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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2887 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-06-22 21:17:38 +00:00
parent fd89022784
commit a9318bc28e
6 changed files with 130 additions and 5 deletions
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8
doc/Section_commands.html
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@ -322,10 +322,10 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</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></TR>
<TR ALIGN="center"><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><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_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><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><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
<TR ALIGN="center"><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><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_berendsen.html">temp/berendsen</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</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>These are fix styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -422,6 +422,7 @@ of each style or click on the style itself for a full description:
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"rdf"_fix_rdf.html,
"reax/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"rigid"_fix_rigid.html,
"setforce"_fix_setforce.html,

2
doc/fix.html
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@ -150,7 +150,7 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by Berendsen barostat
<LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
<LI><A HREF = "fix_rdf.html">rdf</A> - compute radial distribution functions
<LI><A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms
<LI><A HREF = "fix_reax_bonds.html">reax/bonds</A> - write out ReaxFF bond information <A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms
<LI><A HREF = "fix_rigid.html">rigid</A> - constrain one or more clusters of atoms to move as a rigid body
<LI><A HREF = "fix_setforce.html">setforce</A> - set the force on each atom
<LI><A HREF = "fix_shake.html">shake</A> - SHAKE constraints on bonds and/or angles

1
doc/fix.txt
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@ -151,6 +151,7 @@ list of fix styles available in LAMMPS:
Berendsen barostat
"print"_fix_print.html - print text and variables during a simulation
"rdf"_fix_rdf.html - compute radial distribution functions
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
"recenter"_fix_recenter.html - constrain the center-of-mass position \
of a group of atoms
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \

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doc/fix_reax_bonds.html Normal file
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@ -0,0 +1,64 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix reax/bonds command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID reax/bonds Nevery filename
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>reax/bonds = style name of this fix command
<LI>Nevery = output interval in timesteps
<LI>filename = name of output file
</UL>
<P><B>Examples:</B>
</P>
<P>fix 1 all reax/bonds 100 bonds.tatb
</P>
<P><B>Description:</B>
</P>
<P>Write out the bond information computed by the ReaxFF potential
specified by <A HREF = "pair_reax.html">pair_style reax</A>. The bond information
is written to <I>filename</I> on timesteps that are multiples of <I>Nevery</I>,
including timestep 0.
</P>
<P>The format of the output file should be self-explantory.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. No parameter of this fix can be
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix requires that the <A HREF = "pair_reax.html">pair_style reax</A> be
invoked. This fix is part of the "reax" package. It is only enabled
if LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. 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 = "pair_reax.html">pair_style reax</A>
</P>
<P><B>Default:</B>
</P>
<P>none
</P>
</HTML>

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doc/fix_reax_bonds.txt Normal file
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@ -0,0 +1,59 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix reax/bonds command :h3
[Syntax:]
fix ID group-ID reax/bonds Nevery filename :pre
ID, group-ID are documented in "fix"_fix.html command
reax/bonds = style name of this fix command
Nevery = output interval in timesteps
filename = name of output file :ul
[Examples:]
fix 1 all reax/bonds 100 bonds.tatb
[Description:]
Write out the bond information computed by the ReaxFF potential
specified by "pair_style reax"_pair_reax.html. The bond information
is written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0.
The format of the output file should be self-explantory.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
commands"_Section_howto.html#4_15. No parameter of this fix can be
used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that the "pair_style reax"_pair_reax.html be
invoked. This fix is part of the "reax" package. It is only enabled
if LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
"pair_style reax"_pair_reax.html
[Default:]
none