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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9741 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2013-04-03 17:06:31 +00:00
parent cbc01e5758
commit 984b4c962b
10 changed files with 175 additions and 7 deletions
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4
doc/Section_commands.html
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@ -306,7 +306,7 @@ 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_restart.html">write_restart</A>
<A HREF = "write_data.html">write_data</A>, <A HREF = "write_restart.html">write_restart</A>
</P>
<P>Actions:
</P>
@ -350,7 +350,7 @@ 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_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_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<HR>

3
doc/Section_commands.txt
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@ -302,7 +302,7 @@ 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_restart"_write_restart.html
"write_data"_write_data.html, "write_restart"_write_restart.html
Actions:
@ -416,6 +416,7 @@ in the command's documentation.
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_data"_write_data.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
:line

7
doc/Section_tools.html
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@ -402,6 +402,13 @@ the README.txt file for more info.
<H4><A NAME = "restart"></A>restart2data tool
</H4>
<P>IMPORTANT NOTE: LAMMPS now has a <A HREF = "write_data.html">write_data</A> command,
which can create a data file from within an input script. This means
a two line input script can read a restart file, and write it as a
data file. When the write_data command is fully functional, the
restart2data tool will be obsolete, and will be retired from the
distribution.
</P>
<P>The file restart2data.cpp converts a binary LAMMPS restart file into
an ASCII data file. The syntax for running the tool is
</P>

7
doc/Section_tools.txt
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@ -398,6 +398,13 @@ These tools were written by Aidan Thompson at Sandia.
restart2data tool :h4,link(restart)
IMPORTANT NOTE: LAMMPS now has a "write_data"_write_data.html command,
which can create a data file from within an input script. This means
a two line input script can read a restart file, and write it as a
data file. When the write_data command is fully functional, the
restart2data tool will be obsolete, and will be retired from the
distribution.
The file restart2data.cpp converts a binary LAMMPS restart file into
an ASCII data file. The syntax for running the tool is

2
doc/read_data.html
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@ -911,7 +911,7 @@ LAMMPS</A> section of the documentation.
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "create_atoms.html">create_atoms</A>
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "write_data.html">write_data</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/read_data.txt
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@ -806,6 +806,6 @@ LAMMPS"_Section_start.html#start_2 section of the documentation.
[Related commands:]
"read_dump"_read_dump.html, "read_restart"_read_restart.html,
"create_atoms"_create_atoms.html
"create_atoms"_create_atoms.html, "write_data"_write_data.html
[Default:] none

78
doc/write_data.html Normal file
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@ -0,0 +1,78 @@
<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_data command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>write_data file
</PRE>
<UL><LI>file = name of data file to write out
</UL>
<P><B>Examples:</B>
</P>
<PRE>write_data data.polymer
</PRE>
<P><B>Description:</B>
</P>
<P>Write a text data file of the current state of the simulation.
</P>
<P>During a long simulation, the <A HREF = "restart.html">restart</A> command is
typically used to dump restart files periodically. The write_restart
command is useful after a minimization or whenever you wish to write
out a single current restart file.
</P>
<P>Similar to <A HREF = "dump.html">dump</A> files, the restart filename can contain
two wild-card characters. If a "*" appears in the filename, it is
replaced with the current timestep value. If a "%" character appears
in the filename, then one file is written by each processor and the
"%" character is replaced with the processor ID from 0 to P-1. An
additional file with the "%" replaced by "base" is also written, which
contains global information. For example, the files written for
filename restart.% would be restart.base, restart.0, restart.1, ...
restart.P-1. This creates smaller files and can be a fast mode of
output and subsequent input on parallel machines that support parallel
I/O.
</P>
<P>Restart files can be read by a <A HREF = "read_restart.html">read_restart</A>
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, the restart2data program in the tools
directory can be used to convert a restart file to an ASCII data file.
Both the read_restart command and restart2data tool can read in a
restart file that was written with the "%" character so that multiple
files were created.
</P>
<P>IMPORTANT NOTE: Although the purpose of restart files is to enable
restarting a simulation from where it left off, not all information
about a simulation is stored in the file. For example, the list of
fixes that were specified during the initial run is not stored, which
means the new input script must specify any fixes you want to use.
Even when restart information is stored in the file, as it is for some
fixes, commands may need to be re-specified in the new input script,
in order to re-use that information. See the
<A HREF = "read_restart.html">read_restart</A> command for information about what is
stored in a restart file.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command requires inter-processor communication to migrate atoms
before the data file is written. This means that your system must be
ready to perform a simulation before using this command (force fields
setup, atom masses initialized, etc).
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "write_restart.html">write_restart</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

73
doc/write_data.txt Normal file
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@ -0,0 +1,73 @@
"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_data command :h3
[Syntax:]
write_data file :pre
file = name of data file to write out :ul
[Examples:]
write_data data.polymer :pre
[Description:]
Write a text data file of the current state of the simulation.
During a long simulation, the "restart"_restart.html command is
typically used to dump restart files periodically. The write_restart
command is useful after a minimization or whenever you wish to write
out a single current restart file.
Similar to "dump"_dump.html files, the restart filename can contain
two wild-card characters. If a "*" appears in the filename, it is
replaced with the current timestep value. If a "%" character appears
in the filename, then one file is written by each processor and the
"%" character is replaced with the processor ID from 0 to P-1. An
additional file with the "%" replaced by "base" is also written, which
contains global information. For example, the files written for
filename restart.% would be restart.base, restart.0, restart.1, ...
restart.P-1. This creates smaller files and can be a fast mode of
output and subsequent input on parallel machines that support parallel
I/O.
Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, the restart2data program in the tools
directory can be used to convert a restart file to an ASCII data file.
Both the read_restart command and restart2data tool can read in a
restart file that was written with the "%" character so that multiple
files were created.
IMPORTANT NOTE: Although the purpose of restart files is to enable
restarting a simulation from where it left off, not all information
about a simulation is stored in the file. For example, the list of
fixes that were specified during the initial run is not stored, which
means the new input script must specify any fixes you want to use.
Even when restart information is stored in the file, as it is for some
fixes, commands may need to be re-specified in the new input script,
in order to re-use that information. See the
"read_restart"_read_restart.html command for information about what is
stored in a restart file.
[Restrictions:]
This command requires inter-processor communication to migrate atoms
before the data file is written. This means that your system must be
ready to perform a simulation before using this command (force fields
setup, atom masses initialized, etc).
[Related commands:]
"read_data"_read_data.html, "write_restart"_write_restart.html
[Default:] none

3
doc/write_restart.html
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@ -72,7 +72,8 @@ fields setup, atom masses initialized, etc).
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "restart.html">restart</A>, <A HREF = "read_restart.html">read_restart</A>
<P><A HREF = "restart.html">restart</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "write_data.html">write_data</A>
</P>
<P><B>Default:</B> none
</P>

3
doc/write_restart.txt
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@ -69,6 +69,7 @@ fields setup, atom masses initialized, etc).
[Related commands:]
"restart"_restart.html, "read_restart"_read_restart.html
"restart"_restart.html, "read_restart"_read_restart.html,
"write_data"_write_data.html
[Default:] none