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84
doc/write_data.html
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@ -19,48 +19,62 @@
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>write_data data.polymer <PRE>write_data data.polymer
write_data data.*
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Write a text data file of the current state of the simulation. <P>Write a data file in text format of the current state of the
simulation. Data files can be read by the <A HREF = "read_data.html">read data</A>
command to begin a simulation. The <A HREF = "read_data.html">read_data</A> command
also describes their format.
</P> </P>
<P>During a long simulation, the <A HREF = "restart.html">restart</A> command is <P>Similar to <A HREF = "dump.html">dump</A> files, the data filename can contain a "*"
typically used to dump restart files periodically. The write_restart wild-card character. The "*" is replaced with the current timestep
command is useful after a minimization or whenever you wish to write value.
out a single current restart file.
</P> </P>
<P>Similar to <A HREF = "dump.html">dump</A> files, the restart filename can contain <P>IMPORTANT NOTE: The write-data command is not yet fully implemented in
two wild-card characters. If a "*" appears in the filename, it is two respects. First, most pair, bond, angle, dihedral, improper
replaced with the current timestep value. If a "%" character appears styles do not yet write their coefficient information into the data
in the filename, then one file is written by each processor and the file. This means you will need to specify that information in your
"%" character is replaced with the processor ID from 0 to P-1. An input script that reads the data file, e.g. with the
additional file with the "%" replaced by "base" is also written, which <A HREF = "pair_coeff.html">pair_coeff</A> command. Second, a few of the <A HREF = "atom_style.html">atom
contains global information. For example, the files written for styles</A> (body, ellipsoid, line, tri) that store
filename restart.% would be restart.base, restart.0, restart.1, ... auxiliary "bonus" information about aspherical particles, do not yet
restart.P-1. This creates smaller files and can be a fast mode of write the bonus info into the data file. Both these functionalities
output and subsequent input on parallel machines that support parallel will be added to the write_data command later.
I/O.
</P> </P>
<P>Restart files can be read by a <A HREF = "read_restart.html">read_restart</A> <P>Because a data file is in text format, if you use a data file written
command to restart a simulation from a particular state. Because the out by this command to restart a simulation, the initial state of the
file is binary (to enable exact restarts), it may not be readable on new run will be slightly different than the final state of the old run
another machine. In this case, the restart2data program in the tools (when the file was written) which was represented internally by LAMMPS
directory can be used to convert a restart file to an ASCII data file. in binary format. A new simulation which reads the data file will
Both the read_restart command and restart2data tool can read in a thus typically diverge from a simulation that continued in the
restart file that was written with the "%" character so that multiple original input script.
files were created.
</P> </P>
<P>IMPORTANT NOTE: Although the purpose of restart files is to enable <P>If you want to do more exact restarts, using binary files, see the
restarting a simulation from where it left off, not all information <A HREF = "restart.html">restart</A>, <A HREF = "write_restart.html">write_restart</A>, and
about a simulation is stored in the file. For example, the list of <A HREF = "read_restart.html">read_restart</A> commands. You can also convert
fixes that were specified during the initial run is not stored, which binary restart files to text data files, after a simulation has run,
means the new input script must specify any fixes you want to use. using the <A HREF = "Section_tools.html#restart2data">restart2data</A> tool in the
Even when restart information is stored in the file, as it is for some tools directory. When the write_data command is fully implemented
fixes, commands may need to be re-specified in the new input script, (see NOTE above), the restart2data command will be obsolete and will
in order to re-use that information. See the be removed from the LAMMPS distribution.
<A HREF = "read_restart.html">read_restart</A> command for information about what is </P>
stored in a restart file. <P>IMPORTANT NOTE: Only limited information about a simulation is stored
in a data file. For example, no information about atom
<A HREF = "group.html">groups</A> and <A HREF = "fix.html">fixes</A> are stored. <A HREF = "read_restart.html">Binary restart
files</A> store more information.
</P>
<P>Bond interactions (angle, etc) that have been turned off by the <A HREF = "fix_shake.html">fix
shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> command will
be written to a data file as if they are turned on. This means they
will need to be turned off again in a new run after the data file is
read.
</P>
<P>Bonds that are broken (e.g. by a bond-breaking potential) are not
written to the data file. Thus these bonds will not exist when the
data file is read.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>

84
doc/write_data.txt
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@ -16,48 +16,62 @@ file = name of data file to write out :ul
[Examples:] [Examples:]
write_data data.polymer :pre write_data data.polymer
write_data data.* :pre
[Description:] [Description:]
Write a text data file of the current state of the simulation. Write a data file in text format of the current state of the
simulation. Data files can be read by the "read data"_read_data.html
command to begin a simulation. The "read_data"_read_data.html command
also describes their format.
During a long simulation, the "restart"_restart.html command is Similar to "dump"_dump.html files, the data filename can contain a "*"
typically used to dump restart files periodically. The write_restart wild-card character. The "*" is replaced with the current timestep
command is useful after a minimization or whenever you wish to write value.
out a single current restart file.
Similar to "dump"_dump.html files, the restart filename can contain IMPORTANT NOTE: The write-data command is not yet fully implemented in
two wild-card characters. If a "*" appears in the filename, it is two respects. First, most pair, bond, angle, dihedral, improper
replaced with the current timestep value. If a "%" character appears styles do not yet write their coefficient information into the data
in the filename, then one file is written by each processor and the file. This means you will need to specify that information in your
"%" character is replaced with the processor ID from 0 to P-1. An input script that reads the data file, e.g. with the
additional file with the "%" replaced by "base" is also written, which "pair_coeff"_pair_coeff.html command. Second, a few of the "atom
contains global information. For example, the files written for styles"_atom_style.html (body, ellipsoid, line, tri) that store
filename restart.% would be restart.base, restart.0, restart.1, ... auxiliary "bonus" information about aspherical particles, do not yet
restart.P-1. This creates smaller files and can be a fast mode of write the bonus info into the data file. Both these functionalities
output and subsequent input on parallel machines that support parallel will be added to the write_data command later.
I/O.
Restart files can be read by a "read_restart"_read_restart.html Because a data file is in text format, if you use a data file written
command to restart a simulation from a particular state. Because the out by this command to restart a simulation, the initial state of the
file is binary (to enable exact restarts), it may not be readable on new run will be slightly different than the final state of the old run
another machine. In this case, the restart2data program in the tools (when the file was written) which was represented internally by LAMMPS
directory can be used to convert a restart file to an ASCII data file. in binary format. A new simulation which reads the data file will
Both the read_restart command and restart2data tool can read in a thus typically diverge from a simulation that continued in the
restart file that was written with the "%" character so that multiple original input script.
files were created.
IMPORTANT NOTE: Although the purpose of restart files is to enable If you want to do more exact restarts, using binary files, see the
restarting a simulation from where it left off, not all information "restart"_restart.html, "write_restart"_write_restart.html, and
about a simulation is stored in the file. For example, the list of "read_restart"_read_restart.html commands. You can also convert
fixes that were specified during the initial run is not stored, which binary restart files to text data files, after a simulation has run,
means the new input script must specify any fixes you want to use. using the "restart2data"_Section_tools.html#restart2data tool in the
Even when restart information is stored in the file, as it is for some tools directory. When the write_data command is fully implemented
fixes, commands may need to be re-specified in the new input script, (see NOTE above), the restart2data command will be obsolete and will
in order to re-use that information. See the be removed from the LAMMPS distribution.
"read_restart"_read_restart.html command for information about what is
stored in a restart file. IMPORTANT NOTE: Only limited information about a simulation is stored
in a data file. For example, no information about atom
"groups"_group.html and "fixes"_fix.html are stored. "Binary restart
files"_read_restart.html store more information.
Bond interactions (angle, etc) that have been turned off by the "fix
shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will
be written to a data file as if they are turned on. This means they
will need to be turned off again in a new run after the data file is
read.
Bonds that are broken (e.g. by a bond-breaking potential) are not
written to the data file. Thus these bonds will not exist when the
data file is read.
[Restrictions:] [Restrictions:]