From 22c1957a2c2a8fe057bdedcf8bbec55a2c921bc7 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 2 Nov 2013 00:02:27 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10917
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.html |   5 +-
 doc/Section_commands.txt  |   4 +-
 doc/velocity.html         |   2 +-
 doc/velocity.txt          |   2 +-
 doc/write_dump.html       | 101 ++++++++++++++++++++++++++++++++++++++
 doc/write_dump.txt        |  89 +++++++++++++++++++++++++++++++++
 6 files changed, 198 insertions(+), 5 deletions(-)
 create mode 100644 doc/write_dump.html
 create mode 100644 doc/write_dump.txt

diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index 0e33a986f3..033506abbd 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -317,7 +317,8 @@ in the command's documentation.
 <A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "restart.html">restart</A>,
 <A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_modify.html">thermo_modify</A>,
 <A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "undump.html">undump</A>,
-<A HREF = "write_data.html">write_data</A>, <A HREF = "write_restart.html">write_restart</A>
+<A HREF = "write_data.html">write_data</A>, <A HREF = "write_dump.html">write_dump</A>,
+<A HREF = "write_restart.html">write_restart</A>
 </P>
 <P>Actions:
 </P>
@@ -361,7 +362,7 @@ in the command's documentation.
 <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 = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><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></TR>
 <TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</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></TR>
-<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_restart.html">write_restart</A> 
+<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD><TD ><A HREF = "write_restart.html">write_restart</A> 
 </TD></TR></TABLE></DIV>
 
 <P>These are commands contributed by users, which can be used if <A HREF = "Section_start.html#start_3">LAMMPS
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 082ef2c076..9f61187228 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -313,7 +313,8 @@ Output:
 "dump_modify"_dump_modify.html, "restart"_restart.html,
 "thermo"_thermo.html, "thermo_modify"_thermo_modify.html,
 "thermo_style"_thermo_style.html, "undump"_undump.html,
-"write_data"_write_data.html, "write_restart"_write_restart.html
+"write_data"_write_data.html, "write_dump"_write_dump.html,
+"write_restart"_write_restart.html
 
 Actions:
 
@@ -428,6 +429,7 @@ in the command's documentation.
 "variable"_variable.html,
 "velocity"_velocity.html,
 "write_data"_write_data.html,
+"write_dump"_write_dump.html,
 "write_restart"_write_restart.html :tb(c=6,ea=c)
 
 These are commands contributed by users, which can be used if "LAMMPS
diff --git a/doc/velocity.html b/doc/velocity.html
index 372b008ca7..69afb8b6ca 100644
--- a/doc/velocity.html
+++ b/doc/velocity.html
@@ -13,7 +13,7 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>velocity group-ID style args keyword args ... 
+<PRE>velocity group-ID style args keyword value ... 
 </PRE>
 <UL><LI>group-ID = ID of group of atoms whose velocity will be changed 
 
diff --git a/doc/velocity.txt b/doc/velocity.txt
index 8e8615e4dc..b2f18c0dbe 100644
--- a/doc/velocity.txt
+++ b/doc/velocity.txt
@@ -10,7 +10,7 @@ velocity command :h3
 
 [Syntax:]
 
-velocity group-ID style args keyword args ... :pre
+velocity group-ID style args keyword value ... :pre
 
 group-ID = ID of group of atoms whose velocity will be changed :ulb,l
 style = {create} or {set} or {scale} or {ramp} or {zero} :l
diff --git a/doc/write_dump.html b/doc/write_dump.html
new file mode 100644
index 0000000000..a375eec63b
--- /dev/null
+++ b/doc/write_dump.html
@@ -0,0 +1,101 @@
+<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>write_dump command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>write_dump ID group-ID style N file dump-args modify dump-modify-args 
+</PRE>
+<UL><LI>ID = user-assigned name for the dump (ignored) 
+
+<LI>group-ID = ID of the group of atoms to be dumped 
+
+<LI>style = any of the supported <A HREF = "dump.html">dump styles</A> 
+
+<LI>N = dump every this many timesteps (ignored) 
+
+<LI>file = name of file to write dump info to 
+
+<LI>dump-args = any additional args needed for a particular <A HREF = "dump.html">dump style</A> 
+
+<LI>modify = all args after this keyword are passed to <A HREF = "dump_modify.html">dump_modify</A> (optional) 
+
+<LI>dump-modify-args = args for <A HREF = "dump_modify.html">dump_modify</A> (optional) 
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>write_dump 1 all atom 0 dump.atom
+write_dump 1 subgroup atom 0 dump.run.bin
+write_dump 1 all custom 0 dump.myforce.* id type x y vx fx
+write_dump 1 flow custom 0 dump.%.myforce id type c_myF[3] v_ke modify sort id
+write_dump 1 all xyz 0 system.xyz modify sort id elements O H 
+write_dump 1 all image 0 snap*.jpg type type size 960 960 modify backcolor white
+write_dump 1 all image 0 snap*.jpg element element &
+   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
+   modify backcolor white element C C O H N C C C O H H S O H 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Dump a single snapshot of atom quantities to one or more files for the
+current state of the system.  This is a one-time operation, in
+contrast to the <A HREF = "dump.html">dump</A> command which will write out multiple
+snapshots periodically during a running simulation.
+</P>
+<P>The syntax for this command is identical to that of the
+<A HREF = "dump.html">dump</A> and <A HREF = "dump_modify.html">dump_modify</A> commands as if
+they were concatenated together, with one exception.  This is so that
+the full range of <A HREF = "dump_modify.html">dump_modify</A> options can be
+specified for the single snapshot, just as they can be for multiple
+snapshots.  The syntax exception is that if a second set of
+dump-modify-args is specified, they must be preceeded by the "modify"
+keyword, so that LAMMPS can cleanly separate the two sets of args.
+</P>
+<P>Note that the dump ID and frequency <I>N</I> arguments are ignored, since
+they are irrelevant when only a single snapshot is being written.
+</P>
+<P>Also note that if the specified filename uses the wildcard characters
+"*" or "%", as supported by the <A HREF = "dump.html">dump</A> commmand, they will
+operate in the same fashion to create the new filename(s).
+</P>
+<HR>
+
+<P><B>Restrictions:</B>
+</P>
+<P>All restrictions for the <A HREF = "dump.html">dump</A> and
+<A HREF = "dump_modify.html">dump_modify</A> commands apply to this command as well.
+For the <A HREF = "dump_image.html">dump image</A> dump style, this means the
+filename is required to contain a '*' character, which will be
+replaced by the current timestep.
+</P>
+<P>Since dumps are normally written during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy
+minimization</A>, the simulation has to be ready to run
+before this command can be used.  Similarly, if the dump requires
+information from a compute, fix, or variable, the information needs to
+have been calculated for the current timestep (e.g. by a prior run),
+else LAMMPS will generate an error message.
+</P>
+<P>For example, it is not possible to dump per-atom energy with this
+command before a run has been performed, since no energies and forces
+have yet been calculated.  See the <A HREF = "variable.html">variable</A> doc page
+sectinn on Variable Accuracy for more information on this topic.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>, <A HREF = "dump_modify.html">dump_modify</A>
+</P>
+<P><B>Default:</B>
+</P>
+<P>The defaults are listed on the doc pages for the <A HREF = "dump.html">dump</A> and
+<A HREF = "dump_image.html">dump image</A> and <A HREF = "dump_modify.html">dump_modify</A>
+commands.
+</P>
+</HTML>
diff --git a/doc/write_dump.txt b/doc/write_dump.txt
new file mode 100644
index 0000000000..7ec1268cff
--- /dev/null
+++ b/doc/write_dump.txt
@@ -0,0 +1,89 @@
+ "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
+   
+write_dump command :h3
+
+[Syntax:]
+
+write_dump ID group-ID style N file dump-args modify dump-modify-args :pre
+
+ID = user-assigned name for the dump (ignored) :ulb,l
+group-ID = ID of the group of atoms to be dumped :l
+style = any of the supported "dump styles"_dump.html :l
+N = dump every this many timesteps (ignored) :l
+file = name of file to write dump info to :l
+dump-args = any additional args needed for a particular "dump style"_dump.html :l
+modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l
+dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l,ule
+
+[Examples:]
+
+write_dump 1 all atom 0 dump.atom
+write_dump 1 subgroup atom 0 dump.run.bin
+write_dump 1 all custom 0 dump.myforce.* id type x y vx fx
+write_dump 1 flow custom 0 dump.%.myforce id type c_myF\[3\] v_ke modify sort id
+write_dump 1 all xyz 0 system.xyz modify sort id elements O H 
+write_dump 1 all image 0 snap*.jpg type type size 960 960 modify backcolor white
+write_dump 1 all image 0 snap*.jpg element element &
+   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
+   modify backcolor white element C C O H N C C C O H H S O H :pre
+
+[Description:]
+
+Dump a single snapshot of atom quantities to one or more files for the
+current state of the system.  This is a one-time operation, in
+contrast to the "dump"_dump.html command which will write out multiple
+snapshots periodically during a running simulation.
+
+The syntax for this command is identical to that of the
+"dump"_dump.html and "dump_modify"_dump_modify.html commands as if
+they were concatenated together, with one exception.  This is so that
+the full range of "dump_modify"_dump_modify.html options can be
+specified for the single snapshot, just as they can be for multiple
+snapshots.  The syntax exception is that if a second set of
+dump-modify-args is specified, they must be preceeded by the "modify"
+keyword, so that LAMMPS can cleanly separate the two sets of args.
+
+Note that the dump ID and frequency {N} arguments are ignored, since
+they are irrelevant when only a single snapshot is being written.
+
+Also note that if the specified filename uses the wildcard characters
+"*" or "%", as supported by the "dump"_dump.html commmand, they will
+operate in the same fashion to create the new filename(s).
+
+:line
+
+[Restrictions:]
+
+All restrictions for the "dump"_dump.html and
+"dump_modify"_dump_modify.html commands apply to this command as well.
+For the "dump image"_dump_image.html dump style, this means the
+filename is required to contain a '*' character, which will be
+replaced by the current timestep.
+
+Since dumps are normally written during a "run"_run.html or "energy
+minimization"_minimize.html, the simulation has to be ready to run
+before this command can be used.  Similarly, if the dump requires
+information from a compute, fix, or variable, the information needs to
+have been calculated for the current timestep (e.g. by a prior run),
+else LAMMPS will generate an error message.
+
+For example, it is not possible to dump per-atom energy with this
+command before a run has been performed, since no energies and forces
+have yet been calculated.  See the "variable"_variable.html doc page
+sectinn on Variable Accuracy for more information on this topic.
+
+[Related commands:]
+
+"dump"_dump.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html
+
+[Default:]
+
+The defaults are listed on the doc pages for the "dump"_dump.html and
+"dump image"_dump_image.html and "dump_modify"_dump_modify.html
+commands.