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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@150 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2006-11-13 22:18:34 +00:00
parent ecaf8734e1
commit ac60b08b69
14 changed files with 492 additions and 159 deletions
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31
doc/Section_commands.html
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@ -161,10 +161,10 @@ or restart file via the <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
<A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>, <A HREF = "region.html">region</A>,
<A HREF = "create_box.html">create_box</A>, <A HREF = "create_atoms.html">create_atoms</A>. The
entire set of atoms can be duplicated to make a larger simulation
using the <A HREF = "replicate.html">replicate</A> command.
<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
duplicated to make a larger simulation using the
<A HREF = "replicate.html">replicate</A> command.
</P>
<P>(3) Settings
</P>
@ -222,9 +222,9 @@ in the command's documentation.
<P>Atom definition:
</P>
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "lattice.html">lattice</A>, <A HREF = "orient.html">orient</A>, <A HREF = "origin.html">origin</A>,
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, <A HREF = "region.html">region</A>,
<A HREF = "replicate.html">replicate</A>
</P>
<P>Force fields:
</P>
@ -293,13 +293,12 @@ in the command's documentation.
<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 = "orient.html">orient</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "origin.html">origin</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 = "temp_modify.html">temp_modify</A></TD><TD ><A HREF = "temper.html">temper</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "write_restart.html">write_restart</A>
<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>
</TD></TR></TABLE></DIV>
<P>Fix styles. See the <A HREF = "fix.html">fix</A> command for one-line descriptions
@ -312,8 +311,8 @@ or click on the command itself for a full description:
<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_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><TD ><A HREF = "fix_shake.html">fix shake</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "fix_uniaxial.html">fix uniaxial</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wiggle.html">fix wiggle</A>
<TR ALIGN="center"><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><TD ><A HREF = "fix_wall_lj126.html">fix wall/lj126</A></TD></TR>
<TR ALIGN="center"><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>
<P>Pair styles. See the <A HREF = "pair_style.html">pair_style</A> command for an