed along
with minimal instructions. The best way to add a new feature is to
find a similar feature in LAMMPS and look at the corresponding source
and header files to figure out what it does. You will need some
knowledge of C++ to be able to understand the hi-level structure of
LAMMPS and its class organization, but functions (class methods) that
do actual computations are written in vanilla C-style code and operate
on simple C-style data structures (vectors and arrays).
Most of the new features described in this section require you to
write a new C++ class (except for dump, thermo, and variable options,
described below, where you can make small edits to existing files).
Creating a new class requires 2 files, a source code file (*.cpp) and
a header file (*.h). Their contents are briefly discussed below.
Enabling LAMMPS to invoke the new class is as simple as adding two
definition lines to the style_user.h file, in the same syntax as the
existing LAMMPS classes are defined in the style.h file.
write a new C++ derived class (except for exceptions described below,
where you can make small edits to existing files). Creating a new
class requires 2 files, a source code file (*.cpp) and a header file
(*.h). The derived class must provide certain methods to work as a
new option. Depending on how different your new feature is compared
to existing features, you can either derive from the base class
itself, or from a derived class that already exists. Enabling LAMMPS
to invoke the new class is as simple as adding two lines to the
style_user.h file, in the same syntax as other LAMMPS classes are
specified in the style.h file.
The power of C++ and its object-orientation is that usually, all the
code and variables needed to define the new feature are contained in
the 2 files you write, and thus shouldn't make the rest of the code
more complex or cause side-effect bugs.
The advantage of C++ and its object-orientation is that all the code
and variables needed to define the new feature are in the 2 files you
write, and thus shouldn't make the rest of LAMMPS more complex or
cause side-effect bugs.
Here is a concrete example. Suppose you write 2 files pair_foo.cpp
and pair_foo.h that define a new class PairFoo that computes pairwise
@ -43,8 +48,8 @@ command like
pair_style foo 0.1 3.5 :pre
you simply need to put your 2 files in the LAMMPS src directory, add 2
lines to the style_user.h file, and re-make the code.
you put your 2 files in the LAMMPS src directory, add 2 lines to the
style_user.h file, and re-make the code.
The first line added to style_user.h would be
@ -66,107 +71,119 @@ the executable and can be invoked with a pair_style command like the
example above. Arguments like 0.1 and 3.5 can be defined and
processed by your new class.
Note that if you are using Makefile.list instead of Makefile to build
LAMMPS, you will need to explicitly add the names of your new .cpp and
.h file to Makefile.list.
Here is a list of the new features that can be added in this way:
Here is a list of the kinds of new features that can be added in this
way. The dump and thermo options do not typically require new styles;
LAMMPS can simply be recompiled after new code is added to
dump_custom.cpp or thermo_custom.cpp.
"Pairwise potentials"_#pair
"Atom styles"_#atom
"Bond, angle, dihedral, improper potentials"_#bond
"Dump options"_#dump
"Thermodynamic output options"_#thermo
"Temperature computation options"_#temp
"Region geometry options"_#region
"Fix options"_#fix which include integrators, \
"Compute styles"_#compute
"Dump styles"_#dump
"Fix styles"_#fix which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
"Atom options"_#atom
"Variable options"_#variable
"New top-level commands"_#command :ul
"Input script commands"_#command
"Kspace computations"_#kspace
"Minimization solvers"_#min
"Pairwise potentials"_#pair
"Region styles"_#region :ul
As illustrated by the pairwise example, these options are
referred to in the LAMMPS documentation as the "style" of a particular
command.
As illustrated by the pairwise example, these options are referred to
in the LAMMPS documentation as the "style" of a particular command.
The instructions below for each category will list the header file for
the parent class that these styles are sub-classes of. Public
variables in that file are ones used and set by the sub-classes which
are also used by the parent class. Sometimes they are also used by
the rest of LAMMPS. Virtual functions in the header file which are
set = 0 are ones you must define in your new class to give it the
functionality LAMMPS expects. Virtual functions that are not set to 0
are functions you can optionally define.
The instructions below give the header file for the base class that
these styles are derived from. Public variables in that file are ones
used and set by the derived classes which are also used by the base
class. Sometimes they are also used by the rest of LAMMPS. Virtual
functions in the base class header file which are set = 0 are ones you
must define in your new derived class to give it the functionality
LAMMPS expects. Virtual functions that are not set to 0 are functions
you can optionally define.
Here are some additional guidelines for modifying LAMMPS and adding
new functionality:
Additionally, new output options can be added directly to the
thermo.cpp, dump_custom.cpp, and variable.cpp files as explained in
these sections:
"Dump custom output options"_#dump_custom
"Thermodynamic output options"_#thermo
"Variable options"_#variable :ul
:line
Here are additional guidelines for modifying LAMMPS and adding new
functionality:
Think about whether what you want to do would be better as a pre- or
post-processing step. Many computations are more easily and more
quickly done that way.
quickly done that way. :ulb,l
Don't do anything within the timestepping of a run that isn't
parallel. E.g. don't accumulate a bunch of data on a single processor
and analyze it. You run the risk of seriously degrading the parallel
efficiency.
efficiency. :l
If your new feature reads arguments or writes output, make sure you
follow the unit conventions discussed by the "units"_units.html
command.
command. :l
If you add something you think is truly useful and doesn't impact
LAMMPS performance when it isn't used, send an email to the
"developers"_http://lammps.sandia.gov/authors.html. We might be
interested in adding it to the LAMMPS distribution.
interested in adding it to the LAMMPS distribution. :l,ule
:line
:line
Pairwise potentials :link(pair),h4
Atom styles :link(atom),h4
All classes that compute pairwise interactions are sub-classes of the
Pair class. See the pair.h file for a list of methods this class
defines.
Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
A new atom style can be created if one of the existing atom styles
does not define all the arrays you need to store and communicate with
atoms.
Pair_lj_cut.cpp and pair_lj_cut.h are the simplest example of a Pair
class. They implement the {lj/cut} style of the
"pair_style"_pair_style.html command.
Atom_vec_atomic.cpp is a simple example of an atom style.
Here is a brief description of the class methods in pair.h:
Here is a brief description of methods you define in your new derived
class. See atom.h for details.
compute: the workhorse routine that computes the pairwise interactions
settings: reads the input script line with any arguments you define
coeff: set coefficients for one i,j type pair
init_one: perform initialization for one i,j type pair
write & read_restart: write/read i,j pair coeffs to restart files
write & read_restart_settings: write/read global settings to restart files
single: force and energy of a single pairwise interaction between 2 atoms
compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:)
grow: re-allocate atom arrays to longer lengths
copy: copy info for one atom to another atom's array locations
pack_comm: store an atom's info in a buffer communicated every timestep
unpack_comm: retrieve an atom's info from the buffer
pack_reverse: store an atom's info in a buffer communicating partial forces
unpack_reverse: retrieve an atom's info from the buffer
pack_border: store an atom's info in a buffer communicated on neighbor re-builds
unpack_border: retrieve an atom's info from the buffer
pack_exchange: store all an atom's info to migrate to another processor
unpack_exchange: retrieve an atom's info from the buffer
size_restart: number of restart quantities associated with proc's atoms
pack_restart: pack atom quantities into a buffer
unpack_restart: unpack atom quantities from a buffer
create_atom: create an individual atom of this style
data_atom: parse an atom line from the data file
memory_usage: tally memory allocated by atom arrays :tb(s=:)
The inner/middle/outer routines are optional. Only a few of the
pairwise potentials use these in conjunction with rRESPA as set by the
"run_style"_run_style.html command.
The constructor of the derived class sets values for several variables
that you must set when defining a new atom style. The atom arrays
themselves are defined in atom.cpp. Search for the word "customize"
and you will find locations you will need to modify.
:line
Bond, angle, dihedral, improper potentials :link(bond),h4
All classes that compute molecular interactions are sub-classes of the
Bond, Angle, Dihedral, and Improper classes. See the bond.h, angle.h,
dihedral.h, and improper.h file for a list of methods these classes
defines.
Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
add new potentials to LAMMPS.
Bond_harmonic.cpp and bond_harmonic.h are the simplest example of a
Bond class. Ditto for the harmonic forms of the angle, dihedral, and
improper style commands. The bond_harmonic files implement the
{harmonic} style of the "bond_style"_bond_style.html command.
Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
the harmonic forms of the angle, dihedral, and improper style
commands.
Here is a brief description of the class methods in bond.h, angle.h,
etc:
Here is a brief description of methods you define in your new derived
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
details.
compute: the workhorse routine that computes the molecular interactions
compute: compute the molecular interactions
coeff: set coefficients for one bond type
equilibrium_distance: length of bond, used by SHAKE
write & read_restart: writes/reads coeffs to restart files
@ -174,141 +191,80 @@ single: force and energy of a single bond :tb(s=:)
:line
Dump options :link(dump),h4
Compute styles :link(compute),h4
There are several classes that print dump files (snapshots of atoms)
that are sub-classes of the Dump class. These include the
dump_atom.cpp, dump_bond.cpp, and dump_custom.cpp files.
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
quantities like kinetic energy and the centro-symmetry parameter
are derived from the Compute class. New styles can be created
to add new calculations to LAMMPS.
New dump classes can be added, but it is typically simpler to modify
the DumpCustom class contained in the dump_custom.cpp file. See the
"dump"_dump.html command and its {custom} style for a list of what
atom information can already be dumped by DumpCustom. If the
attribute you want to dump is not in the list, or if you define a "new
atom style"_#atom with new attributes (e.g. atoms that store their own
magnetic moment), here is how to dump it out in a snapshot file:
Compute_temp.cpp is a simple example of computing a scalar
temperature. Compute_ke_atom.cpp is a simple example of computing
per-atom kinetic energy.
Search the dump_custom.cpp and dump_custom.h files for the word
"customize". It appears in roughly half a dozen locations. In each
of the locations you can add a bit of code that will extend the
DumpCustom class to enable it to dump a new quantity. E.g. you will
add a keyword, add an if test, add a new small method that packs the
requested data into a buffer, etc. For the latter, you can perform a
modest amount of computation in this method; see the pack_xs()
function for an example.
Here is a brief description of methods you define in your new derived
class. See compute.h for details.
If desired, a dump custom option can also compute more complicated
quantities by invoking a fix that computed quantities at the end of a
timestep (should be the same timestep the dump is invoked on). See
the ENERGY, CENTRO, and stress options (SXX, SYY, etc) in
dump_custom.cpp for examples.
When you re-make LAMMPS, your new option should now be useable via the
dump custom command.
compute_scalar: compute a scalar quantity
compute_vector: compute a vector of quantities
compute_peratom: compute one or more quantities per atom
pack_comm: pack a buffer with items to communicate
unpack_comm: unpack the buffer
pack_reverse: pack a buffer with items to reverse communicate
unpack_reverse: unpack the buffer
memory_usage: tally memory usage :tb(s=:)
:line
Thermodynamic output options :link(thermo),h4
Dump styles :link(dump),h4
Dump custom output options :link(dump_custom),h4
There is only one class that computes and prints thermodynamic
information to the screen and log file, although the
"thermo_style"_thermo_style.html command treats its options as styles.
Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
class can be added, but it is typically simpler to modify the
DumpCustom class contained in the dump_custom.cpp file.
There are several styles defined in thermo.cpp: "one", "multi", and
"granular". There is also a flexible "custom" style which allows you
to specify what quantities will be printed each timestep where
thermodynamics is computed. See the "thermo_style"_thermo_style.html
command for a list of pre-defined quantities.
Dump_atom.cpp is a simple example of a derived dump class.
Here is how you can extend the thermo output capabilities. Search the
thermo.cpp and thermo.h files for the word "customize" which will tell
you where to make these additions. Note that fixes can also print-out
thermodynamic quantities via the "fix_modify"_fix_modify.html command,
so you do not need to modify thermo.cpp to print fix information.
Here is a brief description of methods you define in your new derived
class. See dump.h for details.
If you want to create a new style (like "one" or "granular") that
prints a collection of pre-defined quantities, you add a few lines
that define the new style to thermo.cpp. First, add a #DEFINE line at
the top of the file which lists the quantities to print. Then add the
style name you have chosen to the if test in the constructor to copy
the defined string to the line[] variable.
write_header: write the header section of a snapshot of atoms
count: count the number of lines a processor will output
pack: pack a proc's output data into a buffer
write_data: write a proc's data to a file :tb(s=:)
You can also add new quantities to the custom list. Add your new
keyword to the if test in the parse_fields() function where the call
to addfield() specifies the text string (8 character max) that will be
printed with the quantity, the function that will compute it, and the
data type (INT,FLOAT) of the quantity. Then at the bottom of the
file, add a function compute_*() which computes the quantity you wish
to print. The function assigns the quantity to the variable "dvalue"
if it is a floating-point quantity, or to "ivalue" if it is an
integer. See the other compute_*() functions for examples of how
various quantities can be accessed, computed, summed across
processors, normalized as per-atom values, etc. Also, if it makes
sense to allow the quantity to be stored in a variable in the input
script, add a couple of lines to the compute_value() function that is
called when a variable is evaluated. Finally, add a prototype for
your new compute method to thermo.h.
See the "dump"_dump.html command and its {custom} style for a list of
keywords for atom information that can already be dumped by
DumpCustom. It includes options to dump per-atom info from Compute
classes, so adding a new derived Compute class is one way to calculate
new quantities to dump.
Alternatively, you can add new keywords to the dump custom command.
Search for the word "customize" in dump_custom.cpp to see the
half-dozen or so locations where code will need to be added.
:line
Temperature computation options :link(temp),h4
All classes that compute the temperature of the system are sub-classes
of the Temperature class. See the temperature.h file for a list of
methods these classes defines. Temperatures are computed by LAMMPS
when velocities are set, when thermodynamics are computed, and when
temperature is controlled by various thermostats like the "fix
nvt"_fix_nvt.html of "fix langevin"_fix_langevin.html commands.
Temp_full.cpp and temp_full.h are the simplest example of a
Temperature class. They implement the {full} style of the
"temperature"_temperature.html command.
Here is a brief description of the class methods in temperature.h:
init: setup the temperature computation
compute: compute and return temperature :tb(s=:)
:line
Region geometry options :link(region),h4
All classes that define geometric regions are sub-classes of the
Region class. See the region.h file for a list of methods these
classes defines. Regions are used elsewhere in LAMMPS to group atoms,
delete atoms to create a void, insert atoms in a specified region,
etc.
Region_sphere.cpp and region_sphere.h are the simplest example of a
Region class. They implement the {sphere} style of the
"region"_region.html command.
Here is a brief description of the single class method required:
match: determine whether a point is in the region :tb(s=:)
:line
Fix options :link(fix),h4
Fix styles :link(fix),h4
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
everything that happens during a simulation besides force computation,
neighbor list manipulation, and output, is a "fix". This includes
time integration (update of velocity and coordinates), force
constraints (SHAKE or walls), and diagnostics (compute a diffusion
coefficient). See the fix.h file for a list of methods these classes
defines.
neighbor list construction, and output, is a "fix". This includes
time integration (update of coordinates and velocities), force
constraints or boundary conditions (SHAKE or walls), and diagnostics
(compute a diffusion coefficient). New styles can be created to add
new options to LAMMPS.
There are dozens of fix options in LAMMPS; choose one as a template
that is similar to what you want to implement. They can be as simple
as zeroing out forces (see "fix enforce2d"_fix_enforce2d.html which
corresponds to the {enforce2d} style) or as complicated as applying
SHAKE constraints on bonds and angles (see "fix shake"_fix_shake.html
which corresponds to the {shake} style) which involves many extra
computations.
Fix_setforce.cpp is a simple example of setting forces on atoms to
prescribed values. There are dozens of fix options already in LAMMPS;
choose one as a template that is similar to what you want to
implement.
Here is a brief description of the class methods in fix.h:
Here is a brief description of methods you can define in your new
derived class. See fix.h for details.
setmask: determines when the fix is called during the timestep
init: initialization before a run
@ -337,8 +293,7 @@ pack_comm: pack a buffer to communicate a per-atom quantity
unpack_comm: unpack a buffer to communicate a per-atom quantity
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity
thermo_fields: define quantities for thermodynamic output
thermo_compute: compute thermodynamic quantities :tb(s=:)
thermo: compute quantities for thermodynamic output :tb(s=:)
Typically, only a small fraction of these methods are defined for a
particular fix. Setmask is mandatory, as it determines when the fix
@ -352,122 +307,188 @@ when to call the fix. By convention, this is the first argument the
fix defines (after the ID, group-ID, style).
If the fix needs to store information for each atom that persists from
timestep to timestep, it can manage that memory and migrate it with
the atoms as they move from processors to processor by implementing
the grow_arrays, copy_arrays, pack_exchange, and unpack_exchange
methods. Similarly, the pack_restart and unpack_restart methods can be
implemented to store information about the fix in restart files. If
you wish an integrator or force constraint fix to work with rRESPA (see
the "run_style"_run_style.html command), the initial_integrate,
post_force_integrate, and final_integrate_respa methods can be
implemented. The thermo_fields and thermo_compute methods enable a
fix to contribute values to thermodynamic output, as printed
timestep to timestep, it can manage that memory and migrate the info
with the atoms as they move from processors to processor by
implementing the grow_arrays, copy_arrays, pack_exchange, and
unpack_exchange methods. Similarly, the pack_restart and
unpack_restart methods can be implemented to store information about
the fix in restart files. If you wish an integrator or force
constraint fix to work with rRESPA (see the "run_style"_run_style.html
command), the initial_integrate, post_force_integrate, and
final_integrate_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.
:line
Atom options :link(atom),h4
Input script commands :link(command),h4
All classes that define an atom style are sub-classes of the Atom
class. See the atom.h file for a list of methods these classes
defines. The atom style determines what quantities are associated
with an atom in a LAMMPS simulation. If one of the existing atom
styles does not define all the arrays you need to store with an atom,
then a new atom class can be created.
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method and are listed in the Command
sections of style.h (or style_user.h). For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on LAMMPS data structures.
Atom_atomic.cpp and atom_atomic.h are the simplest example of an Atom
class. They implement the {atomic} style of the
"atom_style"_atom_style.html command.
The single method your new class must define is as follows:
Here is a brief description of the class methods in atom.h:
command: operations performed by the new command :tb(s=:)
copy: copy info for one atom to another atom's array location
pack_comm: store an atom's info in a buffer communicated every timestep
unpack_comm: retrieve an atom's info from the buffer
pack_reverse: store an atom's info in a buffer communicating partial forces
unpack_reverse: retrieve an atom's info from the buffer
pack_border: store an atom's info in a buffer communicated on neighbor re-builds
unpack_border: retrieve an atom's info from the buffer
pack_exchange: store all an atom's info to migrate to another processor
unpack_exchange: retrieve an atom's info from the buffer
:tb(s=:)
Of course, the new class can define other methods and variables as
needed.
There are also several methods in atom.cpp you will need to augment
with information about your new atom class, following the patterns of
the other atom styles. These routines are so similar for all classes,
that it was simpler to just have one master routine for all classes.
:line
constructor: create style variable and atom array ptrs to NULL
destructor: free memory for atom arrays
set_style: set style variable
check_style: check for pure style vs hybrid style
style2arg: convert style variables to keywords
grow: re-allocate atom arrays to longer lengths
unpack_data: parse atom lines from data file
create_one: create an individual atom of this style
size_restart: number of restart quantities associated with proc's atoms
pack_restart: pack atom quantities into a buffer
unpack_restart: unpack atom quantities from a buffer
memory_usage: memory allocated by atom arrays
:tb(s=:)
Kspace computations :link(kspace),h4
Classes that compute long-range Coulombic interactions via K-space
represenations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS.
Ewald.cpp is an example of computing K-space interactions.
Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
init: initialize the calculation before a run
setup: computation before the 1st timestep of a run
compute: every-timestep computation
memory_usage: tally of memory usage :tb(s=:)
:line
Minimization solvers :link(min),h4
Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
LAMMPS.
Min_cg.cpp is an example of conjugate gradient minimization.
Here is a brief description of methods you define in your new derived
class. See min.h for details.
init: initialize the minimization before a run
run: perform the minimization
memory_usage: tally of memory usage :tb(s=:)
:line
Pairwise potentials :link(pair),h4
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
Here is a brief description of the class methods in pair.h:
compute: workhorse routine that computes pairwise interactions
settings: reads the input script line with arguments you define
coeff: set coefficients for one i,j type pair
init_one: perform initialization for one i,j type pair
init_style: initialization specific to this pair style
write & read_restart: write/read i,j pair coeffs to restart files
write & read_restart_settings: write/read global settings to restart files
single: force and energy of a single pairwise interaction between 2 atoms
compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:)
The inner/middle/outer routines are optional.
:line
Region styles :link(region),h4
Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
atoms to create a void, insert atoms in a specified region, etc. New
styles can be created to add new region shapes to LAMMPS.
Region_sphere.cpp is an example of a spherical region.
Here is a brief description of methods you define in your new derived
class. See region.h for details.
match: determine whether a point is in the region :tb(s=:)
:line
Thermodynamic output options :link(thermo),h4
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
There are several styles defined in thermo.cpp: "one", "multi",
"granular", etc. There is also a flexible "custom" style which allows
the user to explicitly list keywords for quantities to print when
thermodynamic info is output. See the
"thermo_style"_thermo_style.html command for a list of defined
quantities.
The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requies defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
Note that the "thermo_style custom"_thermo.html command already allows
for thermo output of quantities calculated by "fixes"_fix.html,
"computes"_compute.html, and "variables"_variable.html. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
:line
Variable options :link(variable),h4
The variable class stores and evaluates input script variables $a, $b,
... $z, as described in "this section"_Section_commands.html#3_2.
{Equal}-style variables are defined by an equation that is evaluated
each time the variable is used. The equation can include functions,
vectors, keywords, and numbers as described in the
"variable"_variable.html command. The list of valid functions,
vectors, and keywords, can be extended by adding a few lines of code
to the evaluate() method at the end of the variable.cpp file. Search
for the word "customize" to find the correct locations for adding
code.
There is one class that computes and stores "variable"_variable.html
information in LAMMPS; see the file variable.cpp. The value
associated with a variable can be periodically printed to the screen
via the "print"_print.html, "fix print"_fix_print.html, or
"thermo_style custom"_thermo_style.html commands. Variables of style
"equal" can compute complex equations that involve the following types
of arguments:
A new function (e.g. foo(arg1,arg2,...)) can be added in the section
that starts with the comment
thermo keywords = ke, vol, atoms, ...
other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x[123], y[3], vx[34], ...
compute values = c_mytemp[0], c_thermo_press[3], ...
// customize by adding function to this list and to if statement :pre
Adding keywords for the "thermo_style custom"_themo_style.html command
(which can then be accessed by variables) was discussed
"here"_Section_modify.html#thermo on this page.
A new vector (e.g. q[]) can be added in the section that starts with
the comment
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaulate() method. Search for
the word "customize" to find the appropriate location.
// customize by adding vector to this list and to if statement :pre
Adding a new group function can be done by editing one section of the
Variable::evaulate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
A new keyword (e.g. mysum) can be added in the section that starts with
the comment
Accessing a new atom-based vector can be done by editing one section
of the Variable::evaulate() method. Search for the word "customize"
to find the appropriate location.
// customize by adding keyword to this list and to if statement :pre
Note that keywords supported by the "thermo_style
custom"_themo_style.html command are evaluated by the thermo routines,
so do not need to be added to variable.cpp.
Adding new "compute styles"_compute.html (whose calculated values can
then be accessed by variables) was discussed
"here"_Section_modify.html#compute on this page.
:line
New top-level commands :link(command),h4
It is possible to add a new command to a LAMMPS input script as
opposed to adding a new style to an existing command (atom_style,
pair_style, fix, etc). For example the create_atoms, read_data,
velocity, and run commands are all top-level LAMMPS commands that are
listed in the Command section of style.h. When such a command is
encountered in the LAMMPS input script, the topmost level of LAMMPS
(lammps.cpp) simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on the LAMMPS data structures.
Thus to add a new command, you simply need to add a *.cpp and *.h file
containing a single class:
command: operations performed by the new command :tb(s=:)
Of course, the new class can define other methods and variables that
it uses internally.
:line
:link(Foo)

276
doc/Section_start.html
View File

@ -16,16 +16,18 @@ new and experienced users.
</P>
2.1 <A HREF = "#2_1">What's in the LAMMPS distribution</A><BR>
2.2 <A HREF = "#2_2">Making LAMMPS</A><BR>
2.3 <A HREF = "#2_3">Running LAMMPS</A><BR>
2.4 <A HREF = "#2_4">Command-line options</A><BR>
2.5 <A HREF = "#2_5">Screen output</A><BR>
2.6 <A HREF = "#2_6">Tips for users of previous versions</A> <BR>
2.3 <A HREF = "#2_3">Making LAMMPS with optional packages</A><BR>
2.4 <A HREF = "#2_4">Building LAMMPS as a library</A><BR>
2.5 <A HREF = "#2_5">Running LAMMPS</A><BR>
2.6 <A HREF = "#2_6">Command-line options</A><BR>
2.7 <A HREF = "#2_7">Screen output</A><BR>
2.8 <A HREF = "#2_8">Tips for users of previous versions</A> <BR>
<HR>
<H4><A NAME = "2_1"></A>2.1 What's in the LAMMPS distribution
</H4>
<P>When you download LAMMPS you will need to unzip and untar the
<P>When you download SLAMMPS you will need to unzip and untar the
downloaded file with the following commands, after placing the file in
an appropriate directory.
</P>
@ -57,20 +59,19 @@ makefile, there are compiler options, additional libraries can be used
(MPI, FFT), etc. Please read this section carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many of the emails we get about build and run problems are not
really about LAMMPS - they are peculiar to the user's system,
compilers, libraries, etc. Such questions are better answered by a
local expert.
you. Many compiling, linking, and run problems users have do not
really have to do with LAMMPS - they are peculiar to the user's
system, compilers, libraries, etc. Such questions are better answered
by a local expert.
</P>
<P>If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. Note that doesn't
include linking problems - that's a question for a local expert!
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
</P>
<P>Also, if you succeed in building LAMMPS on a new kind of machine
(which there isn't a similar Makefile for in the distribution), send
it to the developers and we'll include it in future LAMMPS releases.
<P>If you succeed in building LAMMPS on a new kind of machine (which
there isn't a similar Makefile for in the distribution), send it to
the developers and we'll include it in future LAMMPS releases.
</P>
<P><B><I>Building a LAMMPS executable:</I></B>
</P>
@ -85,12 +86,9 @@ type a command like:
gmake mac
</PRE>
<P>If you get no errors and an executable like lmp_linux or lmp_mac is
produced, you're done; it's your lucky day. The remainder of this
section addressed the following topics: errors that occur when making
LAMMPS, editing a new low-level Makefile.foo, how to make LAMMPS with
and without packages, and additional build tips.
produced, you're done; it's your lucky day.
</P>
<P><B><I>Errors that occur when making LAMMPS:</I></B>
<P><B><I>Errors that can occur when making LAMMPS:</I></B>
</P>
<P>(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
@ -210,98 +208,6 @@ gmake foo
</PRE>
<P>You should get the executable lmp_foo when the build is complete.
</P>
<P><B><I>How to make LAMMPS with and without packages:</I></B>
</P>
<P>The source code for LAMMPS is structured as a large set of core files
that are always used plus additional packages, which are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>
<TR><TD >manybody </TD><TD > metal, 3-body, bond-order potentials</TD></TR>
<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
</TD></TR></TABLE></DIV>
<P>Any or all of these packages can be included or excluded when LAMMPS
is built. The default is to include only the kspace, manybody, and
molecule packages. You may wish to exclude certain packages if you
will never run certain kinds of simulations. This will produce a
smaller executable which in some cases will also run a bit faster.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
"make yes-all" or "make no-all" to include/exclude all optional
packages. These commands work by simply moving files back and forth
between the main src directory and sub-directories with the package
name, so that the files are not seen when LAMMPS is built. After you
have included or excluded a package, you must re-make LAMMPS.
</P>
<P>Additional make options exist to help manage LAMMPS files that exist
in both the src directory and in package sub-directories. Typing
"make package-update" will overwrite src files with files from the
package directories if the package has been included. Typing "make
package-overwrite" will overwrite files in the package directories
with src files. Typing "make package-check" will list differences
between src and package versions of the same files.
</P>
<P>To use the poems package you must build LAMMPS with the POEMS library,
which computes the constrained rigid-body motion of articulated
(jointed) multibody systems. POEMS was written and is distributed by
Prof Kurt Anderson's group at Rensselaer Polytechnic Institute (RPI).
It is included in the LAMMPS distribution. To build LAMMPS with
POEMS, you must use a low-level LAMMPS Makefile that includes the
POEMS directory in its paths. See Makefile.g++.poems as an example.
You must also build POEMS itself as a library before building LAMMPS,
so that LAMMPS can link against it. The POEMS library is built by
typing "make" from within the poems directory in the LAMMPS
distribution. By default this uses Makefile which uses the gcc
compiler. If you need to use another compiler (so that the POEMS
library and LAMMPS are consistent), use another poems/Makefile.* or
create your own and invoke it as "make -f Makefile.*".
</P>
<P><B><I>Building LAMMPS as a library:</I></B>
</P>
<P>LAMMPS can be built as a library, which can then be called from
another application or a scripting language. See <A HREF = "Section_howto.html#4_10">this
section</A> for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
</P>
<PRE>make makelib
make -f Makefile.lib foo
</PRE>
<P>where foo is the machine name. The first "make" command will create a
current Makefile.lib with all the file names in your src dir. The 2nd
"make" command will use it to build LAMMPS as a library. This
requires that Makefile.foo have a library target (lib) and
system-specific settings for ARCHIVE and ARFLAGS. See Makefile.linux
for an example. The build will create the file liblmp_foo.a which
another application can link to. The callable functions in the
library are listed in library.h, but you can add as many functions as
you wish to library.h and library.cpp, which can access LAMMPS data
and return it to the caller or set LAMMPS data values as specified by
the caller. These 3 functions are included in the library:
</P>
<PRE>void lammps_open(int, char **, MPI_Comm);
void lammps_close();
int lammps_command(char *);
</PRE>
<P>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <A HREF = "#2_4">command-line arguments</A> when
LAMMPS is run from the command line and a MPI communicator for LAMMPS
to run under. The lammps_close() function is used to shut down LAMMPS
and free all its memory. The lammps_command() function is used to
pass a string to LAMMPS as if it were an input command read from an
input script. See the library.h file for more information about the
arguments and return values for these 3 functions.
</P>
<P><B><I>Additional build tips:</I></B>
</P>
<P>(1) Building LAMMPS for multiple platforms.
@ -337,11 +243,149 @@ make. Or you should be able to pull all the source files into Visual
C++ (ugh) or some similar development environment and build it. In
the src/MAKE/Windows directory are some notes from users on how they
built LAMMPS under Windows, so you can look at their instructions for
tips. Good luck - I can't help you on this one.
tips. Good luck - we can't help you on this one.
</P>
<H4><A NAME = "2_3"></A>2.3 Making LAMMPS with optional packages
</H4>
<P>The source code for LAMMPS is structured as a large set of core files
that are always used plus additional packages, which are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>
<TR><TD >manybody </TD><TD > metal, 3-body, bond-order potentials</TD></TR>
<TR><TD >meam </TD><TD > modified embedded atom method (MEAM) potential</TD></TR>
<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
<TR><TD >opt </TD><TD > optimized versions of a few pair potentials</TD></TR>
<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
</TD></TR></TABLE></DIV>
<P>Any or all packages can be included or excluded when LAMMPS is built.
The one exception is that to use the "opt" package, you must also be
using the "molecule" and "manybody" packages. You may wish to exclude
certain packages if you will never run certain kinds of simulations.
This will produce a smaller executable which may run a bit faster.
</P>
<P>By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages. As described below, some packages require LAMMPS
be linked to separately built library files, which will require
editing of your machine Makefile.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
"make yes-all" or "make no-all" to include/exclude all optional
packages. These commands work by simply moving files back and forth
between the main src directory and sub-directories with the package
name, so that the files are seen or not seen when LAMMPS is built.
After you have included or excluded a package, you must re-make
LAMMPS.
</P>
<P>Additional make options exist to help manage LAMMPS files that exist
in both the src directory and in package sub-directories. You do not
normally need to use these commands unless you are editing LAMMPS
files or have downloaded a patch from the LAMMPS WWW site. Typing
"make package-update" will overwrite src files with files from the
package directories if the package has been included. It should be
used after a patch is installed, since patches only update the master
package version of a file. Typing "make package-overwrite" will
overwrite files in the package directories with src files. Typing
"make package-check" will list differences between src and package
versions of the same files.
</P>
<P>To use the "poems" package you must build LAMMPS with the POEMS
library, which computes the constrained rigid-body motion of
articulated (jointed) multibody systems. POEMS was written and is
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI) and a version is included in the LAMMPS distribution
under the "lib" directory. To build LAMMPS with POEMS, you must use a
low-level LAMMPS Makefile that includes the POEMS directory in its
paths. See Makefile.g++_poems as an example. You must also build
POEMS itself as a library before building LAMMPS, so that LAMMPS can
link against it. The POEMS library is built by typing "make" from
within the poems directory with the appropriate Makefile, e.g. "make
-f Makefile.g++". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
</P>
<P>To use the "meam" package you must build LAMMPS with the MEAM library,
which computes the modified embedded atom method potential, which is a
generalization of EAM potentials that can be used to model a wider
variety of materials. This MEAM implementation was written by Greg
Wagner at Sandia and is included under the "lib" directory. To build
LAMMPS with MEAM, you must use a low-level LAMMPS Makefile that
includes the MEAM directory in its paths. See Makefile.linux_meam as
an example. You must also build MEAM itself as a library before
building LAMMPS, so that LAMMPS can link against it. This requires a
F90 compiler. The library is built by typing "make" from within the
meam directory with the appropriate Makefile, e.g. "make -f
Makefile.icc". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
</P>
<P>Linking a Fortran library to a C++ code can be problematic
(e.g. non-matching underscore conventions). If you have problems with
a particular compiler/machine, please send an email to the developers.
</P>
<H4><A NAME = "2_4"></A>2.4 Building LAMMPS as a library
</H4>
<P>LAMMPS can be built as a library, which can then be called from
another application or a scripting language. See <A HREF = "Section_howto.html#4_10">this
section</A> for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
</P>
<PRE>make makelib
make -f Makefile.lib foo
</PRE>
<P>where foo is the machine name. The first "make" command will create a
current Makefile.lib with all the file names in your src dir. The 2nd
"make" command will use it to build LAMMPS as a library. This
requires that Makefile.foo have a library target (lib) and
system-specific settings for ARCHIVE and ARFLAGS. See Makefile.linux
for an example. The build will create the file liblmp_foo.a which
another application can link to.
</P>
<P>When used from a C++ program, the library allows one or more LAMMPS
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within your application code, as needed. See the sample code
examples/couple/c++_driver.cpp as an example.
</P>
<P>When used from a C or Fortran program or a scripting language, the
library has a simple function-style interface, provided in library.cpp
and library.h. See the sample code examples/couple/c_driver.cpp as an
example.
</P>
<P>You can add as many functions as you wish to library.cpp and
library.h. In a general sense, those functions can access LAMMPS data
and return it to the caller or set LAMMPS data values as specified by
the caller. These 4 functions are currently included in library.cpp:
</P>
<PRE>void lammps_open(int, char **, MPI_Comm, void **ptr);
void lammps_close(void *ptr);
int lammps_file(void *ptr, char *);
int lammps_command(void *ptr, char *);
</PRE>
<P>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <A HREF = "#2_6">command-line arguments</A> when
LAMMPS is run from the command line and a MPI communicator for LAMMPS
to run under. It returns a ptr to the LAMMPS object that is created,
and which should be used in subsequent library calls. Note that
lammps_open() can be called multiple times to create multiple LAMMPS
objects.
</P>
<P>The lammps_close() function is used to shut down LAMMPS and free all
its memory. The lammps_file() and lammps_command() functions are used
to pass a file or string to LAMMPS as if it were an input file or
single command read from an input script.
</P>
<HR>
<H4><A NAME = "2_3"></A>2.3 Running LAMMPS
<H4><A NAME = "2_5"></A>2.5 Running LAMMPS
</H4>
<P>By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
@ -388,7 +432,7 @@ more processors or setup a smaller problem.
</P>
<HR>
<H4><A NAME = "2_4"></A>2.4 Command-line options
<H4><A NAME = "2_6"></A>2.6 Command-line options
</H4>
<P>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. For example, lmp_ibm might be
@ -476,7 +520,7 @@ variables in scripts.
</P>
<HR>
<H4><A NAME = "2_5"></A>2.5 LAMMPS screen output
<H4><A NAME = "2_7"></A>2.7 LAMMPS screen output
</H4>
<P>As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
@ -573,7 +617,7 @@ communication, roughly 75% in the example above.
</P>
<HR>
<H4><A NAME = "2_6"></A>2.6 Tips for users of previous LAMMPS versions
<H4><A NAME = "2_8"></A>2.8 Tips for users of previous LAMMPS versions
</H4>
<P>LAMMPS 2003 is a complete C++ rewrite of LAMMPS 2001, which was
written in F90. Features of earlier versions of LAMMPS are listed in

272
doc/Section_start.txt
View File

@ -13,16 +13,18 @@ new and experienced users.
2.1 "What's in the LAMMPS distribution"_#2_1
2.2 "Making LAMMPS"_#2_2
2.3 "Running LAMMPS"_#2_3
2.4 "Command-line options"_#2_4
2.5 "Screen output"_#2_5
2.6 "Tips for users of previous versions"_#2_6 :all(b)
2.3 "Making LAMMPS with optional packages"_#2_3
2.4 "Building LAMMPS as a library"_#2_4
2.5 "Running LAMMPS"_#2_5
2.6 "Command-line options"_#2_6
2.7 "Screen output"_#2_7
2.8 "Tips for users of previous versions"_#2_8 :all(b)
:line
2.1 What's in the LAMMPS distribution :h4,link(2_1)
When you download LAMMPS you will need to unzip and untar the
When you download SLAMMPS you will need to unzip and untar the
downloaded file with the following commands, after placing the file in
an appropriate directory.
@ -52,20 +54,19 @@ makefile, there are compiler options, additional libraries can be used
(MPI, FFT), etc. Please read this section carefully. If you are not
comfortable with makefiles, or building codes on a Unix platform, or
running an MPI job on your machine, please find a local expert to help
you. Many of the emails we get about build and run problems are not
really about LAMMPS - they are peculiar to the user's system,
compilers, libraries, etc. Such questions are better answered by a
local expert.
you. Many compiling, linking, and run problems users have do not
really have to do with LAMMPS - they are peculiar to the user's
system, compilers, libraries, etc. Such questions are better answered
by a local expert.
If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please send an email to the
"developers"_http://lammps.sandia.gov/authors.html. Note that doesn't
include linking problems - that's a question for a local expert!
"developers"_http://lammps.sandia.gov/authors.html.
Also, if you succeed in building LAMMPS on a new kind of machine
(which there isn't a similar Makefile for in the distribution), send
it to the developers and we'll include it in future LAMMPS releases.
If you succeed in building LAMMPS on a new kind of machine (which
there isn't a similar Makefile for in the distribution), send it to
the developers and we'll include it in future LAMMPS releases.
[{Building a LAMMPS executable:}]
@ -80,12 +81,9 @@ make linux
gmake mac :pre
If you get no errors and an executable like lmp_linux or lmp_mac is
produced, you're done; it's your lucky day. The remainder of this
section addressed the following topics: errors that occur when making
LAMMPS, editing a new low-level Makefile.foo, how to make LAMMPS with
and without packages, and additional build tips.
produced, you're done; it's your lucky day.
[{Errors that occur when making LAMMPS:}]
[{Errors that can occur when making LAMMPS:}]
(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
@ -205,96 +203,6 @@ gmake foo :pre
You should get the executable lmp_foo when the build is complete.
[{How to make LAMMPS with and without packages:}]
The source code for LAMMPS is structured as a large set of core files
that are always used plus additional packages, which are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
class2 : class 2 force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers
manybody : metal, 3-body, bond-order potentials
molecule : force fields for molecular systems
poems : coupled rigid body motion
xtc : dump atom snapshots in XTC format :tb(s=:)
Any or all of these packages can be included or excluded when LAMMPS
is built. The default is to include only the kspace, manybody, and
molecule packages. You may wish to exclude certain packages if you
will never run certain kinds of simulations. This will produce a
smaller executable which in some cases will also run a bit faster.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
"make yes-all" or "make no-all" to include/exclude all optional
packages. These commands work by simply moving files back and forth
between the main src directory and sub-directories with the package
name, so that the files are not seen when LAMMPS is built. After you
have included or excluded a package, you must re-make LAMMPS.
Additional make options exist to help manage LAMMPS files that exist
in both the src directory and in package sub-directories. Typing
"make package-update" will overwrite src files with files from the
package directories if the package has been included. Typing "make
package-overwrite" will overwrite files in the package directories
with src files. Typing "make package-check" will list differences
between src and package versions of the same files.
To use the poems package you must build LAMMPS with the POEMS library,
which computes the constrained rigid-body motion of articulated
(jointed) multibody systems. POEMS was written and is distributed by
Prof Kurt Anderson's group at Rensselaer Polytechnic Institute (RPI).
It is included in the LAMMPS distribution. To build LAMMPS with
POEMS, you must use a low-level LAMMPS Makefile that includes the
POEMS directory in its paths. See Makefile.g++.poems as an example.
You must also build POEMS itself as a library before building LAMMPS,
so that LAMMPS can link against it. The POEMS library is built by
typing "make" from within the poems directory in the LAMMPS
distribution. By default this uses Makefile which uses the gcc
compiler. If you need to use another compiler (so that the POEMS
library and LAMMPS are consistent), use another poems/Makefile.* or
create your own and invoke it as "make -f Makefile.*".
[{Building LAMMPS as a library:}]
LAMMPS can be built as a library, which can then be called from
another application or a scripting language. See "this
section"_Section_howto.html#4_10 for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
make makelib
make -f Makefile.lib foo :pre
where foo is the machine name. The first "make" command will create a
current Makefile.lib with all the file names in your src dir. The 2nd
"make" command will use it to build LAMMPS as a library. This
requires that Makefile.foo have a library target (lib) and
system-specific settings for ARCHIVE and ARFLAGS. See Makefile.linux
for an example. The build will create the file liblmp_foo.a which
another application can link to. The callable functions in the
library are listed in library.h, but you can add as many functions as
you wish to library.h and library.cpp, which can access LAMMPS data
and return it to the caller or set LAMMPS data values as specified by
the caller. These 3 functions are included in the library:
void lammps_open(int, char **, MPI_Comm);
void lammps_close();
int lammps_command(char *); :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line arguments"_#2_4 when
LAMMPS is run from the command line and a MPI communicator for LAMMPS
to run under. The lammps_close() function is used to shut down LAMMPS
and free all its memory. The lammps_command() function is used to
pass a string to LAMMPS as if it were an input command read from an
input script. See the library.h file for more information about the
arguments and return values for these 3 functions.
[{Additional build tips:}]
(1) Building LAMMPS for multiple platforms.
@ -330,11 +238,147 @@ make. Or you should be able to pull all the source files into Visual
C++ (ugh) or some similar development environment and build it. In
the src/MAKE/Windows directory are some notes from users on how they
built LAMMPS under Windows, so you can look at their instructions for
tips. Good luck - I can't help you on this one.
tips. Good luck - we can't help you on this one.
2.3 Making LAMMPS with optional packages :h4,link(2_3)
The source code for LAMMPS is structured as a large set of core files
that are always used plus additional packages, which are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of packages by typing "make package". The current
list of packages is as follows:
class2 : class 2 force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers
manybody : metal, 3-body, bond-order potentials
meam : modified embedded atom method (MEAM) potential
molecule : force fields for molecular systems
opt : optimized versions of a few pair potentials
poems : coupled rigid body motion
xtc : dump atom snapshots in XTC format :tb(s=:)
Any or all packages can be included or excluded when LAMMPS is built.
The one exception is that to use the "opt" package, you must also be
using the "molecule" and "manybody" packages. You may wish to exclude
certain packages if you will never run certain kinds of simulations.
This will produce a smaller executable which may run a bit faster.
By default, LAMMPS includes only the "kspace", "manybody", and
"molecule" packages. As described below, some packages require LAMMPS
be linked to separately built library files, which will require
editing of your machine Makefile.
Packages are included or excluded by typing "make yes-name" or "make
no-name", where "name" is the name of the package. You can also type
"make yes-all" or "make no-all" to include/exclude all optional
packages. These commands work by simply moving files back and forth
between the main src directory and sub-directories with the package
name, so that the files are seen or not seen when LAMMPS is built.
After you have included or excluded a package, you must re-make
LAMMPS.
Additional make options exist to help manage LAMMPS files that exist
in both the src directory and in package sub-directories. You do not
normally need to use these commands unless you are editing LAMMPS
files or have downloaded a patch from the LAMMPS WWW site. Typing
"make package-update" will overwrite src files with files from the
package directories if the package has been included. It should be
used after a patch is installed, since patches only update the master
package version of a file. Typing "make package-overwrite" will
overwrite files in the package directories with src files. Typing
"make package-check" will list differences between src and package
versions of the same files.
To use the "poems" package you must build LAMMPS with the POEMS
library, which computes the constrained rigid-body motion of
articulated (jointed) multibody systems. POEMS was written and is
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
Institute (RPI) and a version is included in the LAMMPS distribution
under the "lib" directory. To build LAMMPS with POEMS, you must use a
low-level LAMMPS Makefile that includes the POEMS directory in its
paths. See Makefile.g++_poems as an example. You must also build
POEMS itself as a library before building LAMMPS, so that LAMMPS can
link against it. The POEMS library is built by typing "make" from
within the poems directory with the appropriate Makefile, e.g. "make
-f Makefile.g++". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
To use the "meam" package you must build LAMMPS with the MEAM library,
which computes the modified embedded atom method potential, which is a
generalization of EAM potentials that can be used to model a wider
variety of materials. This MEAM implementation was written by Greg
Wagner at Sandia and is included under the "lib" directory. To build
LAMMPS with MEAM, you must use a low-level LAMMPS Makefile that
includes the MEAM directory in its paths. See Makefile.linux_meam as
an example. You must also build MEAM itself as a library before
building LAMMPS, so that LAMMPS can link against it. This requires a
F90 compiler. The library is built by typing "make" from within the
meam directory with the appropriate Makefile, e.g. "make -f
Makefile.icc". If one of the provided Makefiles is not appropriate
for your system you can edit or add one as needed.
Linking a Fortran library to a C++ code can be problematic
(e.g. non-matching underscore conventions). If you have problems with
a particular compiler/machine, please send an email to the developers.
2.4 Building LAMMPS as a library :h4,link(2_4)
LAMMPS can be built as a library, which can then be called from
another application or a scripting language. See "this
section"_Section_howto.html#4_10 for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
make makelib
make -f Makefile.lib foo :pre
where foo is the machine name. The first "make" command will create a
current Makefile.lib with all the file names in your src dir. The 2nd
"make" command will use it to build LAMMPS as a library. This
requires that Makefile.foo have a library target (lib) and
system-specific settings for ARCHIVE and ARFLAGS. See Makefile.linux
for an example. The build will create the file liblmp_foo.a which
another application can link to.
When used from a C++ program, the library allows one or more LAMMPS
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within your application code, as needed. See the sample code
examples/couple/c++_driver.cpp as an example.
When used from a C or Fortran program or a scripting language, the
library has a simple function-style interface, provided in library.cpp
and library.h. See the sample code examples/couple/c_driver.cpp as an
example.
You can add as many functions as you wish to library.cpp and
library.h. In a general sense, those functions can access LAMMPS data
and return it to the caller or set LAMMPS data values as specified by
the caller. These 4 functions are currently included in library.cpp:
void lammps_open(int, char **, MPI_Comm, void **ptr);
void lammps_close(void *ptr);
int lammps_file(void *ptr, char *);
int lammps_command(void *ptr, char *); :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line arguments"_#2_6 when
LAMMPS is run from the command line and a MPI communicator for LAMMPS
to run under. It returns a ptr to the LAMMPS object that is created,
and which should be used in subsequent library calls. Note that
lammps_open() can be called multiple times to create multiple LAMMPS
objects.
The lammps_close() function is used to shut down LAMMPS and free all
its memory. The lammps_file() and lammps_command() functions are used
to pass a file or string to LAMMPS as if it were an input file or
single command read from an input script.
:line
2.3 Running LAMMPS :h4,link(2_3)
2.5 Running LAMMPS :h4,link(2_5)
By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
@ -381,7 +425,7 @@ more processors or setup a smaller problem.
:line
2.4 Command-line options :h4,link(2_4)
2.6 Command-line options :h4,link(2_6)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. For example, lmp_ibm might be
@ -469,7 +513,7 @@ variables in scripts.
:line
2.5 LAMMPS screen output :h4,link(2_5)
2.7 LAMMPS screen output :h4,link(2_7)
As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
@ -566,7 +610,7 @@ communication, roughly 75% in the example above.
:line
2.6 Tips for users of previous LAMMPS versions :h4,link(2_6)
2.8 Tips for users of previous LAMMPS versions :h4,link(2_8)
LAMMPS 2003 is a complete C++ rewrite of LAMMPS 2001, which was
written in F90. Features of earlier versions of LAMMPS are listed in

14
doc/angle_coeff.html
View File

@ -62,14 +62,14 @@ corresponds to the 1st example above would be listed as
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command:
</P>
<UL><LI><A HREF = "angle_style_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_style_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
</UL>
<UL><LI><A HREF = "angle_style_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_style_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_style_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_style_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_style_harmonic.html">angle_style harmonic</A> - harmonic angle
<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
</UL>
<HR>

14
doc/angle_coeff.txt
View File

@ -59,14 +59,14 @@ Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command:
"angle_style none"_angle_style_none.html - turn off angle interactions
"angle_style hybrid"_angle_style_hybrid.html - define multiple styles of angle interactions :ul
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_style_charmm.html - CHARMM angle
"angle_style class2"_angle_style_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_style_cosine.html - cosine angle potential
"angle_style cosine/squared"_angle_style_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_style_harmonic.html - harmonic angle :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle :ul
:line

14
doc/angle_style.html
View File

@ -51,14 +51,14 @@ exist between the 3 bonded atoms.
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command:
</P>
<UL><LI><A HREF = "angle_style_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_style_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
</UL>
<UL><LI><A HREF = "angle_style_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_style_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_style_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_style_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_style_harmonic.html">angle_style harmonic</A> - harmonic angle
<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
</UL>
<HR>

14
doc/angle_style.txt
View File

@ -49,14 +49,14 @@ Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command:
"angle_style none"_angle_style_none.html - turn off angle interactions
"angle_style hybrid"_angle_style_hybrid.html - define multiple styles of angle interactions :ul
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_style_charmm.html - CHARMM angle
"angle_style class2"_angle_style_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_style_cosine.html - cosine angle potential
"angle_style cosine/squared"_angle_style_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_style_harmonic.html - harmonic angle :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle :ul
:line

16
doc/atom_style.html
View File

@ -15,14 +15,15 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>dpd</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dpd</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more styles
<I>hybrid</I> args = list of one or more sub-styles
</PRE>
<P><B>Examples:</B>
</P>
<PRE>atom_style bond
<PRE>atom_style atomic
atom_style bond
atom_style full
atom_style hybrid charge bond
</PRE>
@ -51,11 +52,10 @@ velocities, atom IDs and types.
<LI><I>atomic</I> = only the default values
<LI><I>bond</I> = bonds - e.g. bead-spring polymers
<LI><I>charge</I> = charge
<LI><I>dipole</I> = charge + dipole moments
<LI><I>dpd</I> = default values, also communicates velocities
<LI><I>molecular</I> = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
<LI><I>full</I> = molecular + charge - e.g. biomolecules, charged polymers
<LI><I>granular</I> = granular material with rotational properties
<LI><I>granular</I> = granular atoms with rotational properties
</UL>
<P>Typical simulations with a single pair potential will use only one of
these styles. For cases where multiple pair potentials will be used
@ -77,13 +77,15 @@ section</A>.
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
"molecular" package. The <I>granular</I> style is part of the "granular"
package. The <I>dpd</I> style is part of the "dpd" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "pair_style.html">pair_style</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>atom_style atomic
</P>
</HTML>

14
doc/atom_style.txt
View File

@ -12,13 +12,14 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or {dpd} or \
style = {angle} or {atomic} or {bond} or {charge} or {dpd} or \
{full} or {granular} or {molecular} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more styles :pre
{hybrid} args = list of one or more sub-styles :pre
[Examples:]
atom_style atomic
atom_style bond
atom_style full
atom_style hybrid charge bond :pre
@ -48,11 +49,10 @@ velocities, atom IDs and types.
{atomic} = only the default values
{bond} = bonds - e.g. bead-spring polymers
{charge} = charge
{dipole} = charge + dipole moments
{dpd} = default values, also communicates velocities
{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
{full} = molecular + charge - e.g. biomolecules, charged polymers
{granular} = granular material with rotational properties :ul
{granular} = granular atoms with rotational properties :ul
Typical simulations with a single pair potential will use only one of
these styles. For cases where multiple pair potentials will be used
@ -75,10 +75,12 @@ The {angle}, {bond}, {full}, and {molecular} styles are part of the
"molecular" package. The {granular} style is part of the "granular"
package. The {dpd} style is part of the "dpd" package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"read_data"_read_data.html, "pair_style"_pair_style.html
[Default:] none
[Default:]
atom_style atomic

18
doc/bond_coeff.html
View File

@ -63,16 +63,16 @@ corresponds to the 1st example above would be listed as
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</P>
<UL><LI><A HREF = "bond_style_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_style_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
</UL>
<UL><LI><A HREF = "bond_style_class.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_style_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_style_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_style_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_style_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_style_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_style_quartic.html">bond_style quartic</A> - breakable quartic bond
<UL><LI><A HREF = "bond_class.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
</UL>
<HR>

18
doc/bond_coeff.txt
View File

@ -60,16 +60,16 @@ Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command:
"bond_style none"_bond_style_none.html - turn off bonded interactions
"bond_style hybrid"_bond_style_hybrid.html - define multiple styles of bond interactions :ul
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_style_class.html - COMPASS (class 2) bond
"bond_style fene"_bond_style_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_style_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_style_harmonic.html - harmonic bond
"bond_style morse"_bond_style_morse.html - Morse bond
"bond_style nonlinear"_bond_style_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_style_quartic.html - breakable quartic bond :ul
"bond_style class2"_bond_class.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond :ul
:line

18
doc/bond_style.html
View File

@ -60,16 +60,16 @@ exist between 2 bonded atoms.
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</P>
<UL><LI><A HREF = "bond_style_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_style_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
</UL>
<UL><LI><A HREF = "bond_style_class2.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_style_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_style_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_style_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_style_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_style_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_style_quartic.html">bond_style quartic</A> - breakable quartic bond
<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
</UL>
<HR>

18
doc/bond_style.txt
View File

@ -57,16 +57,16 @@ Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command:
"bond_style none"_bond_style_none.html - turn off bonded interactions
"bond_style hybrid"_bond_style_hybrid.html - define multiple styles of bond interactions :ul
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_style_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_style_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_style_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_style_harmonic.html - harmonic bond
"bond_style morse"_bond_style_morse.html - Morse bond
"bond_style nonlinear"_bond_style_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_style_quartic.html - breakable quartic bond :ul
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond :ul
:line

16
doc/dihedral_coeff.html
View File

@ -64,15 +64,15 @@ corresponds to the 1st example above would be listed as
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command:
</P>
<UL><LI><A HREF = "dihedral_style_none.html">dihedral_style none</A> - turn off dihedral interactions
<LI><A HREF = "dihedral_style_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
<UL><LI><A HREF = "dihedral_none.html">dihedral_style none</A> - turn off dihedral interactions
<LI><A HREF = "dihedral_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
</UL>
<UL><LI><A HREF = "dihedral_style_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
<LI><A HREF = "dihedral_style_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
<LI><A HREF = "dihedral_style_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
<LI><A HREF = "dihedral_style_helix.html">dihedral_style helix</A> - helix dihedral
<LI><A HREF = "dihedral_style_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
<LI><A HREF = "dihedral_style_opls.html">dihedral_style opls</A> - OPLS dihedral
<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
<LI><A HREF = "dihedral_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
<LI><A HREF = "dihedral_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
<LI><A HREF = "dihedral_helix.html">dihedral_style helix</A> - helix dihedral
<LI><A HREF = "dihedral_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
<LI><A HREF = "dihedral_opls.html">dihedral_style opls</A> - OPLS dihedral
</UL>
<HR>

16
doc/dihedral_coeff.txt
View File

@ -61,15 +61,15 @@ Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command:
"dihedral_style none"_dihedral_style_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_style_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_style_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_style_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_style_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_style_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_style_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_style_opls.html - OPLS dihedral :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
:line

16
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View File

@ -66,15 +66,15 @@ torsions that contain the j-k bond in an i-j-k-l torsion.
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command:
</P>
<UL><LI><A HREF = "dihedral_style_none.html">dihedral_style none</A> - turn off dihedral interactions
<LI><A HREF = "dihedral_style_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
<UL><LI><A HREF = "dihedral_none.html">dihedral_style none</A> - turn off dihedral interactions
<LI><A HREF = "dihedral_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
</UL>
<UL><LI><A HREF = "dihedral_style_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
<LI><A HREF = "dihedral_style_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
<LI><A HREF = "dihedral_style_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
<LI><A HREF = "dihedral_style_helix.html">dihedral_style helix</A> - helix dihedral
<LI><A HREF = "dihedral_style_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
<LI><A HREF = "dihedral_style_opls.html">dihedral_style opls</A> - OPLS dihedral
<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
<LI><A HREF = "dihedral_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
<LI><A HREF = "dihedral_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
<LI><A HREF = "dihedral_helix.html">dihedral_style helix</A> - helix dihedral
<LI><A HREF = "dihedral_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
<LI><A HREF = "dihedral_opls.html">dihedral_style opls</A> - OPLS dihedral
</UL>
<HR>

16
doc/dihedral_style.txt
View File

@ -64,15 +64,15 @@ Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command:
"dihedral_style none"_dihedral_style_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_style_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_style_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_style_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_style_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_style_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_style_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_style_opls.html - OPLS dihedral :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
:line

165
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View File

@ -19,7 +19,7 @@
<LI>group-ID = ID of the group of atoms to be dumped
<LI>style = <I>atom</I> or <I>bond</I> or <I>custom</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I>
<LI>style = <I>atom</I> or <I>bond</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>custom</I>
<LI>N = dump every this many timesteps
@ -29,11 +29,18 @@
<PRE> <I>atom</I> args = none
<I>bond</I> args = none
<I>dcd</I> args = none
<I>xtc</I> args = precision (optional)
precision = power-of-10 value from 10 to 1000000 (default = 1000)
<I>xyz</I> args = none
<I>custom</I> args = list of atom attributes
possible attributes = tag, mol, type, x, y, z, xs, ys, zs, xu, yu, zu,
ix, iy, iz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, tqx, tqy, tqz,
etotal, ke, epair, centro, sxx, syy, szz, sxy, sxz, syz
possible attributes = tag, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, tqx, tqy, tqz,
epair, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID[N]
tag = atom ID
mol = molecule ID
type = atom type
@ -46,15 +53,13 @@
q = atom charge
mux,muy,muz = orientation of dipolar atom
tqx,tqy,tqz = torque on dipolar atoms
etotal = per-atom total energy (ke + epair)
ke = per-atom kinetic energy
epair = per-atom pairwise energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
centro = per-atom centro-symmetry parameter
sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
<I>dcd</I> args = none
<I>xtc</I> args = precision (optional)
precision = power-of-10 value from 10 to 1000000 (default = 1000)
<I>xyz</I> args = none
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID
</PRE>
</UL>
@ -63,7 +68,7 @@
<PRE>dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz c_myF[3]
dump 1 all xtc 1000 file.xtc 100.0
</PRE>
<P><B>Description:</B>
@ -207,87 +212,71 @@ styles.
part of the <I>custom</I> style.
</P>
<P>The <I>tag</I>, <I>mol</I>, <I>type</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, <I>q</I> attributes are self-explanatory. <I>Tag</I> is the atom ID.
<I>Mol</I> is the molecule ID, included in the data file for molecular
systems. The <I>x</I>, <I>y</I>, <I>z</I> attributes write atom coordinates
"unscaled", in the appropriate distance units (Angstroms, sigma, etc).
Use <I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box
size, so that each value is 0.0 to 1.0. Use <I>xu</I>, <I>yu</I>, <I>zu</I> if you
want the coordinates "unwrapped" by the image flags for each atom.
Unwrapped means that if the atom has passed thru a periodic boundary
one or more times, the value is printed for what the coordinate would
be if it had not been wrapped back into the periodic box. Note that
using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the coordinate values may be far
outside the box size printed with the snapshot. The image flags can
be printed directly using the <I>ix</I>, <I>iy</I>, <I>iz</I> attributes. The
<A HREF = "dump_modify.html">dump_modify</A> documentation describes in more detail
what is meant by scaled vs unscaled coordinates and the image flags.
<I>fz</I>, <I>q</I> keywords are self-explanatory. <I>Tag</I> is the atom ID. <I>Mol</I>
is the molecule ID, included in the data file for molecular systems.
The <I>x</I>, <I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
appropriate distance units (Angstroms, sigma, etc). Use <I>xs</I>, <I>ys</I>,
<I>zs</I> if you want the coordinates "scaled" to the box size, so that
each value is 0.0 to 1.0. Use <I>xu</I>, <I>yu</I>, <I>zu</I> if you want the
coordinates "unwrapped" by the image flags for each atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that using <I>xu</I>,
<I>yu</I>, <I>zu</I> means that the coordinate values may be far outside the box
size printed with the snapshot. The image flags can be printed
directly using the <I>ix</I>, <I>iy</I>, <I>iz</I> keywords. The
<A HREF = "dump_modify.html">dump_modify</A> command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
</P>
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I>, <I>tqy</I>, <I>tqx</I>, <I>tqy</I> attributes are specific
to dipolar systems defined with an atom style of <I>dipole</I>.
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I>, <I>tqy</I>, <I>tqx</I>, <I>tqy</I> keywords are specific
to dipolar systems defined with an atom style of <I>dipole</I>. The first
3 give the orientation of the atom's dipole. The latter 3 give the
torque on the dipolar atoms.
</P>
<P>The <I>etotal</I> attribute computes the total energy of each atom, which
is the <I>ke</I> plus <I>epair</I> values. Note that it does not include
contributions due to bonds, angles, etc that the atom is part of.
<P>The <I>epair</I>, <I>ke</I>, <I>etotal</I>, <I>centro</I>, and <I>sxx</I>, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
kinetic), centro-symmetry parameter, and components of the per-atom
stress tensor for each atom. These quantities are calculated by
computes that the dump defines, as if these commands had been issued:
</P>
<P>The <I>ke</I> attribute computes the kinetic energy of each atom
which is simply 0.5 m v^2.
<PRE>compute dump-ID_epair/atom group-ID <A HREF = "compute_epair_atom.html">epair/atom</A>
compute dump-ID_ke/atom group-ID <A HREF = "compute_ke_atom.html">ke/atom</A>
compute dump-ID_etotal/atom group-ID <A HREF = "compute_etotal_atom.html">etotal/atom</A>
compute dump-ID_centro/atom group-ID <A HREF = "compute_centro_atom.html">centro/atom</A>
compute dump-ID_stress/atom group-ID <A HREF = "compute_stress_atom.html">stress/atom</A>
</PRE>
<P>See the corresponding <A HREF = "compute.html">compute</A> style commands for
details on what is computed for each atom. Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore). The group for each new compute is the same as the dump
group.
</P>
<P>The <I>epair</I> attribute computes the pairwise energy for each atom.
This is its pairwise interaction with all of its neighbors (divided by
2). Summed over all atoms, this should equal the pairwise energy of
the entire system (Van der Waals + Coulombic). However, for force
fields that include a contribution to the pairwise energy that is
computed as part of dihedral terms (i.e. 1-4 interactions), this
contribution is not included in the per-atom pairwise energy.
Computation of the per-atom energy requires a loop thru the neighbor
list and inter-processor communication, so it can be inefficient to
dump this quantity too frequently or to have multiple dump commands,
each with a <I>epair</I> attribute.
<P>Note that the <I>etotal</I> keyword does not include energy contributions
due to bonds, angles, etc that the atom is part of.
</P>
<P>The <I>centro</I> attribute causes the centro-symmetry parameter to be
computed for each atom in the dump group using the following formula
from <A HREF = "#Kelchner">(Kelchner)</A>
<P>The <I>sxx</I>, <I>syy</I>, <I>szz</I>, <I>sxy</I>, <I>sxz</I>, <I>syz</I> keywords access the 6
components of the stress tensor calculated for each atom by the
<A HREF = "compute_stress_atom.html">compute stress/atom</A> style.
</P>
<CENTER><IMG SRC = "Eqs/centro_symmetry.jpg">
</CENTER>
<P>where the 12 nearest neighbors are found and Ri and Ri+6 are the
vectors from the central atom to the opposite pair of nearest
neighbors. In solid state systems this is a useful measure of the
local lattice disorder around an atom and can be used to characterize
whether the atom is part of a perfect lattice, a local defect (e.g. a
dislocation or stacking fault), or at a surface. The neighbor list
needed to compute this quantity is constructed each time the dump is
performed. Thus it can be inefficient to dump this quantity too
frequently or to have multiple dump commands, each with a <I>centro</I>
attribute.
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector per-atom
quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
<A HREF = "compute.html">compute</A> command for details. Note that scalar and
vector quantities that are not calculated on a per-atoms basis
(e.g. global temperature or pressure) cannot be output in a dump.
Rather, these quantities are output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command.
</P>
<P>The <I>sxx</I>, <I>syy</I>, <I>szz</I>, <I>sxy</I>, <I>sxz</I>, <I>syz</I> attributes compute the
pairwise stress tensor for each atom where the <I>ab</I> component of the
stress on atom <I>i</I> is given by
<P>If <I>c_ID</I> is used as a keyword, then the a single per-atom quantity
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N in
the range from 1-M will print a specific component of the per-atom
vector calculated by the compute. A value of N=0 will output the
single per-atom quantity.
</P>
<CENTER><IMG SRC = "Eqs/stress_tensor.jpg">
</CENTER>
<P>where the first term is a kinetic energy component for atom <I>i</I>, <I>j</I>
loops over the <I>N</I> neighbors of atom <I>i</I>, and <I>Fb</I> is one of 3
components of force on atom <I>i</I> due to atom <I>j</I>. Both <I>a</I> and <I>b</I> can
take on values x,y,z to generate the 6 components of the symmetric
tensor.
</P>
<P>Note that this formula for stress does not include virial
contributions from intra-molecular interactions (e.g. bonds, angles,
torsions, etc). Also note that this quantity is the negative of the
per-atom pressure tensor. It is also really a stress-volume
formulation. It would need to be divided by a per-atom volume to have
units of stress, but an individual atom's volume is not easy to
compute in a deformed solid. Computation of stress tensor components
requires a loop thru the neighbor list and inter-processor
communication, so it can be inefficient to dump this quantity too
frequently or to have multiple dump commands, each with stress tensor
attributes.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> for information on how to modify
LAMMPS to dump other kinds of per-atom quantities.
<P>See <A HREF = "Section_modify.html">this section</A> for information on how to add
new compute styles to LAMMPS that calculate per-atom quantities which
could then be output with these keywords.
</P>
<HR>
@ -319,10 +308,4 @@ gran/diag</A> command should be used instead.
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kelchner"></A>
<P><B>(Kelchner)</B> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
</P>
</HTML>

162
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View File

@ -14,17 +14,24 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {bond} or {custom} or {dcd} or {xtc} or {xyz} :l
style = {atom} or {bond} or {dcd} or {xtc} or {xyz} or {custom} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
{atom} args = none
{bond} args = none
{dcd} args = none
{xtc} args = precision (optional)
precision = power-of-10 value from 10 to 1000000 (default = 1000)
{xyz} args = none
{custom} args = list of atom attributes
possible attributes = tag, mol, type, x, y, z, xs, ys, zs, xu, yu, zu,
ix, iy, iz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, tqx, tqy, tqz,
etotal, ke, epair, centro, sxx, syy, szz, sxy, sxz, syz
possible attributes = tag, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, tqx, tqy, tqz,
epair, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID\[N\]
tag = atom ID
mol = molecule ID
type = atom type
@ -37,15 +44,13 @@ args = list of arguments for a particular style :l
q = atom charge
mux,muy,muz = orientation of dipolar atom
tqx,tqy,tqz = torque on dipolar atoms
etotal = per-atom total energy (ke + epair)
ke = per-atom kinetic energy
epair = per-atom pairwise energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
centro = per-atom centro-symmetry parameter
sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
{dcd} args = none
{xtc} args = precision (optional)
precision = power-of-10 value from 10 to 1000000 (default = 1000)
{xyz} args = none :pre
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
c_ID\[N\] = Nth per-atom vector quantity calculated by a compute identified by its ID :pre
:ule
[Examples:]
@ -53,7 +58,7 @@ args = list of arguments for a particular style :l
dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz
dump 4b flow custom 100 dump.%.myforce tag type epair sxx syy szz c_myF\[3\]
dump 1 all xtc 1000 file.xtc 100.0 :pre
[Description:]
@ -197,87 +202,71 @@ This section explains the atom quantities that can be specified as
part of the {custom} style.
The {tag}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} attributes are self-explanatory. {Tag} is the atom ID.
{Mol} is the molecule ID, included in the data file for molecular
systems. The {x}, {y}, {z} attributes write atom coordinates
"unscaled", in the appropriate distance units (Angstroms, sigma, etc).
Use {xs}, {ys}, {zs} if you want the coordinates "scaled" to the box
size, so that each value is 0.0 to 1.0. Use {xu}, {yu}, {zu} if you
want the coordinates "unwrapped" by the image flags for each atom.
Unwrapped means that if the atom has passed thru a periodic boundary
one or more times, the value is printed for what the coordinate would
be if it had not been wrapped back into the periodic box. Note that
using {xu}, {yu}, {zu} means that the coordinate values may be far
outside the box size printed with the snapshot. The image flags can
be printed directly using the {ix}, {iy}, {iz} attributes. The
"dump_modify"_dump_modify.html documentation describes in more detail
what is meant by scaled vs unscaled coordinates and the image flags.
{fz}, {q} keywords are self-explanatory. {Tag} is the atom ID. {Mol}
is the molecule ID, included in the data file for molecular systems.
The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the
appropriate distance units (Angstroms, sigma, etc). Use {xs}, {ys},
{zs} if you want the coordinates "scaled" to the box size, so that
each value is 0.0 to 1.0. Use {xu}, {yu}, {zu} if you want the
coordinates "unwrapped" by the image flags for each atom. Unwrapped
means that if the atom has passed thru a periodic boundary one or more
times, the value is printed for what the coordinate would be if it had
not been wrapped back into the periodic box. Note that using {xu},
{yu}, {zu} means that the coordinate values may be far outside the box
size printed with the snapshot. The image flags can be printed
directly using the {ix}, {iy}, {iz} keywords. The
"dump_modify"_dump_modify.html command describes in more detail what
is meant by scaled vs unscaled coordinates and the image flags.
The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} attributes are specific
to dipolar systems defined with an atom style of {dipole}.
The {mux}, {muy}, {muz}, {tqy}, {tqx}, {tqy} keywords are specific
to dipolar systems defined with an atom style of {dipole}. The first
3 give the orientation of the atom's dipole. The latter 3 give the
torque on the dipolar atoms.
The {etotal} attribute computes the total energy of each atom, which
is the {ke} plus {epair} values. Note that it does not include
contributions due to bonds, angles, etc that the atom is part of.
The {epair}, {ke}, {etotal}, {centro}, and {sxx}, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
kinetic), centro-symmetry parameter, and components of the per-atom
stress tensor for each atom. These quantities are calculated by
computes that the dump defines, as if these commands had been issued:
The {ke} attribute computes the kinetic energy of each atom
which is simply 0.5 m v^2.
compute dump-ID_epair/atom group-ID "epair/atom"_compute_epair_atom.html
compute dump-ID_ke/atom group-ID "ke/atom"_compute_ke_atom.html
compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html
compute dump-ID_centro/atom group-ID "centro/atom"_compute_centro_atom.html
compute dump-ID_stress/atom group-ID "stress/atom"_compute_stress_atom.html :pre
The {epair} attribute computes the pairwise energy for each atom.
This is its pairwise interaction with all of its neighbors (divided by
2). Summed over all atoms, this should equal the pairwise energy of
the entire system (Van der Waals + Coulombic). However, for force
fields that include a contribution to the pairwise energy that is
computed as part of dihedral terms (i.e. 1-4 interactions), this
contribution is not included in the per-atom pairwise energy.
Computation of the per-atom energy requires a loop thru the neighbor
list and inter-processor communication, so it can be inefficient to
dump this quantity too frequently or to have multiple dump commands,
each with a {epair} attribute.
See the corresponding "compute"_compute.html style commands for
details on what is computed for each atom. Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore). The group for each new compute is the same as the dump
group.
The {centro} attribute causes the centro-symmetry parameter to be
computed for each atom in the dump group using the following formula
from "(Kelchner)"_#Kelchner
Note that the {etotal} keyword does not include energy contributions
due to bonds, angles, etc that the atom is part of.
:c,image(Eqs/centro_symmetry.jpg)
The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} keywords access the 6
components of the stress tensor calculated for each atom by the
"compute stress/atom"_compute_stress_atom.html style.
where the 12 nearest neighbors are found and Ri and Ri+6 are the
vectors from the central atom to the opposite pair of nearest
neighbors. In solid state systems this is a useful measure of the
local lattice disorder around an atom and can be used to characterize
whether the atom is part of a perfect lattice, a local defect (e.g. a
dislocation or stacking fault), or at a surface. The neighbor list
needed to compute this quantity is constructed each time the dump is
performed. Thus it can be inefficient to dump this quantity too
frequently or to have multiple dump commands, each with a {centro}
attribute.
The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom
quantities calculated by a compute to be output. The ID in the
keyword should be replaced by the actual ID of the compute that has
been defined elsewhere in the input script. See the
"compute"_compute.html command for details. Note that scalar and
vector quantities that are not calculated on a per-atoms basis
(e.g. global temperature or pressure) cannot be output in a dump.
Rather, these quantities are output by the "thermo_style
custom"_thermo_style.html command.
The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} attributes compute the
pairwise stress tensor for each atom where the {ab} component of the
stress on atom {i} is given by
If {c_ID} is used as a keyword, then the a single per-atom quantity
calculated by the compute is printed. If {c_ID\[N\]} is used, then N in
the range from 1-M will print a specific component of the per-atom
vector calculated by the compute. A value of N=0 will output the
single per-atom quantity.
:c,image(Eqs/stress_tensor.jpg)
where the first term is a kinetic energy component for atom {i}, {j}
loops over the {N} neighbors of atom {i}, and {Fb} is one of 3
components of force on atom {i} due to atom {j}. Both {a} and {b} can
take on values x,y,z to generate the 6 components of the symmetric
tensor.
Note that this formula for stress does not include virial
contributions from intra-molecular interactions (e.g. bonds, angles,
torsions, etc). Also note that this quantity is the negative of the
per-atom pressure tensor. It is also really a stress-volume
formulation. It would need to be divided by a per-atom volume to have
units of stress, but an individual atom's volume is not easy to
compute in a deformed solid. Computation of stress tensor components
requires a loop thru the neighbor list and inter-processor
communication, so it can be inefficient to dump this quantity too
frequently or to have multiple dump commands, each with stress tensor
attributes.
See "this section"_Section_modify.html for information on how to modify
LAMMPS to dump other kinds of per-atom quantities.
See "this section"_Section_modify.html for information on how to add
new compute styles to LAMMPS that calculate per-atom quantities which
could then be output with these keywords.
:line
@ -308,8 +297,3 @@ gran/diag"_fix_gran_diag.html command should be used instead.
"dump_modify"_dump_modify.html, "undump"_undump.html
[Default:] none
:line
:link(Kelchner)
[(Kelchner)] Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).

12
doc/fix_indent.html
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@ -100,12 +100,12 @@ choice affects not only the indenter's physical geometry, but also its
velocity and force constant since they are defined in terms of
distance as well.
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed,
where the energy of each particle interacting with the indenter is K/3
(r - R)^3. The latter will add this contribution to the total
potential energy (PotEng).
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The energy of each
particle interacting with the indenter is K/3 (r - R)^3. The
contribution can also be printed by itself via the keyword <I>f_fix-ID</I>
in the <A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command. If you

12
doc/fix_indent.txt
View File

@ -91,12 +91,12 @@ choice affects not only the indenter's physical geometry, but also its
velocity and force constant since they are defined in terms of
distance as well.
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed,
where the energy of each particle interacting with the indenter is K/3
(r - R)^3. The latter will add this contribution to the total
potential energy (PotEng).
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The energy of each
particle interacting with the indenter is K/3 (r - R)^3. The
contribution can also be printed by itself via the keyword {f_fix-ID}
in the "thermo_style custom"_thermo_style.html command.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command. If you

56
doc/fix_modify.html
View File

@ -19,18 +19,18 @@
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>temp</I> or <I>energy</I> or <I>thermo</I>
<LI>keyword = <I>temp</I> or <I>press</I> or <I>thermo</I>
<PRE> <I>temp</I> value = temperature ID
<I>energy</I> value = <I>yes</I> or <I>no</I>
<PRE> <I>temp</I> value = compute ID that calculates a temperature
<I>press</I> value = compute ID that calculates a pressure
<I>thermo</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix_modify 3 temp myTemp
fix_modify 1 thermo yes energy no
<PRE>fix_modify 3 temp myTemp press myPress
fix_modify 1 thermo yes
</PRE>
<P><B>Description:</B>
</P>
@ -38,30 +38,29 @@ fix_modify 1 thermo yes energy no
fix styles support all parameters.
</P>
<P>The <I>temp</I> keyword is used to determine how a fix computes
temperature. The specified temperature ID must have been previously
defined by the user via the <A HREF = "temperature.html">temperature</A> command.
The default setting for <I>temp</I> is temperature ID = <I>default</I>. Fix
styles that use the <I>temp</I> setting are
<A HREF = "fix_temp_rescale.html">temp/rescale</A>, <A HREF = "fix_nvt.html">nvt</A>, and
<A HREF = "fix_npt.html">npt</A>.
temperature. The specified compute ID must have been previously
defined by the user via the <A HREF = "compute.html">compute</A> command and it must
be a style of compute that calculates a temperature. All fixes that
compute temperatures defined their own compute by default, as
described in their documentation. Thus this option allows the user to
override the default method for computing T.
</P>
<P>The <I>energy</I> and <I>thermo</I> keywords enable a fix to compute and/or
print quantities as part of the thermodynamic output to the screen and
log file (if the fix defines such quantities). When the <I>energy</I>
keyword is set to <I>yes</I>, the fix computes a contribution to the total
potential energy that is printed as PotEng during thermodynamic
output. When the <I>thermo</I> keyword is set to yes, the fix prints one
or more values that are appended to the list of thermodynamic outputs.
See the <A HREF = "thermo_style.html">thermo_style</A> command for how this printing
is formatted.
<P>The <I>press</I> keyword is used to determine how a fix computes pressure.
The specified compute ID must have been previously defined by the user
via the <A HREF = "compute.html">compute</A> command and it must be a style of
compute that calculates a pressure. All fixes that compute pressures
defined their own compute by default, as described in their
documentation. Thus this option allows the user to override the
default method for computing P.
</P>
<P>The fixes that support the <I>energy</I> and <I>thermo</I> options include: <A HREF = "fix_indent.html">fix
indent</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nph.html">fix
nph</A>, <A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_orient_fcc.html">fix
orient/fcc</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, and <A HREF = "fix_wall_lj93.html">fix
wall/lj93</A>. See the individual fix commands for
more info on what is computed and/or printed.
<P>For fixes that calculates a contribution to the potential energy of
the system, the <I>thermo</I> keyword will include that contribution in
thermodyanmic output of the potential energy, as invoked by the
<A HREF = "thermo_style.html">thermo_style</A> command. The value of the
contribution can also be printed by itself using the <A HREF = "thermo_style.html">thermo_style
custom</A> keywords. The documentation for individual
fix commands specifies whether they make a contribution to the
potential energy.
</P>
<P><B>Restrictions:</B> none
</P>
@ -72,6 +71,7 @@ more info on what is computed and/or printed.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are temp = default, energy = no, thermo = no.
<P>The option defaults are temp = ID defined by fix, press = ID defined
by fix, thermo = no.
</P>
</HTML>

56
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@ -14,16 +14,16 @@ fix_modify fix-ID keyword value ... :pre
fix-ID = ID of the fix to modify :ulb,l
one or more keyword/value pairs may be appended :l
keyword = {temp} or {energy} or {thermo} :l
{temp} value = temperature ID
{energy} value = {yes} or {no}
keyword = {temp} or {press} or {thermo} :l
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
{thermo} value = {yes} or {no} :pre
:ule
[Examples:]
fix_modify 3 temp myTemp
fix_modify 1 thermo yes energy no :pre
fix_modify 3 temp myTemp press myPress
fix_modify 1 thermo yes :pre
[Description:]
@ -31,30 +31,29 @@ Modify one or more parameters of a previously defined fix. Not all
fix styles support all parameters.
The {temp} keyword is used to determine how a fix computes
temperature. The specified temperature ID must have been previously
defined by the user via the "temperature"_temperature.html command.
The default setting for {temp} is temperature ID = {default}. Fix
styles that use the {temp} setting are
"temp/rescale"_fix_temp_rescale.html, "nvt"_fix_nvt.html, and
"npt"_fix_npt.html.
temperature. The specified compute ID must have been previously
defined by the user via the "compute"_compute.html command and it must
be a style of compute that calculates a temperature. All fixes that
compute temperatures defined their own compute by default, as
described in their documentation. Thus this option allows the user to
override the default method for computing T.
The {energy} and {thermo} keywords enable a fix to compute and/or
print quantities as part of the thermodynamic output to the screen and
log file (if the fix defines such quantities). When the {energy}
keyword is set to {yes}, the fix computes a contribution to the total
potential energy that is printed as PotEng during thermodynamic
output. When the {thermo} keyword is set to yes, the fix prints one
or more values that are appended to the list of thermodynamic outputs.
See the "thermo_style"_thermo_style.html command for how this printing
is formatted.
The {press} keyword is used to determine how a fix computes pressure.
The specified compute ID must have been previously defined by the user
via the "compute"_compute.html command and it must be a style of
compute that calculates a pressure. All fixes that compute pressures
defined their own compute by default, as described in their
documentation. Thus this option allows the user to override the
default method for computing P.
The fixes that support the {energy} and {thermo} options include: "fix
indent"_fix_indent.html, "fix nvt"_fix_nvt.html, "fix
nph"_fix_nph.html, "fix npt"_fix_npt.html, "fix
orient/fcc"_fix_orient_fcc.html, "fix
temp/rescale"_fix_temp_rescale.html, and "fix
wall/lj93"_fix_wall_lj93.html. See the individual fix commands for
more info on what is computed and/or printed.
For fixes that calculates a contribution to the potential energy of
the system, the {thermo} keyword will include that contribution in
thermodyanmic output of the potential energy, as invoked by the
"thermo_style"_thermo_style.html command. The value of the
contribution can also be printed by itself using the "thermo_style
custom"_thermo_style.html keywords. The documentation for individual
fix commands specifies whether they make a contribution to the
potential energy.
[Restrictions:] none
@ -65,4 +64,5 @@ more info on what is computed and/or printed.
[Default:]
The option defaults are temp = default, energy = no, thermo = no.
The option defaults are temp = ID defined by fix, press = ID defined
by fix, thermo = no.

74
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View File

@ -71,26 +71,8 @@ only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<P>This fix computes a temperature each timestep, to contribute to the
pressure. The fix creates its own method for computing T, as if it
had been defined by the command:
</P>
<PRE>temperature fix-ID all full
</PRE>
<P>See the <A HREF = "temperature.html">temperature</A> command for details. Note that
this is NOT the temperature with ID = <I>default</I>. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the <A HREF = "temp_modify.html">temp_modify</A> command or
print the temperature with thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
@ -130,17 +112,49 @@ oscillations after a few periods.
shape. Parinello-Rahman boundary conditions (tilted box) are not
implemented in LAMMPS.
</P>
<P>For all styles, the <I>Pdamp</I> parameter is specified in time units and
determines how rapidly the pressure is relaxed. For example, a value
of 1000.0 means to relax the temperature in a timespan of (roughly)
1000 time units (tau or fmsec or psec - see the <A HREF = "units.html">units</A>
command).
<P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>This fix supports the "fix_modify" options for <I>thermo</I> and <I>energy</I>.
The former will print the contribution the fix makes to the energy of
the system when thermodynamics is printed. The latter will add this
contribution to the total potential energy (PotEng) so that energy
conservation can be monitored.
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<PRE>compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html<A HREF = "temp"<A HREF = "press"">>>compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID with </A> or </A>
appended and the group for the new computes is the same as the fix
group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P><B>Restrictions:</B>
</P>

71
doc/fix_nph.txt
View File

@ -62,25 +62,7 @@ only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
This fix computes a temperature each timestep, to contribute to the
pressure. The fix creates its own method for computing T, as if it
had been defined by the command:
temperature fix-ID all full :pre
See the "temperature"_temperature.html command for details. Note that
this is NOT the temperature with ID = {default}. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the "temp_modify"_temp_modify.html command or
print the temperature with thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
@ -121,17 +103,48 @@ For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not
implemented in LAMMPS.
For all styles, the {Pdamp} parameter is specified in time units and
determines how rapidly the pressure is relaxed. For example, a value
of 1000.0 means to relax the temperature in a timespan of (roughly)
1000 time units (tau or fmsec or psec - see the "units"_units.html
command).
For all styles, the {Pdamp} parameter operates like the {Tdamp}
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
"units"_units.html command).
This fix supports the "fix_modify" options for {thermo} and {energy}.
The former will print the contribution the fix makes to the energy of
the system when thermodynamics is printed. The latter will add this
contribution to the total potential energy (PotEng) so that energy
conservation can be monitored.
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
compute fix-ID_temp group-ID temp :pre
compute fix-ID_press group-ID pressure fix-ID_temp :pre
See the "compute temp"_compute_temp.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID with "_temp" or "_press"
appended and the group for the new computes is the same as the fix
group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restrictions:]

67
doc/fix_npt.html
View File

@ -76,26 +76,8 @@ only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<P>This fix computes a temperature each timestep, to contribute to the
pressure. The fix creates its own method for computing T, as if it
had been defined by the command:
</P>
<PRE>temperature fix-ID all full
</PRE>
<P>See the <A HREF = "temperature.html">temperature</A> command for details. Note that
this is NOT the temperature with ID = <I>default</I>. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the <A HREF = "temp_modify.html">temp_modify</A> command or
print the temperature with thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
@ -137,12 +119,47 @@ implemented in LAMMPS.
</P>
<P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng) so that energy conservation can be monitored.
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<PRE>compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html<A HREF = "temp"<A HREF = "press"">>>compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID with </A> or </A>
appended and the group for the new computes is the same as the fix
group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P><B>Restrictions:</B>
</P>

64
doc/fix_npt.txt
View File

@ -65,25 +65,7 @@ only the atoms in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of atoms in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
This fix computes a temperature each timestep, to contribute to the
pressure. The fix creates its own method for computing T, as if it
had been defined by the command:
temperature fix-ID all full :pre
See the "temperature"_temperature.html command for details. Note that
this is NOT the temperature with ID = {default}. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the "temp_modify"_temp_modify.html command or
print the temperature with thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
:line
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
@ -126,12 +108,46 @@ implemented in LAMMPS.
For all styles, the {Pdamp} parameter operates like the {Tdamp}
parameter, determining the time scale on which pressure is relaxed.
For example, a value of 1000.0 means to relax the pressure in a
timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
"units"_units.html command).
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng) so that energy conservation can be monitored.
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
compute fix-ID_temp group-ID temp :pre
compute fix-ID_press group-ID pressure fix-ID_temp :pre
See the "compute temp"_compute_temp.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID with "_temp" or "_press"
appended and the group for the new computes is the same as the fix
group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restrictions:]

42
doc/fix_nvt.html
View File

@ -61,27 +61,33 @@ Performing a short run and monitoring the temperature is the best way
to determine if the drag term is working. Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.
</P>
<P>This fix computes a temperature each timestep. The fix creates its
own method for computing T, as if it had been defined by the command:
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
</P>
<PRE>temperature fix-ID group-ID full
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<P>See the <A HREF = "temperature.html">temperature</A> command for details. Note that
this is NOT the temperature with ID = <I>default</I>. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the <A HREF = "temp_modify.html">temp_modify</A> command or
print the temperature with thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
<A HREF = "fix_modify.html">fix_modify</A> command.
<P>See the <A HREF = "compute_temp.html<A HREF = "temp"">>compute temp</A> command for details. Note
that the ID of the new compute is the fix-ID with </A> appended and
the group for the new compute is the same as the fix group.
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng) so that energy conservation can be monitored.
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P><B>Restrictions:</B>
</P>

42
doc/fix_nvt.txt
View File

@ -52,27 +52,33 @@ Performing a short run and monitoring the temperature is the best way
to determine if the drag term is working. Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.
This fix computes a temperature each timestep. The fix creates its
own method for computing T, as if it had been defined by the command:
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
temperature fix-ID group-ID full :pre
compute fix-ID_temp group-ID temp :pre
See the "temperature"_temperature.html command for details. Note that
this is NOT the temperature with ID = {default}. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the "temp_modify"_temp_modify.html command or
print the temperature with thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
"fix_modify"_fix_modify.html command.
See the "compute temp"_compute_temp.html command for details. Note
that the ID of the new compute is the fix-ID with "_temp" appended and
the group for the new compute is the same as the fix group.
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng) so that energy conservation can be monitored.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the "fix_modify"_fix_modify.html command.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restrictions:]

10
doc/fix_orient_fcc.html
View File

@ -116,11 +116,11 @@ symmetry, so the list must include one from each pair of
equal-and-opposite neighbors. A pair of orientation files for a
Sigma=5 tilt boundary are show below.
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng).
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P><B>Restrictions:</B>
</P>

10
doc/fix_orient_fcc.txt
View File

@ -113,11 +113,11 @@ symmetry, so the list must include one from each pair of
equal-and-opposite neighbors. A pair of orientation files for a
Sigma=5 tilt boundary are show below.
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng).
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restrictions:]

33
doc/fix_print.html
View File

@ -30,28 +30,29 @@
simulation run. This can be used for diagnostic purposes or even as a
debugging tool to monitor some quantity during a run. The text string
must be a single argument, so it should be enclosed in double quotes
if it is more than one word. If it contains variables ($a thru $z) it
must be enclosed in double quotes to insure they are not evaluated
when the input script is read, but will instead be evaluated when the
string is printed.
if it is more than one word. If it contains variables it must be
enclosed in double quotes to insure they are not evaluated when the
input script is read, but will instead be evaluated when the string is
printed.
</P>
<P>See the <A HREF = "variable.html">variable</A> command for a description of <I>equal</I>
style variables which are the most useful ones to use with the fix
print command, since they are evaluated afresh each timestep that the
fix print line is output.
fix print line is output. Equal-style variables can calculate complex
formulas involving atom and group properties, mathematical operations,
other variables, etc.
</P>
<P>Note that if <I>equal</I>-style variables are used in the print line which
contain <A HREF = "thermo_style.html">thermo_style custom</A> keywords for potential
energy such as pe, eng, evdwl, ebond, etc, they will only be
up-to-date on timesteps where thermodynamics are computed. Hence, if
you output thermodynamics every 100 steps, but issue a fix print
command with N = 2 that contains such a variable, the printed value
will only be current on timesteps that are a multiple of 100. This is
because the potential functions in LAMMPS (pairwise, bond, etc) only
compute energies on timesteps when thermodynamic output is being
performed.
<P><B>Restrictions:</B>
</P>
<P><B>Restrictions:</B> none
<P>If <I>equal</I>-style variables are used which contain
<A HREF = "thermo_style.html">thermo_style custom</A> keywords for energy such as
pe, eng, evdwl, ebond, etc, then they will only be up-to-date on
timesteps where thermodynamics are computed. For example, if you
output thermodynamics every 100 steps, but issue a fix print command
with N = 2 that contains such a variable, the printed value will only
be current on timesteps that are a multiple of 100. This is because
the potential functions in LAMMPS (pairwise, bond, etc) only compute
energies on timesteps when thermodynamic output is being performed.
</P>
<P><B>Related commands:</B>
</P>

33
doc/fix_print.txt
View File

@ -27,28 +27,29 @@ Print a text string to the screen and logfile every N steps during a
simulation run. This can be used for diagnostic purposes or even as a
debugging tool to monitor some quantity during a run. The text string
must be a single argument, so it should be enclosed in double quotes
if it is more than one word. If it contains variables ($a thru $z) it
must be enclosed in double quotes to insure they are not evaluated
when the input script is read, but will instead be evaluated when the
string is printed.
if it is more than one word. If it contains variables it must be
enclosed in double quotes to insure they are not evaluated when the
input script is read, but will instead be evaluated when the string is
printed.
See the "variable"_variable.html command for a description of {equal}
style variables which are the most useful ones to use with the fix
print command, since they are evaluated afresh each timestep that the
fix print line is output.
fix print line is output. Equal-style variables can calculate complex
formulas involving atom and group properties, mathematical operations,
other variables, etc.
Note that if {equal}-style variables are used in the print line which
contain "thermo_style custom"_thermo_style.html keywords for potential
energy such as pe, eng, evdwl, ebond, etc, they will only be
up-to-date on timesteps where thermodynamics are computed. Hence, if
you output thermodynamics every 100 steps, but issue a fix print
command with N = 2 that contains such a variable, the printed value
will only be current on timesteps that are a multiple of 100. This is
because the potential functions in LAMMPS (pairwise, bond, etc) only
compute energies on timesteps when thermodynamic output is being
performed.
[Restrictions:]
[Restrictions:] none
If {equal}-style variables are used which contain
"thermo_style custom"_thermo_style.html keywords for energy such as
pe, eng, evdwl, ebond, etc, then they will only be up-to-date on
timesteps where thermodynamics are computed. For example, if you
output thermodynamics every 100 steps, but issue a fix print command
with N = 2 that contains such a variable, the printed value will only
be current on timesteps that are a multiple of 100. This is because
the potential functions in LAMMPS (pairwise, bond, etc) only compute
energies on timesteps when thermodynamic output is being performed.
[Related commands:]

93
doc/fix_temp_rescale.html
View File

@ -15,26 +15,17 @@
</P>
<PRE>fix ID group-ID temp/rescale N Tstart Tstop window fraction keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale = style name of this fix command
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale = style name of this fix command
<LI>N = perform rescaling every N steps
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
<LI>fraction = rescale to target temperature by this fraction
<LI>zero or more keyword/value pairs may be appended to the args
<PRE>keyword = <I>region</I>
<I>region</I> values = region-ID
region-ID = ID of region to apply rescaling to
</PRE>
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
<LI>fraction = rescale to target temperature by this fraction
<LI>zero or more keyword/value pairs may be appended to the args
<LI>keyword = <I>region</I>
</UL>
<PRE> <I>region</I> values = region-ID of region to apply rescaling to
</PRE>
<P><B>Examples:</B>
</P>
<PRE>fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
@ -61,43 +52,47 @@ value.
specified geometric region (and in the fix group). Since atoms can
enter/leave a region, this test is performed each timestep.
</P>
<P>This fix computes a temperature each timestep. The fix creates its
own method for computing T, as if it had been defined by one of these
commands:
</P>
<PRE>temperature fix-ID group-ID full
temperature fix-ID group-ID region region-ID
</PRE>
<P>Which is used depends on whether a region was specified with the fix.
See the <A HREF = "temperature.html">temperature</A> command for details. Note that
this is NOT the temperature with ID = <I>default</I>. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the <A HREF = "temp_modify.html">temp_modify</A> command or
print the temperature with thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. For consistency, if using the
keyword <I>region</I>, the temperature you assign should also be of style
<I>region</I>.
</P>
<P>A temp/rescale fix does not update the coordinates of its atoms. It
is normally used with a fix of style <I>nve</I> that does that. A
temp/rescale fix should not normally be used on atoms that also have
their temperature controlled by another fix - e.g. a
<A HREF = "fix_nvt.html">nvt</A> or <A HREF = "fix_langevin.html">langevin</A> fix.
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng) so that energy conservation can be monitored. Note that the
energy value printed by thermo is not cummulative energy, but energy
added in the most recent rescaling. Also note that because this fix
is invoked every N steps and thermo may be printed every M steps, that
unless M is a multiple of N, the energy info printed by thermo will
not be for the current timestep.
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp" or "temp/region", as if one of
these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
compute fix-ID_temp group-ID temp/region region-ID
</PRE>
<P>Which is used depends on whether a region was specified with the fix.
See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_temp_region.html<A HREF = "temp"">>compute
temp/region</A> commands for details. Note that
the ID of the new compute is the fix-ID with </A> appended and the
group for the new compute is the same as the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the <A HREF = "fix_modify.html">fix_modify</A> command. For consistency, if
using the keyword <I>region</I>, the compute you assign should also be of
style <I>temp/region</I>.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command. Note that because
this fix is invoked every N steps and thermodynamic info may be
printed every M steps, that unless M is a multiple of N, the energy
info accessed will not be for the current timestep.
</P>
<P><B>Restrictions:</B> none
</P>

86
doc/fix_temp_rescale.txt
View File

@ -12,17 +12,15 @@ fix temp/rescale command :h3
fix ID group-ID temp/rescale N Tstart Tstop window fraction keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
temp/rescale = style name of this fix command :l
N = perform rescaling every N steps :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
window = only rescale if temperature is outside this window (temperature units) :l
fraction = rescale to target temperature by this fraction :l
zero or more keyword/value pairs may be appended to the args :l
keyword = {region}
{region} values = region-ID
region-ID = ID of region to apply rescaling to :pre
:ule
ID, group-ID are documented in "fix"_fix.html command
temp/rescale = style name of this fix command
N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units)
fraction = rescale to target temperature by this fraction
zero or more keyword/value pairs may be appended to the args
keyword = {region} :ul
{region} values = region-ID of region to apply rescaling to :pre
[Examples:]
@ -50,43 +48,47 @@ The keyword {region} applies the fix only to atoms that are in the
specified geometric region (and in the fix group). Since atoms can
enter/leave a region, this test is performed each timestep.
This fix computes a temperature each timestep. The fix creates its
own method for computing T, as if it had been defined by one of these
commands:
temperature fix-ID group-ID full
temperature fix-ID group-ID region region-ID :pre
Which is used depends on whether a region was specified with the fix.
See the "temperature"_temperature.html command for details. Note that
this is NOT the temperature with ID = {default}. This means you can
change the attributes of this fix's temperature (e.g. its
degrees-of-freedom) via the "temp_modify"_temp_modify.html command or
print the temperature with thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate temp-ID =
fix-ID. It also means that changing attributes of the default
temperature will have no effect on this fix. Alternatively, you can
directly assign a new temperature to the fix via the
"fix_modify"_fix_modify.html command. For consistency, if using the
keyword {region}, the temperature you assign should also be of style
{region}.
A temp/rescale fix does not update the coordinates of its atoms. It
is normally used with a fix of style {nve} that does that. A
temp/rescale fix should not normally be used on atoms that also have
their temperature controlled by another fix - e.g. a
"nvt"_fix_nvt.html or "langevin"_fix_langevin.html fix.
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed. The
latter will add this contribution to the total potential energy
(PotEng) so that energy conservation can be monitored. Note that the
energy value printed by thermo is not cummulative energy, but energy
added in the most recent rescaling. Also note that because this fix
is invoked every N steps and thermo may be printed every M steps, that
unless M is a multiple of N, the energy info printed by thermo will
not be for the current timestep.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp" or "temp/region", as if one of
these commands had been issued:
compute fix-ID_temp group-ID temp
compute fix-ID_temp group-ID temp/region region-ID :pre
Which is used depends on whether a region was specified with the fix.
See the "compute temp"_compute_temp.html and "compute
temp/region"_compute_temp_region.html commands for details. Note that
the ID of the new compute is the fix-ID with "_temp" appended and the
group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the "fix_modify"_fix_modify.html command. For consistency, if
using the keyword {region}, the compute you assign should also be of
style {temp/region}.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command. Note that because
this fix is invoked every N steps and thermodynamic info may be
printed every M steps, that unless M is a multiple of N, the energy
info accessed will not be for the current timestep.
[Restrictions:] none

11
doc/fix_wall_lj126.html
View File

@ -44,12 +44,11 @@ provided by the <A HREF = "fix_wall_lj93.html">fix wall/lj93</A> command.
<P>The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed,
where the energy of each particle comes from the integrated form of
the equation above. The latter will add this contribution to the
total potential energy (PotEng).
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command. If you

11
doc/fix_wall_lj126.txt
View File

@ -41,12 +41,11 @@ provided by the "fix wall/lj93"_fix_wall_lj93.html command.
The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed,
where the energy of each particle comes from the integrated form of
the equation above. The latter will add this contribution to the
total potential energy (PotEng).
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command. If you

11
doc/fix_wall_lj93.html
View File

@ -45,12 +45,11 @@ wall/lj126</A> command.
<P>The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
</P>
<P>This fix supports the <A HREF = "fix_modify.html">fix_modify</A> options for
<I>thermo</I> and <I>energy</I>. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed,
where the energy of each particle comes from the integrated form of
the equation above. The latter will add this contribution to the
total potential energy (PotEng).
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command. If you

11
doc/fix_wall_lj93.txt
View File

@ -42,12 +42,11 @@ wall/lj126"_fix_wall_lj126.html command.
The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
This fix supports the "fix_modify"_fix_modify.html options for
{thermo} and {energy}. The former will print the contribution the fix
makes to the energy of the system when thermodynamics is printed,
where the energy of each particle comes from the integrated form of
the equation above. The latter will add this contribution to the
total potential energy (PotEng).
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command. If you

10
doc/improper_coeff.html
View File

@ -64,12 +64,12 @@ corresponds to the 1st example above would be listed as
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A> command:
</P>
<UL><LI><A HREF = "improper_style_none.html">improper_style none</A> - turn off improper interactions
<LI><A HREF = "improper_style_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
<UL><LI><A HREF = "improper_none.html">improper_style none</A> - turn off improper interactions
<LI><A HREF = "improper_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
</UL>
<UL><LI><A HREF = "improper_style_class2.html">improper_style class2</A> - COMPASS (class 2) improper
<LI><A HREF = "improper_style_cvff.html">improper_style cvff</A> - CVFF improper
<LI><A HREF = "improper_style_harmonic.html">improper_style harmonic</A> - harmonic improper
<UL><LI><A HREF = "improper_class2.html">improper_style class2</A> - COMPASS (class 2) improper
<LI><A HREF = "improper_cvff.html">improper_style cvff</A> - CVFF improper
<LI><A HREF = "improper_harmonic.html">improper_style harmonic</A> - harmonic improper
</UL>
<HR>

10
doc/improper_coeff.txt
View File

@ -61,12 +61,12 @@ Here is an alphabetic list of improper styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command:
"improper_style none"_improper_style_none.html - turn off improper interactions
"improper_style hybrid"_improper_style_hybrid.html - define multiple styles of improper interactions :ul
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_style_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_style_cvff.html - CVFF improper
"improper_style harmonic"_improper_style_harmonic.html - harmonic improper :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_cvff.html - CVFF improper
"improper_style harmonic"_improper_harmonic.html - harmonic improper :ul
:line

10
doc/improper_style.html
View File

@ -48,12 +48,12 @@ exist between the 4 bonded atoms.
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A> command:
</P>
<UL><LI><A HREF = "improper_style_none.html">improper_style none</A> - turn off improper interactions
<LI><A HREF = "improper_style_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
<UL><LI><A HREF = "improper_none.html">improper_style none</A> - turn off improper interactions
<LI><A HREF = "improper_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
</UL>
<UL><LI><A HREF = "improper_style_class2.html">improper_style class2</A> - COMPASS (class 2) improper
<LI><A HREF = "improper_style_cvff.html">improper_style cvff</A> - CVFF improper
<LI><A HREF = "improper_style_harmonic.html">improper_style harmonic</A> - harmonic improper
<UL><LI><A HREF = "improper_class2.html">improper_style class2</A> - COMPASS (class 2) improper
<LI><A HREF = "improper_cvff.html">improper_style cvff</A> - CVFF improper
<LI><A HREF = "improper_harmonic.html">improper_style harmonic</A> - harmonic improper
</UL>
<HR>

10
doc/improper_style.txt
View File

@ -45,12 +45,12 @@ Here is an alphabetic list of improper styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command:
"improper_style none"_improper_style_none.html - turn off improper interactions
"improper_style hybrid"_improper_style_hybrid.html - define multiple styles of improper interactions :ul
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_style_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_style_cvff.html - CVFF improper
"improper_style harmonic"_improper_style_harmonic.html - harmonic improper :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_cvff.html - CVFF improper
"improper_style harmonic"_improper_harmonic.html - harmonic improper :ul
:line

2
doc/log.html
View File

@ -33,7 +33,7 @@ the same log file.
</P>
<P>The file "log.lammps" is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
switch -log. See <A HREF = "Section_start.html#2_4">this section</A> for details.
switch -log. See <A HREF = "Section_start.html#2_6">this section</A> for details.
</P>
<P><B>Restrictions:</B> none
</P>

2
doc/log.txt
View File

@ -30,7 +30,7 @@ the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The
name of the initial log file can also be set by the command-line
switch -log. See "this section"_Section_start.html#2_4 for details.
switch -log. See "this section"_Section_start.html#2_6 for details.
[Restrictions:] none

2
doc/neighbor.html
View File

@ -48,7 +48,7 @@ stored in the list.
</P>
<P>When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See <A HREF = "Section_start.html#2_5">this
are printed to the screen and log file. See <A HREF = "Section_start.html#2_7">this
section</A> for details.
</P>
<P><B>Restrictions:</B> none

2
doc/neighbor.txt
View File

@ -46,7 +46,7 @@ stored in the list.
When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
are printed to the screen and log file. See "this
section"_Section_start.html#2_5 for details.
section"_Section_start.html#2_7 for details.
[Restrictions:] none

2
doc/next.html
View File

@ -47,7 +47,7 @@ the next command is used with <I>universe</I>- or <I>uloop</I>-style variables,
the next value is assigned to whichever processor partition executes
the command first. All processors in the partition are assigned the
same value. Running LAMMPS on multiple partitions of processors via
the "-partition" command-line switch is described in <A HREF = "Section_start.html#2_4">this
the "-partition" command-line switch is described in <A HREF = "Section_start.html#2_6">this
section</A> of the manual. <I>Universe</I>- and
<I>uloop</I>-style variables are incremented using the files
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will

2
doc/next.txt
View File

@ -45,7 +45,7 @@ the next value is assigned to whichever processor partition executes
the command first. All processors in the partition are assigned the
same value. Running LAMMPS on multiple partitions of processors via
the "-partition" command-line switch is described in "this
section"_Section_start.html#2_4 of the manual. {Universe}- and
section"_Section_start.html#2_6 of the manual. {Universe}- and
{uloop}-style variables are incremented using the files
"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
see in your directory during such a LAMMPS run.

65
doc/pair_coeff.html
View File

@ -83,40 +83,39 @@ the style to display the formula it computes, arguments specified in
the pair_style command, and coefficients specified by the associated
<A HREF = "pair_coeff.html">pair_coeff</A> command:
</P>
<UL><LI><A HREF = "pair_style_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_style_hybrid.html">pair_style hybrid</A> - define multiple styles of pairwise interactions
<UL><LI><A HREF = "pair_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - define multiple styles of pairwise interactions
</UL>
<UL><LI><A HREF = "pair_style_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_style_buck.html">pair_style buck/coul/cut</A> - Buckinhham with cutoff Coulomb
<LI><A HREF = "pair_style_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_style_dipole.html">pair_style dipole/cut</A> - cutoff dipole and charge interactions
<LI><A HREF = "pair_style_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_style_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_style_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_style_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_style_granular.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions
<LI><A HREF = "pair_style_granular.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_style_granular.html">pair_style gran/no_history</A> - granular potential without history effects
<LI><A HREF = "pair_style_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_style_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_style_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_style_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_style_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_style_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye damping added to Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_style_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_style_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_style_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
<LI><A HREF = "pair_style_morse.html">pair_style morse</A> - Morse potential
<LI><A HREF = "pair_style_soft.html">pair_style soft</A> - Soft (cosine) potential
<LI><A HREF = "pair_style_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential
<LI><A HREF = "pair_style_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_style_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_style_yukawa.html">pair_style yukawa</A> - Yukawa potential
<UL><LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckinhham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_granular.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions
<LI><A HREF = "pair_granular.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_granular.html">pair_style gran/no_history</A> - granular potential without history effects
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye damping added to Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential
<LI><A HREF = "pair_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential
<LI><A HREF = "pair_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
</UL>
<HR>

65
doc/pair_coeff.txt
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@ -80,40 +80,39 @@ the style to display the formula it computes, arguments specified in
the pair_style command, and coefficients specified by the associated
"pair_coeff"_pair_coeff.html command:
"pair_style none"_pair_style_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_style_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style buck"_pair_style_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_style_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_style_buck.html - Buckingham with long-range Coulomb
"pair_style dipole/cut"_pair_style_dipole.html - cutoff dipole and charge interactions
"pair_style dpd"_pair_style_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_style_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_style_eam.html - alloy EAM
"pair_style eam/fs"_pair_style_eam.html - Finnis-Sinclair EAM
"pair_style gran/hertzian"_pair_style_granular.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_style_granular.html - granular potential with history effects
"pair_style gran/no_history"_pair_style_granular.html - granular potential without history effects
"pair_style lj/charmm/coul/charmm"_pair_style_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_style_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_style_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/class2"_pair_style_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_style_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_style_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_style_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_style_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_style_lj.html - LJ with Debye damping added to Coulomb
"pair_style lj/cut/coul/long"_pair_style_lj.html - LJ with long-range Coulomb
"pair_style lj/cut/coul/long/tip4p"_pair_style_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/expand"_pair_style_lj_expand.html - Lennard-Jones for variable size particles
"pair_style lj/smooth"_pair_style_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style meam"_pair_style_meam.html - modified embedded atom method (MEAM)
"pair_style morse"_pair_style_morse.html - Morse potential
"pair_style soft"_pair_style_soft.html - Soft (cosine) potential
"pair_style sw"_pair_style_sw.html - Stillinger-Weber 3-body potential
"pair_style table"_pair_style_table.html - tabulated pair potential
"pair_style tersoff"_pair_style_tersoff.html - Tersoff 3-body potential
"pair_style yukawa"_pair_style_yukawa.html - Yukawa potential :ul
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style gran/hertzian"_pair_granular.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_granular.html - granular potential with history effects
"pair_style gran/no_history"_pair_granular.html - granular potential without history effects
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
"pair_style morse"_pair_morse.html - Morse potential
"pair_style soft"_pair_soft.html - Soft (cosine) potential
"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
"pair_style table"_pair_table.html - tabulated pair potential
"pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential
"pair_style yukawa"_pair_yukawa.html - Yukawa potential :ul
:line

92
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View File

@ -17,25 +17,14 @@
</PRE>
<UL><LI>style = one of the following
<UL><LI><I>none</I>
<LI><I>hybrid</I>
<LI><I>buck</I> or <I>buck/coul/cut</I> or <I>buck/coul/long</I>
<LI><I>dipole/cut</I> or <I>dipole/long</I>
<LI><I>dpd</I>
<LI><I>eam</I> or <I>eam/alloy</I> or <I>eam/fs</I>
<LI><I>gran/hertzian</I> or <I>gran/history</I> or <I>gran/no_history</I>
<LI><I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>
<LI><I>lj/class2</I> or <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>
<LI><I>lj/cut</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><I>lj/expand</I>
<LI><I>lj/smooth</I>
<LI><I>meam</I>
<LI><I>morse</I>
<LI><I>soft</I>
<LI><I>sw</I>
<LI><I>table</I>
<LI><I>tersoff</I>
<LI><I>yukawa</I>
<UL><LI><I>none</I>, <I>hybrid</I>, <I>buck</I>, <I>buck/coul/cut</I>, <I>buck/coul/long</I>, <I>dpd</I>,
<LI><I>eam</I>, <I>eam/alloy</I> or <I>eam/fs</I>, <I>gran/hertzian</I>, <I>gran/history</I>,
<LI><I>gran/no_history</I>, <I>lj/charmm/coul/charmm</I>,
<LI><I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>,
<LI><I>lj/class2</I>, <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>, <I>lj/cut</I>,
<LI><I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I>, <I>lj/cut/coul/long</I>,
<LI><I>lj/cut/coul/long/tip4p</I>, <I>lj/expand</I>, <I>lj/smooth</I>, <I>meam</I>, <I>morse</I>,
<LI><I>soft</I>, <I>sw</I>, <I>table</I>, <I>tersoff</I>, <I>yukawa</I>
</UL>
<LI>args = arguments used by a particular style
</UL>
@ -100,40 +89,39 @@ the style to display the formula it computes, arguments specified in
the pair_style command, and coefficients specified by the associated
<A HREF = "pair_coeff.html">pair_coeff</A> command:
</P>
<UL><LI><A HREF = "pair_style_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_style_hybrid.html">pair_style hybrid</A> - define multiple styles of pairwise interactions
<UL><LI><A HREF = "pair_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - define multiple styles of pairwise interactions
</UL>
<UL><LI><A HREF = "pair_style_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_style_buck.html">pair_style buck/coul/cut</A> - Buckinhham with cutoff Coulomb
<LI><A HREF = "pair_style_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_style_dipole.html">pair_style dipole/cut</A> - cutoff dipole and charge interactions
<LI><A HREF = "pair_style_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_style_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_style_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_style_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_style_granular.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions
<LI><A HREF = "pair_style_granular.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_style_granular.html">pair_style gran/no_history</A> - granular potential without history effects
<LI><A HREF = "pair_style_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_style_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_style_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_style_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_style_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_style_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye damping added to Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
<LI><A HREF = "pair_style_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_style_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_style_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_style_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
<LI><A HREF = "pair_style_morse.html">pair_style morse</A> - Morse potential
<LI><A HREF = "pair_style_soft.html">pair_style soft</A> - Soft (cosine) potential
<LI><A HREF = "pair_style_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential
<LI><A HREF = "pair_style_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_style_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_style_yukawa.html">pair_style yukawa</A> - Yukawa potential
<UL><LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckinhham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_granular.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions
<LI><A HREF = "pair_granular.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_granular.html">pair_style gran/no_history</A> - granular potential without history effects
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye damping added to Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential
<LI><A HREF = "pair_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential
<LI><A HREF = "pair_table.html">pair_style table</A> - tabulated pair potential
<LI><A HREF = "pair_tersoff.html">pair_style tersoff</A> - Tersoff 3-body potential
<LI><A HREF = "pair_yukawa.html">pair_style yukawa</A> - Yukawa potential
</UL>
<HR>

92
doc/pair_style.txt
View File

@ -14,25 +14,14 @@ pair_style style args :pre
style = one of the following :ulb,l
{none}
{hybrid}
{buck} or {buck/coul/cut} or {buck/coul/long}
{dipole/cut} or {dipole/long}
{dpd}
{eam} or {eam/alloy} or {eam/fs}
{gran/hertzian} or {gran/history} or {gran/no_history}
{lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}
{lj/class2} or {lj/class2/coul/cut} or {lj/class2/coul/long}
{lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
{lj/expand}
{lj/smooth}
{meam}
{morse}
{soft}
{sw}
{table}
{tersoff}
{yukawa} :ul
{none}, {hybrid}, {buck}, {buck/coul/cut}, {buck/coul/long}, {dpd},
{eam}, {eam/alloy} or {eam/fs}, {gran/hertzian}, {gran/history},
{gran/no_history}, {lj/charmm/coul/charmm},
{lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long},
{lj/class2}, {lj/class2/coul/cut} or {lj/class2/coul/long}, {lj/cut},
{lj/cut/coul/cut} or {lj/cut/coul/debye}, {lj/cut/coul/long},
{lj/cut/coul/long/tip4p}, {lj/expand}, {lj/smooth}, {meam}, {morse},
{soft}, {sw}, {table}, {tersoff}, {yukawa} :ul
args = arguments used by a particular style :l,ule
@ -97,40 +86,39 @@ the style to display the formula it computes, arguments specified in
the pair_style command, and coefficients specified by the associated
"pair_coeff"_pair_coeff.html command:
"pair_style none"_pair_style_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_style_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style buck"_pair_style_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_style_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_style_buck.html - Buckingham with long-range Coulomb
"pair_style dipole/cut"_pair_style_dipole.html - cutoff dipole and charge interactions
"pair_style dpd"_pair_style_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_style_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_style_eam.html - alloy EAM
"pair_style eam/fs"_pair_style_eam.html - Finnis-Sinclair EAM
"pair_style gran/hertzian"_pair_style_granular.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_style_granular.html - granular potential with history effects
"pair_style gran/no_history"_pair_style_granular.html - granular potential without history effects
"pair_style lj/charmm/coul/charmm"_pair_style_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_style_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_style_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/class2"_pair_style_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_style_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_style_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_style_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_style_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_style_lj.html - LJ with Debye damping added to Coulomb
"pair_style lj/cut/coul/long"_pair_style_lj.html - LJ with long-range Coulomb
"pair_style lj/cut/coul/long/tip4p"_pair_style_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/expand"_pair_style_lj_expand.html - Lennard-Jones for variable size particles
"pair_style lj/smooth"_pair_style_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style meam"_pair_style_meam.html - modified embedded atom method (MEAM)
"pair_style morse"_pair_style_morse.html - Morse potential
"pair_style soft"_pair_style_soft.html - Soft (cosine) potential
"pair_style sw"_pair_style_sw.html - Stillinger-Weber 3-body potential
"pair_style table"_pair_style_table.html - tabulated pair potential
"pair_style tersoff"_pair_style_tersoff.html - Tersoff 3-body potential
"pair_style yukawa"_pair_style_yukawa.html - Yukawa potential :ul
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style gran/hertzian"_pair_granular.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_granular.html - granular potential with history effects
"pair_style gran/no_history"_pair_granular.html - granular potential without history effects
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
"pair_style morse"_pair_morse.html - Morse potential
"pair_style soft"_pair_soft.html - Soft (cosine) potential
"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
"pair_style table"_pair_table.html - tabulated pair potential
"pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential
"pair_style yukawa"_pair_yukawa.html - Yukawa potential :ul
:line

25
doc/print.html
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@ -15,7 +15,7 @@
</P>
<PRE>print args
</PRE>
<UL><LI>args = one or more text strings and variables names to print out
<UL><LI>args = a line of text and variables names to print out
</UL>
<P><B>Examples:</B>
</P>
@ -25,14 +25,23 @@
</P>
<P>Print the list of arguments as a line of text to the screen and/or
logfile. If variables are included in the arguments, they will be
evaluated and their values printed. Note that if variables are
included, the print string should not be enclosed in double quotes,
else it will prevent the variables from being evaluated.
evaluated and their current values printed. Note that if variables
are included, the print string should not be enclosed in double
quotes, else it will prevent the variables from being evaluated.
</P>
<P>By using the print command in a section of the input script that is
looped over (see the <A HREF = "jump.html">jump</A> command), and by including
variables of the <I>equal</I> style (see the <A HREF = "variable.html">variable</A>
command), a string with changing values can be printed.
<P>If you want the print command to be executed multiple times (with
changing variable values), there are 3 options. First, consider using
the <A HREF = "fix_print.html">fix print</A> command, which will invoke a print
periodically during a simulation. Second, the print command can be
used as an argument to the <I>every</I> option of the <A HREF = "run.html">run</A>
command. Third, the print command could appear in a section of the
input script that is looped over (see the <A HREF = "jump.html">jump</A> command).
</P>
<P>See the <A HREF = "variable.html">variable</A> command for a description of <I>equal</I>
style variables which are typically the most useful ones to use with
the print command. Equal-style variables can calculate complex
formulas involving atom and group properties, mathematical operations,
other variables, etc.
</P>
<P><B>Restrictions:</B> none
</P>

25
doc/print.txt
View File

@ -12,7 +12,7 @@ print command :h3
print args :pre
args = one or more text strings and variables names to print out :ul
args = a line of text and variables names to print out :ul
[Examples:]
@ -22,14 +22,23 @@ print The system volume is now $v :pre
Print the list of arguments as a line of text to the screen and/or
logfile. If variables are included in the arguments, they will be
evaluated and their values printed. Note that if variables are
included, the print string should not be enclosed in double quotes,
else it will prevent the variables from being evaluated.
evaluated and their current values printed. Note that if variables
are included, the print string should not be enclosed in double
quotes, else it will prevent the variables from being evaluated.
By using the print command in a section of the input script that is
looped over (see the "jump"_jump.html command), and by including
variables of the {equal} style (see the "variable"_variable.html
command), a string with changing values can be printed.
If you want the print command to be executed multiple times (with
changing variable values), there are 3 options. First, consider using
the "fix print"_fix_print.html command, which will invoke a print
periodically during a simulation. Second, the print command can be
used as an argument to the {every} option of the "run"_run.html
command. Third, the print command could appear in a section of the
input script that is looped over (see the "jump"_jump.html command).
See the "variable"_variable.html command for a description of {equal}
style variables which are typically the most useful ones to use with
the print command. Equal-style variables can calculate complex
formulas involving atom and group properties, mathematical operations,
other variables, etc.
[Restrictions:] none

2
doc/processors.html
View File

@ -38,7 +38,7 @@ dramatically over the course of the simulation.
</P>
<P>The product of Px, Py, Pz must equal P, the total # of processors
LAMMPS is running on. If multiple partitions are being used then P is
the number of processors in this partition; see <A HREF = "Section_start.html#2_4">this
the number of processors in this partition; see <A HREF = "Section_start.html#2_6">this
section</A> for an explanation of the -partition
command-line switch.
</P>

2
doc/processors.txt
View File

@ -36,7 +36,7 @@ dramatically over the course of the simulation.
The product of Px, Py, Pz must equal P, the total # of processors
LAMMPS is running on. If multiple partitions are being used then P is
the number of processors in this partition; see "this
section"_Section_start.html#2_4 for an explanation of the -partition
section"_Section_start.html#2_6 for an explanation of the -partition
command-line switch.
If P is large and prime, a grid such as 1 x P x 1 will be required,

76
doc/read_data.html
View File

@ -212,47 +212,39 @@ integers (1, not 1.0).
<P><I>Atoms</I> section:
</P>
<UL><LI>one line per atom
<UL><LI>one line per atom
<LI>line syntax: depends on atom style
</UL>
<P>This is the list of all possible quantities that can appear on each
line of this section:
<P>An <I>Atoms</I> section must appear in the data file if natoms > 0 in the
header section. The atoms can be listed in any order. These are the
line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z
</TD></TR></TABLE></DIV>
<P>where the keywords have these meanings:
</P>
<UL><LI>atom-ID = integer ID of atom
<LI>molecule-ID = integer ID of molecule the atom belongs to
<LI>type-ID = integer type ID of atom (1-Ntype)
<LI>type-ID = type of atom (1-Ntype)
<LI>q = charge on atom
<LI>diameter = diameter of atom
<LI>density = density of atom
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = components of dipole orientation of atom
<LI>nx,ny,nz = image indices for atom
<LI>x,y,z = coordinates of atom
</UL>
<P>Which of these quantities are actually listed depends on the <A HREF = "atom_style.html">atom
style</A>. This is the list of which styles require each
quantity:
</P>
<UL><LI>atom-ID = all styles
<LI>molecule-ID = angle, bond, molecular, full styles
<LI>type-ID = all styles
<LI>q = charge, dipole, full styles
<LI>diameter = granular style
<LI>density = granular style
<LI>x,y,z = all styles
<LI>mux,muy,muz = dipole style
<LI>nx,ny,nz = optional for all styles (see below)
</UL>
<P>Any quantity that is used by the atom style appears in the order
listed above. Thus if the atom style is <I>atomic</I>, an atom line should
have 5 quantities: atom-ID, type-ID, x, y, z. If the atom style is
<I>hybrid dipole molecular</I>, then an atom line should have 10 quantites:
atom-ID, molecule-ID, type-ID, q, x, y, z, mux, muy, muz.
</P>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.
</P>
<P>For 2d simulations specify z as 0.0, or whatever value is within the
<I>zlo zhi</I> setting in the data file header.
<P>For 2d simulations specify z as 0.0, or a value is within the <I>zlo
zhi</I> setting in the data file header.
</P>
<P>The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
@ -266,25 +258,21 @@ be set to 0.
</P>
<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care about
molecule assignments.
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
</P>
<P>An <I>Atoms</I> section must appear in the data file if natoms > 0 in the
header section. The atoms can be listed in any order.
</P>
<P>Atom lines (all or none of them) can optionally list 3 final integer
values: nx,ny,nz. For periodic dimensions, they specify which image
of the box the atom is considered to be in. An image of 0 means the
box as defined. A value of 2 means add 2 box lengths to get the true
value. A value of -1 means subtract 1 box length to get the true
<P>Atom lines (all lines or none of them) can optionally list 3 final
integer values: nx,ny,nz. For periodic dimensions, they specify which
image of the box the atom is considered to be in. An image of 0 means
the box as defined. A value of 2 means add 2 box lengths to get the
true value. A value of -1 means subtract 1 box length to get the true
value. LAMMPS updates these flags as atoms cross periodic boundaries
during the simulation. The flags can be output via the
<A HREF = "dump.html">dump</A> and <A HREF = "dump_modify.html">dump_modify</A> commands. If
nx,ny,nz values are not set in the data file, LAMMPS initializes them
to 0.
during the simulation. The flags can be output with atom snapshots
via the <A HREF = "dump.html">dump</A> command. If nx,ny,nz values are not set in
the data file, LAMMPS initializes them to 0.
</P>
<P>Atom velocities are set to 0.0 when the <I>Atoms</I> section is read. They
may later be set by a <I>Velocities</I> section or by a
may later be set by a <I>Velocities</I> section in the data file or by a
<A HREF = "velocity.html">velocity</A> command in the input script.
</P>
<HR>

74
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View File

@ -191,47 +191,37 @@ line syntax: ID coeffs :l
{Atoms} section:
one line per atom
one line per atom
line syntax: depends on atom style :ul
This is the list of all possible quantities that can appear on each
line of this section:
An {Atoms} section must appear in the data file if natoms > 0 in the
header section. The atoms can be listed in any order. These are the
line formats for each "atom style"_atom_style.html in LAMMPS:
angle: atom-ID molecule-ID atom-type x y z
atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dpd: atom-ID atom-type x y z
full: atom-ID molecule-ID atom-type q x y z
granular: atom-ID atom-type diameter density x y z
molecular: atom-ID molecule-ID atom-type x y z :tb(s=:)
where the keywords have these meanings:
atom-ID = integer ID of atom
molecule-ID = integer ID of molecule the atom belongs to
type-ID = integer type ID of atom (1-Ntype)
type-ID = type of atom (1-Ntype)
q = charge on atom
diameter = diameter of atom
density = density of atom
x,y,z = coordinates of atom
mux,muy,muz = components of dipole orientation of atom
nx,ny,nz = image indices for atom :ul
Which of these quantities are actually listed depends on the "atom
style"_atom_style.html. This is the list of which styles require each
quantity:
atom-ID = all styles
molecule-ID = angle, bond, molecular, full styles
type-ID = all styles
q = charge, dipole, full styles
diameter = granular style
density = granular style
x,y,z = all styles
mux,muy,muz = dipole style
nx,ny,nz = optional for all styles (see below) :ul
Any quantity that is used by the atom style appears in the order
listed above. Thus if the atom style is {atomic}, an atom line should
have 5 quantities: atom-ID, type-ID, x, y, z. If the atom style is
{hybrid dipole molecular}, then an atom line should have 10 quantites:
atom-ID, molecule-ID, type-ID, q, x, y, z, mux, muy, muz.
x,y,z = coordinates of atom :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
For 2d simulations specify z as 0.0, or whatever value is within the
{zlo zhi} setting in the data file header.
For 2d simulations specify z as 0.0, or a value is within the {zlo
zhi} setting in the data file header.
The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
@ -245,25 +235,21 @@ be set to 0.
The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care about
molecule assignments.
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
An {Atoms} section must appear in the data file if natoms > 0 in the
header section. The atoms can be listed in any order.
Atom lines (all or none of them) can optionally list 3 final integer
values: nx,ny,nz. For periodic dimensions, they specify which image
of the box the atom is considered to be in. An image of 0 means the
box as defined. A value of 2 means add 2 box lengths to get the true
value. A value of -1 means subtract 1 box length to get the true
Atom lines (all lines or none of them) can optionally list 3 final
integer values: nx,ny,nz. For periodic dimensions, they specify which
image of the box the atom is considered to be in. An image of 0 means
the box as defined. A value of 2 means add 2 box lengths to get the
true value. A value of -1 means subtract 1 box length to get the true
value. LAMMPS updates these flags as atoms cross periodic boundaries
during the simulation. The flags can be output via the
"dump"_dump.html and "dump_modify"_dump_modify.html commands. If
nx,ny,nz values are not set in the data file, LAMMPS initializes them
to 0.
during the simulation. The flags can be output with atom snapshots
via the "dump"_dump.html command. If nx,ny,nz values are not set in
the data file, LAMMPS initializes them to 0.
Atom velocities are set to 0.0 when the {Atoms} section is read. They
may later be set by a {Velocities} section or by a
may later be set by a {Velocities} section in the data file or by a
"velocity"_velocity.html command in the input script.
:line

2
doc/temper.html
View File

@ -33,7 +33,7 @@ temper 40000 100 $t tempfix 0 32285 $w
<P>Run a parallel tempering (replica exchange) simulation of multiple
ensembles of a system on multiple partitions of processors. The
processor partitions are defined using the -partition command-line
switch (see <A HREF = "Section_start.html#2_4">this section</A>). Each ensemble's
switch (see <A HREF = "Section_start.html#2_6">this section</A>). Each ensemble's
temperature is typically controlled at a different value by a fix with
ID <I>fix-ID</I> that controls temperature. Possible fix styles are
<A HREF = "fix_nvt.html">nvt</A>, <A HREF = "fix_npt.html">npt</A>, and

2
doc/temper.txt
View File

@ -30,7 +30,7 @@ temper 40000 100 $t tempfix 0 32285 $w :pre
Run a parallel tempering (replica exchange) simulation of multiple
ensembles of a system on multiple partitions of processors. The
processor partitions are defined using the -partition command-line
switch (see "this section"_Section_start.html#2_4). Each ensemble's
switch (see "this section"_Section_start.html#2_6). Each ensemble's
temperature is typically controlled at a different value by a fix with
ID {fix-ID} that controls temperature. Possible fix styles are
"nvt"_fix_nvt.html, "npt"_fix_npt.html, and

12
doc/thermo.html
View File

@ -23,10 +23,14 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Compute and print thermodynamics (temperature, energy, pressure) on
timesteps that are a multiple of N and at the beginning and end of a
simulation. A value of 0 will only print thermodynamics at the
beginning and end.
<P>Compute and print thermodynamic info (e.g. temperature, energy,
pressure) on timesteps that are a multiple of N and at the beginning
and end of a simulation. A value of 0 will only print thermodynamics
at the beginning and end.
</P>
<P>The content and format of what is printed is controlled by the
<A HREF = "thermo_style.html">thermo_style</A> and
<A HREF = "thermo_modify.html">thermo_modify</A> commands.
</P>
<P><B>Restrictions:</B> none
</P>

12
doc/thermo.txt
View File

@ -20,10 +20,14 @@ thermo 100 :pre
[Description:]
Compute and print thermodynamics (temperature, energy, pressure) on
timesteps that are a multiple of N and at the beginning and end of a
simulation. A value of 0 will only print thermodynamics at the
beginning and end.
Compute and print thermodynamic info (e.g. temperature, energy,
pressure) on timesteps that are a multiple of N and at the beginning
and end of a simulation. A value of 0 will only print thermodynamics
at the beginning and end.
The content and format of what is printed is controlled by the
"thermo_style"_thermo_style.html and
"thermo_modify"_thermo_modify.html commands.
[Restrictions:] none

95
doc/thermo_modify.html
View File

@ -19,8 +19,7 @@
<LI>keyword = <I>temp</I> or <I>lost</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I>
<PRE> <I>temp</I> value = ID of temperature
<I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
<PRE> <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
<I>norm</I> value = <I>yes</I> or <I>no</I>
<I>flush</I> value = <I>yes</I> or <I>no</I>
<I>line</I> value = <I>one</I> or <I>multi</I>
@ -30,57 +29,95 @@
<I>window</I> value = N
N = number of previous print-outs to average over
</PRE>
<I>temp</I> value = compute ID that calculates a temperature
<I>press</I> value = compute ID that calculates a pressure
<I>drot</I> value = compute ID that calculates rotational energy for dipolar atoms
<I>grot</I> value = compute ID that calculates rotational energy for granular atoms
</UL>
<P><B>Examples:</B>
</P>
<PRE>thermo_modify temp mydef
thermo_modify lost no flush yes
<PRE>thermo_modify lost no flush yes
thermo_modify temp myTemp
thermo_modify line multi format float %g format 3 %15.8g
</PRE>
<P><B>Description:</B>
</P>
<P>Set options for how thermodynamics are computed and printed by LAMMPS.
<P>Set options for how thermodynamic information is computed and printed
by LAMMPS.
</P>
<P>The <I>temp</I> option allows you to specify how temperature is computed
when used to output thermodynamic info (temperature, kinetic energy,
pressure). Different methods of computing temperature can be defined
via the <A HREF = "temperature.html">temperature</A> command.
</P>
<P>The <I>lost</I> option determines whether LAMMPS checks for lost atoms each
time it computes thermodynamics and what it does if atoms are lost.
If the value is <I>ignore</I>, LAMMPS does not check for lost atoms. If
the value is <I>error</I> or <I>warn</I>, LAMMPS checks and either issues an
<P>The <I>lost</I> keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. If the value is <I>ignore</I>, LAMMPS does not check for lost atoms.
If the value is <I>error</I> or <I>warn</I>, LAMMPS checks and either issues an
error or warning. The code will exit with an error and continue with
a warning. This can be a useful debugging option.
</P>
<P>The <I>norm</I> option determines whether the thermodynamic print-out is
<P>The <I>norm</I> keyword determines whether the thermodynamic print-out is
normalized by the number of atoms or is the total summed across all
atoms. Different unit styles have different defaults for this
setting.
</P>
<P>The <I>flush</I> option invokes a flush operation after thermodynamic info
<P>The <I>flush</I> keyword invokes a flush operation after thermodynamic info
is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
</P>
<P>The <I>line</I> option determines whether thermodynamics will be printed as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
<P>The <I>line</I> keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the <I>one</I> and <I>multi</I> thermo_style settings.
</P>
<P>The <I>format</I> option sets the numeric format of individual printed
<P>The <I>format</I> keyword sets the numeric format of individual printed
quantities. The <I>int</I> and <I>float</I> settings set the format for all
integer or floating-point quantities printed. The setting with a
numeric value (e.g. format 5 %10.4g) sets the format of the Nth value
printed. If the format for a specific value has been set, it will
take precedent over the <I>int</I> or <I>float</I> setting.
</P>
<P>The <I>window</I> option sets the number of previous thermodynamic screen
<P>The <I>window</I> keyword sets the number of previous thermodynamic screen
outputs over which <A HREF = "thermo_style.html">thermo_style custom</A> <I>ave</I>
quantities are averaged when printed.
</P>
<P>The <I>temp</I> keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave"). The specified compute ID must have been previously
defined by the user via the <A HREF = "compute.html">compute</A> command and it must
be a style of compute that calculates a temperature. As described in
the <A HREF = "thermo_style.html">thermo_style</A> command, thermo output has a
default compute for temperature with ID = <I>thermo_temp</I>. This option
allows the user to override the default.
</P>
<P>The <I>press</I> keyword is used to determine how thermodynamic pressure is
calculated, which is used by all thermo quantities that require a
pressure ("press", "enthalpy", "pxx etc", "pave"). The specified
compute ID must have been previously defined by the user via the
<A HREF = "compute.html">compute</A> command and it must be a style of compute that
calculates a pressure. As described in the
<A HREF = "thermo_style.html">thermo_style</A> command, thermo output has a default
compute for pressure with ID = <I>thermo_press</I>. This option allows the
user to override the default.
</P>
<P>The <I>drot</I> keyword is used to determine how rotational energy is
calculated for dipolar atoms, which is used by the thermo_style
keyword <I>drot</I>. The specified compute ID must have been previously
defined by the user via the <A HREF = "compute.html">compute</A> command. As
described in the <A HREF = "thermo_style.html">thermo_style</A> command, thermo
output has a default compute for this calculation with ID =
<I>thermo_rotate_dipole</I>. This option allows the user to override the
default.
</P>
<P>The <I>grot</I> keyword is used to determine how rotational energy is
calculated for granular atoms, which is used by the thermo_style
keyword <I>grot</I>. The specified compute ID must have been previously
defined by the user via the <A HREF = "compute.html">compute</A> command. As
described in the <A HREF = "thermo_style.html">thermo_style</A> command, thermo
output has a default compute for this calculation with ID =
<I>thermo_rotate_gran</I>. This option allows the user to override the
default.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
@ -90,12 +127,14 @@ quantities are averaged when printed.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are temp = default, lost = error, norm = yes for
unit style of <I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>,
flush = no, window = 10. The defaults for the line and format options
depend on the thermo style. For styles "one", "granular", and
"custom" the line and format defaults are "one", "%8d", and "%12.8g".
For style "multi", the line and format defaults are "multi", "%8d",
and "%14.4f".
<P>The option defaults are lost = error, norm = yes for unit style of
<I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
window = 10, temp/press/drot/grot = compute IDs defined by
thermo_style.
</P>
<P>The defaults for the line and format options depend on the thermo
style. For styles "one", "granular", and "custom" the line and format
defaults are "one", "%8d", and "%12.8g". For style "multi", the line
and format defaults are "multi", "%8d", and "%14.4f".
</P>
</HTML>

91
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@ -14,7 +14,6 @@ thermo_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {temp} or {lost} or {norm} or {flush} or {line} or {format} :l
{temp} value = ID of temperature
{lost} value = {error} or {warn} or {ignore}
{norm} value = {yes} or {no}
{flush} value = {yes} or {no}
@ -24,57 +23,95 @@ keyword = {temp} or {lost} or {norm} or {flush} or {line} or {format} :l
string = C-style format string
{window} value = N
N = number of previous print-outs to average over :pre
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
{drot} value = compute ID that calculates rotational energy for dipolar atoms
{grot} value = compute ID that calculates rotational energy for granular atoms
:ule
[Examples:]
thermo_modify temp mydef
thermo_modify lost no flush yes
thermo_modify temp myTemp
thermo_modify line multi format float %g format 3 %15.8g :pre
[Description:]
Set options for how thermodynamics are computed and printed by LAMMPS.
Set options for how thermodynamic information is computed and printed
by LAMMPS.
The {temp} option allows you to specify how temperature is computed
when used to output thermodynamic info (temperature, kinetic energy,
pressure). Different methods of computing temperature can be defined
via the "temperature"_temperature.html command.
The {lost} option determines whether LAMMPS checks for lost atoms each
time it computes thermodynamics and what it does if atoms are lost.
If the value is {ignore}, LAMMPS does not check for lost atoms. If
the value is {error} or {warn}, LAMMPS checks and either issues an
The {lost} keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. If the value is {ignore}, LAMMPS does not check for lost atoms.
If the value is {error} or {warn}, LAMMPS checks and either issues an
error or warning. The code will exit with an error and continue with
a warning. This can be a useful debugging option.
The {norm} option determines whether the thermodynamic print-out is
The {norm} keyword determines whether the thermodynamic print-out is
normalized by the number of atoms or is the total summed across all
atoms. Different unit styles have different defaults for this
setting.
The {flush} option invokes a flush operation after thermodynamic info
The {flush} keyword invokes a flush operation after thermodynamic info
is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
The {line} option determines whether thermodynamics will be printed as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
The {line} keyword determines whether thermodynamics will be printed
as a series of numeric values on one line or in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the {one} and {multi} thermo_style settings.
The {format} option sets the numeric format of individual printed
The {format} keyword sets the numeric format of individual printed
quantities. The {int} and {float} settings set the format for all
integer or floating-point quantities printed. The setting with a
numeric value (e.g. format 5 %10.4g) sets the format of the Nth value
printed. If the format for a specific value has been set, it will
take precedent over the {int} or {float} setting.
The {window} option sets the number of previous thermodynamic screen
The {window} keyword sets the number of previous thermodynamic screen
outputs over which "thermo_style custom"_thermo_style.html {ave}
quantities are averaged when printed.
The {temp} keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave"). The specified compute ID must have been previously
defined by the user via the "compute"_compute.html command and it must
be a style of compute that calculates a temperature. As described in
the "thermo_style"_thermo_style.html command, thermo output has a
default compute for temperature with ID = {thermo_temp}. This option
allows the user to override the default.
The {press} keyword is used to determine how thermodynamic pressure is
calculated, which is used by all thermo quantities that require a
pressure ("press", "enthalpy", "pxx etc", "pave"). The specified
compute ID must have been previously defined by the user via the
"compute"_compute.html command and it must be a style of compute that
calculates a pressure. As described in the
"thermo_style"_thermo_style.html command, thermo output has a default
compute for pressure with ID = {thermo_press}. This option allows the
user to override the default.
The {drot} keyword is used to determine how rotational energy is
calculated for dipolar atoms, which is used by the thermo_style
keyword {drot}. The specified compute ID must have been previously
defined by the user via the "compute"_compute.html command. As
described in the "thermo_style"_thermo_style.html command, thermo
output has a default compute for this calculation with ID =
{thermo_rotate_dipole}. This option allows the user to override the
default.
The {grot} keyword is used to determine how rotational energy is
calculated for granular atoms, which is used by the thermo_style
keyword {grot}. The specified compute ID must have been previously
defined by the user via the "compute"_compute.html command. As
described in the "thermo_style"_thermo_style.html command, thermo
output has a default compute for this calculation with ID =
{thermo_rotate_gran}. This option allows the user to override the
default.
[Restrictions:] none
[Related commands:]
@ -84,10 +121,12 @@ quantities are averaged when printed.
[Default:]
The option defaults are temp = default, lost = error, norm = yes for
unit style of {lj}, norm = no for unit style of {real} and {metal},
flush = no, window = 10. The defaults for the line and format options
depend on the thermo style. For styles "one", "granular", and
"custom" the line and format defaults are "one", "%8d", and "%12.8g".
For style "multi", the line and format defaults are "multi", "%8d",
and "%14.4f".
The option defaults are lost = error, norm = yes for unit style of
{lj}, norm = no for unit style of {real} and {metal}, flush = no,
window = 10, temp/press/drot/grot = compute IDs defined by
thermo_style.
The defaults for the line and format options depend on the thermo
style. For styles "one", "granular", and "custom" the line and format
defaults are "one", "%8d", and "%12.8g". For style "multi", the line
and format defaults are "multi", "%8d", and "%14.4f".

186
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View File

@ -27,8 +27,11 @@
pe, ke, etotal, enthalpy,
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
gke, grot, tave, pave, eave, peave, t_ID
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
pxx, pyy, pzz, pxy, pxz, pyz
drot, grot,
tave, pave, eave, peave,
c_ID, c_ID[n], f_ID, f_ID[n], v_name
step = timestep
atoms = # of atoms
cpu = elapsed CPU time
@ -50,11 +53,16 @@
etail = VanderWaal energy long-range tail correction
vol = volume
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
gke = granular translational kinetic energy (without frozen atoms)
grot = granular rotational kinetic energy (without frozen atoms)
drot = rotational energy of dipolar atoms
grot = rotational energy of granular atoms
tave, pave, eave, peave = time-averaged temp, press, etotal, pe
t_ID = termperature as computed by temperature ID
c_ID = scalar quantity calculated by a compute identified by its ID
c_ID[N] = Nth vector quantity calculated by a compute identified by its ID
f_ID = scalar quantity calculated by a fix identified by its ID
f_ID[N] = Nth vector quantity calculated by a fix identified by its ID
v_name = current value of a variable identified by the variable name
</PRE>
</UL>
@ -62,12 +70,12 @@
</P>
<PRE>thermo_style multi
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp t_left t_right etotal
thermo_style custom step temp etotal c_myTemp v_abc
</PRE>
<P><B>Description:</B>
</P>
<P>Set the style in which thermodynamic data is printed to the screen and
log file.
<P>Set the style and content for printing thermodynamic data to the
screen and log file.
</P>
<P>Style <I>one</I> prints a one-line summary of thermodynamic info that is
the equivalent of "thermo_style custom step temp epair emol etotal
@ -80,23 +88,97 @@ numeric values and a string ID for each quantity.
</P>
<P>Style <I>granular</I> is used with <A HREF = "atom_style.html">atom style</A> granular
and prints a one-line numeric summary that is the equivalent of
"thermo_style custom step atoms gke grot".
"thermo_style custom step atoms ke grot".
</P>
<P>Style <I>custom</I> is the most general setting and allows you to specify
which of the quantities listed above you want printed on each
thermodynamic timestep.
which of the keywords listed above you want printed on each
thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
references to <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, and
<A HREF = "variable.html"">variables</A> that have been defined elsewhere in the
input script or can even be new styles which users have added to
LAMMPS (see the <A HREF = "Section_modify.html">Section_modify</A> section of the
documentation). Thus the <I>custom</I> style provides a flexible means of
outputting essentially any desired quantity as a simulation proceeds.
</P>
<P>Also, all styles except <I>custom</I> have <I>vol</I> added to their list of
outputs as a final printed quantity when the simulation box volume
changes during the simulation.
<P>All styles except <I>custom</I> have <I>vol</I> appended to their list of
outputs if the simulation box volume changes during the simulation.
</P>
<P>All thermodynamic quantities which require a temperature (<I>temp, press,
ke, etotal, tave, eave</I>) use the temperature with ID = <I>default</I> that is
defined by LAMMPS (see the <A HREF = "temperature.html">temperature</A> command)
that performs an average over all atoms. This can be changed via the
<A HREF = "thermo_modify.html">thermo_modify</A> command. The exception is the
<I>t_ID</I> quantity which directly specifies which temperature to compute
and print out.
<P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
</P>
<HR>
<P>Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave". To do this, a compute of style "temp" is created, as
if this command had been issued:
</P>
<PRE>compute thermo_temp all temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
that the ID of the new compute is <I>thermo_temp</I> and the group is
<I>all</I>. You can change the attributes of this temperature (e.g. its
degrees-of-freedom) via the <A HREF = "compute_modify.html">compute_modify</A>
command. Alternatively, you can directly assign a new compute (that
calculates temperature) which you have defined, to be used for any
thermodynamic quantity that requires a temperature. This is done via
the <A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>Several of the thermodynamic quantities require a pressure to be
computed: "press", "enthalpy", "pxx etc", "pave". To do this, a
compute of style "pressure" is created, as if this command had been
issued:
</P>
<PRE>compute thermo_press all pressure thermo_temp
</PRE>
<P>See the <A HREF = "compute_pressure.html">compute pressure</A> command for details.
Note that the ID of the new compute is <I>thermo_press</I> and the group is
<I>all</I>. You can change the attributes of this pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
directly assign a new compute (that calculates pressure) which you
have defined, to be used for any thermodynamic quantity that requires
a pressure. This is done via the <A HREF = "thermo_modify.html">thermo_modify</A>
command.
</P>
<P>The <I>drot</I> keyword requires a rotational energy to be compute for
dipolar particles. To do this, a compute of style "rotate/dipole" is
created, as if this command had been issued:
</P>
<PRE>compute thermo_rotate_dipole all rotate/dipole
</PRE>
<P>See the <A HREF = "compute_rotate_dipole.html">compute rotate/dipole</A> command for
details. Note that the ID of the new compute is
<I>thermo_rotate_dipole</I> and the group is <I>all</I>. You can change the
attributes of this computation via the
<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
directly assign a new compute which you have defined, to be used for
<I>drot</I>. This is done via the <A HREF = "thermo_modify.html">thermo_modify</A>
command. For example, this could be useful if you wish to exclude
certain particles from the compuation.
</P>
<P>The <I>grot</I> keyword requires a rotational energy to be compute for
granular particles. To do this, a compute of style "rotate/gran" is
created, as if this command had been issued:
</P>
<PRE>compute thermo_rotate_gran all rotate/gran
</PRE>
<P>See the <A HREF = "compute_rotate_gran.html">compute rotate/gran</A> command for
details. Note that the ID of the new compute is <I>thermo_rotate_gran</I>
and the group is <I>all</I>. You can change the attributes of this
computation via the <A HREF = "compute_modify.html">compute_modify</A> command.
Alternatively, you can directly assign a new compute which you have
defined, to be used for <I>grot</I>. This is done via the
<A HREF = "thermo_modify.html">thermo_modify</A> command. For example, this could
be useful if you wish to exclude frozen particles from the compuation.
</P>
<HR>
<P>The potential energy of the system <I>pe</I> will include contributions
from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option was set
for each fix. For example, the <A HREF = "fix_wall_lj93">fix wall/lj93</A> fix will
contribute the energy of atoms interacting with the wall.
</P>
<P>A long-range tail correction <I>etail</I> for the VanderWaal pairwise
energy will be non-zero only if the <A HREF = "pair_modify.html">pair_modify
@ -105,39 +187,53 @@ is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding
correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
etc.
</P>
<P>The time-averaged quantities <I>tave, pave, eave, peave</I> are averaged
over the last N thermodynamic outputs to the screen (not the last N
<P>The time-averaged keywords <I>tave, pave, eave, peave</I> are averaged over
the last N thermodynamic outputs to the screen (not the last N
timesteps), where N is the value set by the <I>window</I> option of the
<A HREF = "thermo_modify.html">thermo_modify</A> command (N = 10 by default).
</P>
<P>The <I>t_ID</I> quantity allows for user-defined temperatures to be printed
with thermodynamic output. For example, if either of the commands
<HR>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector quantities
calculated by a compute to be output. The ID in the keyword should be
replaced by the actual ID of the compute that has been defined
elsewhere in the input script. See the <A HREF = "compute.html">compute</A> command
for details. Note that per-atom quantities calcalated by a compute
cannot be output as part of thermodynamics. Rather, these quantities
are output by the <A HREF = "dump.html">dump custom</A> command.
</P>
<PRE>temperature mine all region sphere
fix mine all temp/rescale 100 1.0 1.0 0.1 1.0 region sphere
</PRE>
<P>were used to compute or thermostat the temperature of atoms inside a
spherical geometric region, then the keyword <I>t_mine</I> will print that
temperature as part of thermodynamic output.
<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
the compute is printed. If <I>c_ID[N]</I> is used, then N in the range
from 1-M will print a specific component of the vector calculated by
the compute. A value of N=0 will output the scalar quantity.
</P>
<P>Some fixes also generate quantities that can be appended to these
lists each time thermodyanmic info prints out, if enabled by the
<A HREF = "fix_modify.html">fix_modify</A> command. See invidividual fix commands
for more details, e.g. the <A HREF = "fix_nvt.html">fix nvt</A> and <A HREF = "fix_npt.html">fix
npt</A> commands.
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector quantities
calculated by a fix to be output. The ID in the keyword should be
replaced by the actual ID of the fix that has been defined elsewhere
in the input script. See the <A HREF = "fix.html">fix</A> command for details.
</P>
<P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
the fix is printed. If <I>f_ID[N]</I> is used, then N in the range from
1-M will print a specific component of the vector calculated by the
fix. A value of N=0 will output the scalar quantity.
</P>
<P>The <I>v_name</I> keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
of the variable that has been defined elsewhere in the input script.
See the <A HREF = "variable.html">variable</A> command for details. Equal-style
variables can calculate complex formulas involving atom and group
properties, mathematical operations, other variables, etc. This
keyword enables them to be evaluated and their value printed
periodically during a simulation.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> for information on how to add
new compute and fix styles as well as variable options to LAMMPS that
calculate quantities that could then be output with these keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P><A HREF = "atom_style.html">Atom style</A> granular cannot compute the usual
temperature and pressure settings because it stores atom masses
differently. The gke and grot settings should be used instead (or use
thermo style granular).
</P>
<P>This command must come after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
<A HREF = "create_box.html">create_box</A> command.

184
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@ -22,8 +22,11 @@ args = list of arguments for a particular style :l
pe, ke, etotal, enthalpy,
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, lx, ly, lz, pxx, pyy, pzz, pxy, pxz, pyz
gke, grot, tave, pave, eave, peave, t_ID
vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
pxx, pyy, pzz, pxy, pxz, pyz
drot, grot,
tave, pave, eave, peave,
c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
step = timestep
atoms = # of atoms
cpu = elapsed CPU time
@ -45,23 +48,28 @@ args = list of arguments for a particular style :l
etail = VanderWaal energy long-range tail correction
vol = volume
lx,ly,lz = box lengths in x,y,z
xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
gke = granular translational kinetic energy (without frozen atoms)
grot = granular rotational kinetic energy (without frozen atoms)
drot = rotational energy of dipolar atoms
grot = rotational energy of granular atoms
tave, pave, eave, peave = time-averaged temp, press, etotal, pe
t_ID = termperature as computed by temperature ID :pre
c_ID = scalar quantity calculated by a compute identified by its ID
c_ID\[N\] = Nth vector quantity calculated by a compute identified by its ID
f_ID = scalar quantity calculated by a fix identified by its ID
f_ID\[N\] = Nth vector quantity calculated by a fix identified by its ID
v_name = current value of a variable identified by the variable name :pre
:ule
[Examples:]
thermo_style multi
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp t_left t_right etotal :pre
thermo_style custom step temp etotal c_myTemp v_abc :pre
[Description:]
Set the style in which thermodynamic data is printed to the screen and
log file.
Set the style and content for printing thermodynamic data to the
screen and log file.
Style {one} prints a one-line summary of thermodynamic info that is
the equivalent of "thermo_style custom step temp epair emol etotal
@ -74,23 +82,97 @@ numeric values and a string ID for each quantity.
Style {granular} is used with "atom style"_atom_style.html granular
and prints a one-line numeric summary that is the equivalent of
"thermo_style custom step atoms gke grot".
"thermo_style custom step atoms ke grot".
Style {custom} is the most general setting and allows you to specify
which of the quantities listed above you want printed on each
thermodynamic timestep.
which of the keywords listed above you want printed on each
thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are
references to "computes"_compute.html, "fixes"_fix.html, and
"variables"_variable.html" that have been defined elsewhere in the
input script or can even be new styles which users have added to
LAMMPS (see the "Section_modify"_Section_modify.html section of the
documentation). Thus the {custom} style provides a flexible means of
outputting essentially any desired quantity as a simulation proceeds.
Also, all styles except {custom} have {vol} added to their list of
outputs as a final printed quantity when the simulation box volume
changes during the simulation.
All styles except {custom} have {vol} appended to their list of
outputs if the simulation box volume changes during the simulation.
All thermodynamic quantities which require a temperature ({temp, press,
ke, etotal, tave, eave}) use the temperature with ID = {default} that is
defined by LAMMPS (see the "temperature"_temperature.html command)
that performs an average over all atoms. This can be changed via the
"thermo_modify"_thermo_modify.html command. The exception is the
{t_ID} quantity which directly specifies which temperature to compute
and print out.
Options invoked by the "thermo_modify"_thermo_modify.html command can
be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
:line
Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave". To do this, a compute of style "temp" is created, as
if this command had been issued:
compute thermo_temp all temp :pre
See the "compute temp"_compute_temp.html command for details. Note
that the ID of the new compute is {thermo_temp} and the group is
{all}. You can change the attributes of this temperature (e.g. its
degrees-of-freedom) via the "compute_modify"_compute_modify.html
command. Alternatively, you can directly assign a new compute (that
calculates temperature) which you have defined, to be used for any
thermodynamic quantity that requires a temperature. This is done via
the "thermo_modify"_thermo_modify.html command.
Several of the thermodynamic quantities require a pressure to be
computed: "press", "enthalpy", "pxx etc", "pave". To do this, a
compute of style "pressure" is created, as if this command had been
issued:
compute thermo_press all pressure thermo_temp :pre
See the "compute pressure"_compute_pressure.html command for details.
Note that the ID of the new compute is {thermo_press} and the group is
{all}. You can change the attributes of this pressure via the
"compute_modify"_compute_modify.html command. Alternatively, you can
directly assign a new compute (that calculates pressure) which you
have defined, to be used for any thermodynamic quantity that requires
a pressure. This is done via the "thermo_modify"_thermo_modify.html
command.
The {drot} keyword requires a rotational energy to be compute for
dipolar particles. To do this, a compute of style "rotate/dipole" is
created, as if this command had been issued:
compute thermo_rotate_dipole all rotate/dipole :pre
See the "compute rotate/dipole"_compute_rotate_dipole.html command for
details. Note that the ID of the new compute is
{thermo_rotate_dipole} and the group is {all}. You can change the
attributes of this computation via the
"compute_modify"_compute_modify.html command. Alternatively, you can
directly assign a new compute which you have defined, to be used for
{drot}. This is done via the "thermo_modify"_thermo_modify.html
command. For example, this could be useful if you wish to exclude
certain particles from the compuation.
The {grot} keyword requires a rotational energy to be compute for
granular particles. To do this, a compute of style "rotate/gran" is
created, as if this command had been issued:
compute thermo_rotate_gran all rotate/gran :pre
See the "compute rotate/gran"_compute_rotate_gran.html command for
details. Note that the ID of the new compute is {thermo_rotate_gran}
and the group is {all}. You can change the attributes of this
computation via the "compute_modify"_compute_modify.html command.
Alternatively, you can directly assign a new compute which you have
defined, to be used for {grot}. This is done via the
"thermo_modify"_thermo_modify.html command. For example, this could
be useful if you wish to exclude frozen particles from the compuation.
:line
The potential energy of the system {pe} will include contributions
from fixes if the "fix_modify thermo"_fix_modify.html option was set
for each fix. For example, the "fix wall/lj93"_fix_wall_lj93 fix will
contribute the energy of atoms interacting with the wall.
A long-range tail correction {etail} for the VanderWaal pairwise
energy will be non-zero only if the "pair_modify
@ -99,39 +181,53 @@ is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
correction to the pressure is included in {press} and {pxx}, {pyy},
etc.
The time-averaged quantities {tave, pave, eave, peave} are averaged
over the last N thermodynamic outputs to the screen (not the last N
The time-averaged keywords {tave, pave, eave, peave} are averaged over
the last N thermodynamic outputs to the screen (not the last N
timesteps), where N is the value set by the {window} option of the
"thermo_modify"_thermo_modify.html command (N = 10 by default).
The {t_ID} quantity allows for user-defined temperatures to be printed
with thermodynamic output. For example, if either of the commands
:line
temperature mine all region sphere
fix mine all temp/rescale 100 1.0 1.0 0.1 1.0 region sphere :pre
The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector quantities
calculated by a compute to be output. The ID in the keyword should be
replaced by the actual ID of the compute that has been defined
elsewhere in the input script. See the "compute"_compute.html command
for details. Note that per-atom quantities calcalated by a compute
cannot be output as part of thermodynamics. Rather, these quantities
are output by the "dump custom"_dump.html command.
were used to compute or thermostat the temperature of atoms inside a
spherical geometric region, then the keyword {t_mine} will print that
temperature as part of thermodynamic output.
If {c_ID} is used as a keyword, then the scalar quantity calculated by
the compute is printed. If {c_ID\[N\]} is used, then N in the range
from 1-M will print a specific component of the vector calculated by
the compute. A value of N=0 will output the scalar quantity.
Some fixes also generate quantities that can be appended to these
lists each time thermodyanmic info prints out, if enabled by the
"fix_modify"_fix_modify.html command. See invidividual fix commands
for more details, e.g. the "fix nvt"_fix_nvt.html and "fix
npt"_fix_npt.html commands.
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities
calculated by a fix to be output. The ID in the keyword should be
replaced by the actual ID of the fix that has been defined elsewhere
in the input script. See the "fix"_fix.html command for details.
Options invoked by the "thermo_modify"_thermo_modify.html command can
be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
If {f_ID} is used as a keyword, then the scalar quantity calculated by
the fix is printed. If {f_ID\[N\]} is used, then N in the range from
1-M will print a specific component of the vector calculated by the
fix. A value of N=0 will output the scalar quantity.
The {v_name} keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
of the variable that has been defined elsewhere in the input script.
See the "variable"_variable.html command for details. Equal-style
variables can calculate complex formulas involving atom and group
properties, mathematical operations, other variables, etc. This
keyword enables them to be evaluated and their value printed
periodically during a simulation.
See "this section"_Section_modify.html for information on how to add
new compute and fix styles as well as variable options to LAMMPS that
calculate quantities that could then be output with these keywords.
:line
[Restrictions:]
"Atom style"_atom_style.html granular cannot compute the usual
temperature and pressure settings because it stores atom masses
differently. The gke and grot settings should be used instead (or use
thermo style granular).
This command must come after the simulation box is defined by a
"read_data"_read_data.html, "read_restart"_read_restart.html, or
"create_box"_create_box.html command.

210
doc/variable.html
View File

@ -17,21 +17,24 @@
</PRE>
<UL><LI>name = name of variable to define
<LI>style = <I>index</I> or <I>loop</I> or <I>equal</I> or <I>world</I> or <I>universe</I>
<LI>style = <I>index</I> or <I>loop</I> or <I>world</I> or <I>universe</I> or <I>uloop</I> or <I>equal</I>
<PRE> <I>index</I> args = one or more strings
<I>loop</I> args = N = integer size of loop
<I>equal</I> args = one string containing functions, vectors, keywords, numbers
<I>world</I> args = one string for each partition of processors
<I>universe</I> args = one or more strings
<I>uloop</I> args = N = integer size of loop
<I>equal</I> args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
numbers = 0.0, -5.4, 2.8e-4, etc
thermo keywords = vol, ke, press, etc from <A HREF = "thermo_style.html">thermo_style</A>
math functions = add(x,y), sub(x,y), mult(x,y), div(x,y),
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
group functions = mass(group), charge(group), xcm(group,dim),
vcm(group,dim), bound(group,xmin), gyration(group)
vectors = x[5], y[12], z[17], vx[88], vy[19], vz[2],
fx[1], fy[2005], fz[1]
keywords = same keywords (mostly) as in <A HREF = "thermo_style.html">thermo_style custom</A> command
<I>world</I> args = one string for each partition of processors
<I>universe</I> args = one or more strings
<I>uloop</I> args = N = integer size of loop
atom vectors = x[N], y[N], z[N], vx[N], vy[N], vz[N],
fx[N], fy[N], fz[N]
compute references = c_ID[0], c_ID[N]
other variables = v_abc, v_x, etc
</PRE>
</UL>
@ -40,8 +43,9 @@
<PRE>variable x index run1 run2 run3 run4 run5 run6 run7 run8
variable LoopVar loop 20
variable beta equal div(temp,3.0)
variable b1 equal add(x[234],mult(0.5,lx))
variable b equal xcm(mol1,x)
variable b1 equal add(x[234],mult(0.5,col))
variable b equal div(xcm(mol1,x),2.0)
variable b equal c_myTemp[0]
variable temp world 300.0 310.0 320.0 330.0
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
variable x uloop 15
@ -49,15 +53,24 @@ variable x uloop 15
<P><B>Description:</B>
</P>
<P>This command assigns one or more values to a variable name so that the
variable can be used in subsequent input script commands. The "name"
of the variable is an arbitrary string. Each "value" is a string
which could be text or numbers, as in the examples above. As
explained in <A HREF = "Section_commands.html#3_2">this section</A>, occurrences of
the variable name in an input script line are replaced by the
variable can be used in subsequent input script commands or its value
output during a simulation. The "name" of the variable is an
arbitrary string. Each "value" is a string which could be text or
numbers, as in the examples above.
</P>
<P>As explained in <A HREF = "Section_commands.html#3_2">this section</A>, occurrences
of the variable name in an input script line are replaced by the
variable's value. The variable name can be referenced in the input
script as $x if the name "x" is a single character, or as ${LoopVar}
if the name "LoopVar" is one or more characters.
</P>
<P>Variable values can also be accessed for output once or periodically
during a simulation by the <A HREF = "print.html">print</A> command, <A HREF = "fix_print.html">fix
print</A> command, <A HREF = "run.html">run every</A> command, and the
<A HREF = "thermo_style.html">thermo_style</A> command.
</P>
<HR>
<P>As described below, for variable styles <I>index</I>, <I>loop</I>, <I>universe</I>,
and <I>uloop</I>, the value assigned to a variable can be incremented via
the <A HREF = "next.html">next</A> command. When there are no more values to
@ -79,12 +92,14 @@ equal-style variable is encountered. Also, if a variable is iterated
on to the end of its list via the <A HREF = "next.html">next</A> command, it is
available to be re-defined in a subsequent variable command.
</P>
<HR>
<P>For the <I>index</I> style, one or more strings are specified. Initially,
the 1st string is assigned to the variable. Each time a
<A HREF = "next.html">next</A> command is used with the variable name, the next
string is assigned. All processors assign the same string to the
variable. <I>Index</I>-style variables can also be set (with a single
value) by using the command-line switch -var; see <A HREF = "Section_start.html#2_4">this
value) by using the command-line switch -var; see <A HREF = "Section_start.html#2_6">this
section</A> for details.
</P>
<P>The <I>loop</I> style is identical to the <I>index</I> style except that the
@ -95,59 +110,8 @@ Each time a <A HREF = "next.html">next</A> command is used with the variable nam
the next string ("2", "3", etc) is assigned. All processors assign
the same string to the variable.
</P>
<P>For the <I>equal</I> style, a single string is specified which represents
an equation that will be evaluated afresh each time the variable is
used. Thus the variable can take on different values at different
stages of the input script. For example, if the variable is used in a
<A HREF = "fix_print.html">fix print</A> command, it could print different values
each timestep it was invoked. The next command cannot be used with
<I>equal</I>-style variables, since there is only one value. Note that, as
with any other input script command, it is feasible to use another
variable in the <I>equal</I> variable's string, e.g. variable y equal
mult($x,2). However, $x will be replaced immediately by it's current
value when the command is first parsed, not each time that $y is
substituted for.
</P>
<P>The syntax of the equation assigned to <I>equal</I> variables is simple.
It can contain "functions", "vectors", "keywords", or "numbers" in any
combination.
</P>
<UL><LI>Function = a keyword followed by parenthesis with one or two arguments
<LI>Supported arithmetic functions = add(x,y), sub(x,y), mult(x,y), div(x,y), neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
<LI>Supported group functions = mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), bound(ID,dir), gyration(ID)
<LI>Example function usage = div(1.0e20,3.0), neg(x[34]), pow(lx,3.0), xcm(mol,x), bound(lower,zmin)
<LI>Vector = a keyword followed by square brackets containing an atom ID
<LI>Supported vectors = x, y, z, vx, vy, vz, fx, fy, fz
<LI>Example vector usage = x[123], fz[1000]
<LI>Keyword = any keyword supported by the <A HREF = "thermo_style.html">thermo_style custom</A> command except cpu, pressure tensor components (pxx, pyy, etc), time-averaged quantities (tave, pave, etc)
<LI>Example keyword usage = atoms, pow(vol,0.333), mult(elong,0.5)
<LI>Number = 0.2, 1.0e20, -15.4, etc
</UL>
<P>For the group functions, ID is a group-ID, dim is 'x' or 'y' or 'z',
and dir is one of 6 strings: "xmin", "xmax", "ymin", "ymax", "zmin",
or "zmax". The group functions mass() and charge() are the total mass
and charge of the group of atoms. Xcm() and vcm() return components
of the position and velocity of the center of mass of the group.
Bound() returns the min/max of a particular coordinate for all atoms
in the group. Gyration() computes the radius-of-gyration of the group
of atoms. See the <A HREF = "fix_gyration.html">fix gyration</A> command for the
formula.
</P>
<P>Keywords have restrictions on when they can be assigned to variables.
For example, keywords that compute thermodynamic quantites can only be
invoked after the first simulation has begun. A warning is issued if
thermodyanmic keywords are invoked on timesteps when thermodynamic
information is not being printed to the screen, since the values
assigned to the variable may be out-of-date.
</P>
<P>The variable <I>equal</I> equation can also be nested in that function
arguments can be functions, vectors, keywords, or numbers. For
example, this is a valid equation:
</P>
<PRE>variable x equal div(add(pe,ke),pow(vol,div(1,3)))
</PRE>
<P>For the <I>world</I> style, one or more strings are specified. There must
be one string for each processor partition or "world". See <A HREF = "Section_start.html#2_4">this
be one string for each processor partition or "world". See <A HREF = "Section_start.html#2_6">this
section</A> of the manual for information on
running LAMMPS with multiple partitions via the "-partition"
command-line switch. This variable command assigns one string to each
@ -161,7 +125,7 @@ different partitions.
</P>
<P>For the <I>universe</I> style, one or more strings are specified. There
must be at least as many strings as there are processor partitions or
"worlds". See <A HREF = "Section_start.html#2_4">this page</A> for information on
"worlds". See <A HREF = "Section_start.html#2_6">this page</A> for information on
running LAMMPS with multiple partitions via the "-partition"
command-line switch. This variable command initially assigns one
string to each world. When a <A HREF = "next.html">next</A> command is encountered
@ -179,11 +143,117 @@ strings are the integers from 1 to N. This allows you to generate a
long list of runs (e.g. 1000) without having to list N values in your
input script.
</P>
<HR>
<P>For the <I>equal</I> style, a single string is specified which represents
an equation that will be evaluated afresh each time the variable is
used. Thus the variable can take on different values at different
stages of the input script. For example, if the variable is used in a
<A HREF = "fix_print.html">fix print</A> command, different values could be printed
each timestep it was invoked. The next command cannot be used with
<I>equal</I>-style variables, since there is only one value.
</P>
<P>The equation for an <I>equal</I>-style variable can contain a variety of
quantities. The syntax for each kind of quantity is simple, but
multiple quantities can be nested and combined in various ways to
build up formulas of arbitrary complexity. For example, this is a
valid (though strange) variable equation:
</P>
<PRE>variable x equal div(add(pe,c_MyTemp[0]),pow(vol,div(1,3)))
</PRE>
<P>Specifically, an equation can contain numbers, thermo keywords, math
functions, group functions, atom vectors, compute references, and
other variables:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >Number</TD><TD > 0.2, 1.0e20, -15.4, etc</TD></TR>
<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
<TR><TD >Math functions</TD><TD > add(x,y), sub(x,y), mult(x,y), div(x,y), neg(x), pow(x,y), exp(x), ln(x), sqrt(x)</TD></TR>
<TR><TD >Group functions</TD><TD > mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), bound(ID,dir), gyration(ID)</TD></TR>
<TR><TD >Atom vectors</TD><TD > x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR>
<TR><TD >Compute references</TD><TD > c_ID[0], c_ID[N]</TD></TR>
<TR><TD >Other variables</TD><TD > v_abc, v_x, etc
</TD></TR></TABLE></DIV>
<P>The thermo keywords allowed in the equation are those defined by the
"thermo_style custom" command. Note that many thermodyanmic
quantities are only computable after the first simulation has begun.
Likewise, many thermodynamic quantities (such as energies) are only
computed on timesteps when thermodyanmic output is being performed.
If the variable equation these quantities at other times, out-of-date
or invalid values may be used.
</P>
<P>Math functions take one or two arguments, each of which may be an
equation containing any of the quantities defined above. This allows
equations to be nested, as in the examples above.
</P>
<P>Group functions take one or two arguments. The first argument is the
group-ID. The <I>dim</I> argument is <I>x</I> or <I>y</I> or <I>z</I>. The <I>dir</I>
argument is <I>xmin</I>, <I>xmax</I>, <I>ymin</I>, <I>ymax</I>, <I>zmin</I>, or <I>zmax</I>. The
group functions mass() and charge() are the total mass and charge of
the group of atoms. Xcm() and vcm() return components of the position
and velocity of the center of mass of the group. Bound() returns the
min/max of a particular coordinate for all atoms in the group.
Gyration() computes the radius-of-gyration of the group of atoms. See
the <A HREF = "fix_gyration.html">fix gyration</A> command for the formula.
</P>
<P>The atom vectors take a single integer argument from 1-N, which
is the desired atom-ID, e.g. x[243].
</P>
<P>Compute references access allow access to scalar or vector quantities
calculated by a compute. The ID in the reference should be replaced
by the actual ID of the compute that has been defined elsewhere in the
input script. See the <A HREF = "compute.html">compute</A> command for details.
Note that per-atom quantities calcalated by a compute cannot be
accessed this way, but only global scalar or vector quantities.
</P>
<P>If <I>c_ID[0]</I> is used as a keyword, then the scalar quantity
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
in the range from 1-M will print a specific component of the vector
calculated by the compute.
</P>
<P>The current values of other variables can be accessed by prepending a
"v_" to the variable name. This will cause the other variable to be
evaulated. Note that if you do something circular like this:
</P>
<PRE>variable a equal v_b
variable b equal v_a
print $a
</PRE>
<P>then LAMMPS will run for a while when the print statement is invoked.
</P>
<P>Note that there is a subtle difference between using a variable
in a <I>equal</I>-style equation in the form $x versus v_x.
</P>
<P>In the former case, as with any other input script command, the
variable's value is substituted for immediately when the line is read
from the input script. Thus if the current simulation box volume was
1000.0, then these lines:
</P>
<PRE>variable x equal vol
variable y equal mult($x,2)
</PRE>
<P>would associate the equation string "mult(1000.0,2)" with variable y.
</P>
<P>By contrast, these lines:
</P>
<PRE>variable x equal vol
variable y equal mult(v_x,2)
</PRE>
<P>would associate the equation string "mult(v_x,2)" with variable y.
</P>
<P>Thus if the variable y were evaluated periodically during a run where
the box volume changed, the resulting value would always be 500.0 for
the first case, but would change dynamically for the second case.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The use of atom vectors in <I>equal</I> style variables requires the atom
style to use a global mapping in order to look up the vector indices.
Only atom styles with molecular information create global maps.
Only atom styles with molecular information create global maps unless
the <A HREF = "atom_modify.html">atom_modify map</A> command is used.
</P>
<P><B>Related commands:</B>
</P>

217
doc/variable.txt
View File

@ -13,20 +13,23 @@ variable command :h3
variable name style args ... :pre
name = name of variable to define :ulb,l
style = {index} or {loop} or {equal} or {world} or {universe} :l
style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} :l
{index} args = one or more strings
{loop} args = N = integer size of loop
{equal} args = one string containing functions, vectors, keywords, numbers
{world} args = one string for each partition of processors
{universe} args = one or more strings
{uloop} args = N = integer size of loop
{equal} args = one equation containing numbers, thermo keywords, math functions, group functions, atom vectors, compute references, other variables
numbers = 0.0, -5.4, 2.8e-4, etc
thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html
math functions = add(x,y), sub(x,y), mult(x,y), div(x,y),
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
group functions = mass(group), charge(group), xcm(group,dim),
vcm(group,dim), bound(group,xmin), gyration(group)
vectors = x\[5\], y\[12\], z\[17\], vx\[88\], vy\[19\], vz\[2\],
fx\[1\], fy\[2005\], fz\[1\]
keywords = same keywords (mostly) as in "thermo_style custom"_thermo_style.html command
{world} args = one string for each partition of processors
{universe} args = one or more strings
{uloop} args = N = integer size of loop :pre
atom vectors = x\[N\], y\[N\], z\[N\], vx\[N\], vy\[N\], vz\[N\],
fx\[N\], fy\[N\], fz\[N\]
compute references = c_ID\[0\], c_ID\[N\]
other variables = v_abc, v_x, etc :pre
:ule
[Examples:]
@ -34,8 +37,9 @@ style = {index} or {loop} or {equal} or {world} or {universe} :l
variable x index run1 run2 run3 run4 run5 run6 run7 run8
variable LoopVar loop 20
variable beta equal div(temp,3.0)
variable b1 equal add(x\[234\],mult(0.5,lx))
variable b equal xcm(mol1,x)
variable b1 equal add(x\[234\],mult(0.5,col))
variable b equal div(xcm(mol1,x),2.0)
variable b equal c_myTemp\[0\]
variable temp world 300.0 310.0 320.0 330.0
variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
variable x uloop 15 :pre
@ -43,15 +47,24 @@ variable x uloop 15 :pre
[Description:]
This command assigns one or more values to a variable name so that the
variable can be used in subsequent input script commands. The "name"
of the variable is an arbitrary string. Each "value" is a string
which could be text or numbers, as in the examples above. As
explained in "this section"_Section_commands.html#3_2, occurrences of
the variable name in an input script line are replaced by the
variable can be used in subsequent input script commands or its value
output during a simulation. The "name" of the variable is an
arbitrary string. Each "value" is a string which could be text or
numbers, as in the examples above.
As explained in "this section"_Section_commands.html#3_2, occurrences
of the variable name in an input script line are replaced by the
variable's value. The variable name can be referenced in the input
script as $x if the name "x" is a single character, or as $\{LoopVar\}
if the name "LoopVar" is one or more characters.
Variable values can also be accessed for output once or periodically
during a simulation by the "print"_print.html command, "fix
print"_fix_print.html command, "run every"_run.html command, and the
"thermo_style"_thermo_style.html command.
:line
As described below, for variable styles {index}, {loop}, {universe},
and {uloop}, the value assigned to a variable can be incremented via
the "next"_next.html command. When there are no more values to
@ -73,13 +86,15 @@ equal-style variable is encountered. Also, if a variable is iterated
on to the end of its list via the "next"_next.html command, it is
available to be re-defined in a subsequent variable command.
:line
For the {index} style, one or more strings are specified. Initially,
the 1st string is assigned to the variable. Each time a
"next"_next.html command is used with the variable name, the next
string is assigned. All processors assign the same string to the
variable. {Index}-style variables can also be set (with a single
value) by using the command-line switch -var; see "this
section"_Section_start.html#2_4 for details.
section"_Section_start.html#2_6 for details.
The {loop} style is identical to the {index} style except that the
strings are the integers from 1 to N. This allows you to generate a
@ -89,66 +104,9 @@ Each time a "next"_next.html command is used with the variable name,
the next string ("2", "3", etc) is assigned. All processors assign
the same string to the variable.
For the {equal} style, a single string is specified which represents
an equation that will be evaluated afresh each time the variable is
used. Thus the variable can take on different values at different
stages of the input script. For example, if the variable is used in a
"fix print"_fix_print.html command, it could print different values
each timestep it was invoked. The next command cannot be used with
{equal}-style variables, since there is only one value. Note that, as
with any other input script command, it is feasible to use another
variable in the {equal} variable's string, e.g. variable y equal
mult($x,2). However, $x will be replaced immediately by it's current
value when the command is first parsed, not each time that $y is
substituted for.
The syntax of the equation assigned to {equal} variables is simple.
It can contain "functions", "vectors", "keywords", or "numbers" in any
combination.
Function = a keyword followed by parenthesis with one or two arguments
Supported arithmetic functions = add(x,y), sub(x,y), mult(x,y), div(x,y), \
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
Supported group functions = mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), \
bound(ID,dir), gyration(ID)
Example function usage = div(1.0e20,3.0), neg(x\[34\]), pow(lx,3.0), \
xcm(mol,x), bound(lower,zmin)
Vector = a keyword followed by square brackets containing an atom ID
Supported vectors = x, y, z, vx, vy, vz, fx, fy, fz
Example vector usage = x\[123\], fz\[1000\]
Keyword = any keyword supported by the \
"thermo_style custom"_thermo_style.html \
command except cpu, pressure tensor components (pxx, pyy, etc), \
time-averaged quantities (tave, pave, etc)
Example keyword usage = atoms, pow(vol,0.333), mult(elong,0.5)
Number = 0.2, 1.0e20, -15.4, etc :ul
For the group functions, ID is a group-ID, dim is 'x' or 'y' or 'z',
and dir is one of 6 strings: "xmin", "xmax", "ymin", "ymax", "zmin",
or "zmax". The group functions mass() and charge() are the total mass
and charge of the group of atoms. Xcm() and vcm() return components
of the position and velocity of the center of mass of the group.
Bound() returns the min/max of a particular coordinate for all atoms
in the group. Gyration() computes the radius-of-gyration of the group
of atoms. See the "fix gyration"_fix_gyration.html command for the
formula.
Keywords have restrictions on when they can be assigned to variables.
For example, keywords that compute thermodynamic quantites can only be
invoked after the first simulation has begun. A warning is issued if
thermodyanmic keywords are invoked on timesteps when thermodynamic
information is not being printed to the screen, since the values
assigned to the variable may be out-of-date.
The variable {equal} equation can also be nested in that function
arguments can be functions, vectors, keywords, or numbers. For
example, this is a valid equation:
variable x equal div(add(pe,ke),pow(vol,div(1,3))) :pre
For the {world} style, one or more strings are specified. There must
be one string for each processor partition or "world". See "this
section"_Section_start.html#2_4 of the manual for information on
section"_Section_start.html#2_6 of the manual for information on
running LAMMPS with multiple partitions via the "-partition"
command-line switch. This variable command assigns one string to each
world. All processors in the world are assigned the same string. The
@ -161,7 +119,7 @@ different partitions.
For the {universe} style, one or more strings are specified. There
must be at least as many strings as there are processor partitions or
"worlds". See "this page"_Section_start.html#2_4 for information on
"worlds". See "this page"_Section_start.html#2_6 for information on
running LAMMPS with multiple partitions via the "-partition"
command-line switch. This variable command initially assigns one
string to each world. When a "next"_next.html command is encountered
@ -179,11 +137,118 @@ strings are the integers from 1 to N. This allows you to generate a
long list of runs (e.g. 1000) without having to list N values in your
input script.
:line
For the {equal} style, a single string is specified which represents
an equation that will be evaluated afresh each time the variable is
used. Thus the variable can take on different values at different
stages of the input script. For example, if the variable is used in a
"fix print"_fix_print.html command, different values could be printed
each timestep it was invoked. The next command cannot be used with
{equal}-style variables, since there is only one value.
The equation for an {equal}-style variable can contain a variety of
quantities. The syntax for each kind of quantity is simple, but
multiple quantities can be nested and combined in various ways to
build up formulas of arbitrary complexity. For example, this is a
valid (though strange) variable equation:
variable x equal div(add(pe,c_MyTemp\[0\]),pow(vol,div(1,3))) :pre
Specifically, an equation can contain numbers, thermo keywords, math
functions, group functions, atom vectors, compute references, and
other variables:
Number: 0.2, 1.0e20, -15.4, etc
Thermo keywords: vol, pe, ebond, etc
Math functions: add(x,y), sub(x,y), mult(x,y), div(x,y), \
neg(x), pow(x,y), exp(x), ln(x), sqrt(x)
Group functions: mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), \
bound(ID,dir), gyration(ID)
Atom vectors: x\[N\], y\[N\], z\[N\], vx\[N\], vy\[N\], vz\[N\], \
fx\[N\], fy\[N\], fz\[N\]
Compute references: c_ID\[0\], c_ID\[N\]
Other variables: v_abc, v_x, etc :tb(s=:)
The thermo keywords allowed in the equation are those defined by the
"thermo_style custom" command. Note that many thermodyanmic
quantities are only computable after the first simulation has begun.
Likewise, many thermodynamic quantities (such as energies) are only
computed on timesteps when thermodyanmic output is being performed.
If the variable equation these quantities at other times, out-of-date
or invalid values may be used.
Math functions take one or two arguments, each of which may be an
equation containing any of the quantities defined above. This allows
equations to be nested, as in the examples above.
Group functions take one or two arguments. The first argument is the
group-ID. The {dim} argument is {x} or {y} or {z}. The {dir}
argument is {xmin}, {xmax}, {ymin}, {ymax}, {zmin}, or {zmax}. The
group functions mass() and charge() are the total mass and charge of
the group of atoms. Xcm() and vcm() return components of the position
and velocity of the center of mass of the group. Bound() returns the
min/max of a particular coordinate for all atoms in the group.
Gyration() computes the radius-of-gyration of the group of atoms. See
the "fix gyration"_fix_gyration.html command for the formula.
The atom vectors take a single integer argument from 1-N, which
is the desired atom-ID, e.g. x\[243\].
Compute references access allow access to scalar or vector quantities
calculated by a compute. The ID in the reference should be replaced
by the actual ID of the compute that has been defined elsewhere in the
input script. See the "compute"_compute.html command for details.
Note that per-atom quantities calcalated by a compute cannot be
accessed this way, but only global scalar or vector quantities.
If {c_ID\[0\]} is used as a keyword, then the scalar quantity
calculated by the compute is printed. If {c_ID\[N\]} is used, then N
in the range from 1-M will print a specific component of the vector
calculated by the compute.
The current values of other variables can be accessed by prepending a
"v_" to the variable name. This will cause the other variable to be
evaulated. Note that if you do something circular like this:
variable a equal v_b
variable b equal v_a
print $a :pre
then LAMMPS will run for a while when the print statement is invoked.
Note that there is a subtle difference between using a variable
in a {equal}-style equation in the form $x versus v_x.
In the former case, as with any other input script command, the
variable's value is substituted for immediately when the line is read
from the input script. Thus if the current simulation box volume was
1000.0, then these lines:
variable x equal vol
variable y equal mult($x,2) :pre
would associate the equation string "mult(1000.0,2)" with variable y.
By contrast, these lines:
variable x equal vol
variable y equal mult(v_x,2) :pre
would associate the equation string "mult(v_x,2)" with variable y.
Thus if the variable y were evaluated periodically during a run where
the box volume changed, the resulting value would always be 500.0 for
the first case, but would change dynamically for the second case.
:line
[Restrictions:]
The use of atom vectors in {equal} style variables requires the atom
style to use a global mapping in order to look up the vector indices.
Only atom styles with molecular information create global maps.
Only atom styles with molecular information create global maps unless
the "atom_modify map"_atom_modify.html command is used.
[Related commands:]