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@ -20,47 +20,61 @@
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<P><B>Examples:</B>
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</P>
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<PRE>write_data data.polymer
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write_data data.*
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Write a text data file of the current state of the simulation.
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<P>Write a data file in text format of the current state of the
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simulation. Data files can be read by the <A HREF = "read_data.html">read data</A>
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command to begin a simulation. The <A HREF = "read_data.html">read_data</A> command
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also describes their format.
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</P>
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<P>During a long simulation, the <A HREF = "restart.html">restart</A> command is
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typically used to dump restart files periodically. The write_restart
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command is useful after a minimization or whenever you wish to write
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out a single current restart file.
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<P>Similar to <A HREF = "dump.html">dump</A> files, the data filename can contain a "*"
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wild-card character. The "*" is replaced with the current timestep
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value.
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</P>
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<P>Similar to <A HREF = "dump.html">dump</A> files, the restart filename can contain
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two wild-card characters. If a "*" appears in the filename, it is
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replaced with the current timestep value. If a "%" character appears
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in the filename, then one file is written by each processor and the
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"%" character is replaced with the processor ID from 0 to P-1. An
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additional file with the "%" replaced by "base" is also written, which
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contains global information. For example, the files written for
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filename restart.% would be restart.base, restart.0, restart.1, ...
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restart.P-1. This creates smaller files and can be a fast mode of
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output and subsequent input on parallel machines that support parallel
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I/O.
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<P>IMPORTANT NOTE: The write-data command is not yet fully implemented in
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two respects. First, most pair, bond, angle, dihedral, improper
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styles do not yet write their coefficient information into the data
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file. This means you will need to specify that information in your
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input script that reads the data file, e.g. with the
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<A HREF = "pair_coeff.html">pair_coeff</A> command. Second, a few of the <A HREF = "atom_style.html">atom
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styles</A> (body, ellipsoid, line, tri) that store
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auxiliary "bonus" information about aspherical particles, do not yet
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write the bonus info into the data file. Both these functionalities
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will be added to the write_data command later.
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</P>
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<P>Restart files can be read by a <A HREF = "read_restart.html">read_restart</A>
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command to restart a simulation from a particular state. Because the
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file is binary (to enable exact restarts), it may not be readable on
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another machine. In this case, the restart2data program in the tools
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directory can be used to convert a restart file to an ASCII data file.
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Both the read_restart command and restart2data tool can read in a
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restart file that was written with the "%" character so that multiple
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files were created.
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<P>Because a data file is in text format, if you use a data file written
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out by this command to restart a simulation, the initial state of the
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new run will be slightly different than the final state of the old run
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(when the file was written) which was represented internally by LAMMPS
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in binary format. A new simulation which reads the data file will
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thus typically diverge from a simulation that continued in the
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original input script.
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</P>
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<P>IMPORTANT NOTE: Although the purpose of restart files is to enable
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restarting a simulation from where it left off, not all information
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about a simulation is stored in the file. For example, the list of
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fixes that were specified during the initial run is not stored, which
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means the new input script must specify any fixes you want to use.
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Even when restart information is stored in the file, as it is for some
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fixes, commands may need to be re-specified in the new input script,
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in order to re-use that information. See the
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<A HREF = "read_restart.html">read_restart</A> command for information about what is
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stored in a restart file.
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<P>If you want to do more exact restarts, using binary files, see the
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<A HREF = "restart.html">restart</A>, <A HREF = "write_restart.html">write_restart</A>, and
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<A HREF = "read_restart.html">read_restart</A> commands. You can also convert
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binary restart files to text data files, after a simulation has run,
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using the <A HREF = "Section_tools.html#restart2data">restart2data</A> tool in the
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tools directory. When the write_data command is fully implemented
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(see NOTE above), the restart2data command will be obsolete and will
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be removed from the LAMMPS distribution.
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</P>
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<P>IMPORTANT NOTE: Only limited information about a simulation is stored
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in a data file. For example, no information about atom
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<A HREF = "group.html">groups</A> and <A HREF = "fix.html">fixes</A> are stored. <A HREF = "read_restart.html">Binary restart
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files</A> store more information.
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</P>
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<P>Bond interactions (angle, etc) that have been turned off by the <A HREF = "fix_shake.html">fix
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shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A> command will
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be written to a data file as if they are turned on. This means they
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will need to be turned off again in a new run after the data file is
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read.
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</P>
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<P>Bonds that are broken (e.g. by a bond-breaking potential) are not
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written to the data file. Thus these bonds will not exist when the
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data file is read.
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</P>
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<P><B>Restrictions:</B>
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</P>
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@ -16,48 +16,62 @@ file = name of data file to write out :ul
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[Examples:]
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write_data data.polymer :pre
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write_data data.polymer
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write_data data.* :pre
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[Description:]
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Write a text data file of the current state of the simulation.
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Write a data file in text format of the current state of the
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simulation. Data files can be read by the "read data"_read_data.html
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command to begin a simulation. The "read_data"_read_data.html command
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also describes their format.
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During a long simulation, the "restart"_restart.html command is
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typically used to dump restart files periodically. The write_restart
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command is useful after a minimization or whenever you wish to write
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out a single current restart file.
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Similar to "dump"_dump.html files, the data filename can contain a "*"
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wild-card character. The "*" is replaced with the current timestep
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value.
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Similar to "dump"_dump.html files, the restart filename can contain
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two wild-card characters. If a "*" appears in the filename, it is
|
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replaced with the current timestep value. If a "%" character appears
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in the filename, then one file is written by each processor and the
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"%" character is replaced with the processor ID from 0 to P-1. An
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additional file with the "%" replaced by "base" is also written, which
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contains global information. For example, the files written for
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filename restart.% would be restart.base, restart.0, restart.1, ...
|
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restart.P-1. This creates smaller files and can be a fast mode of
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output and subsequent input on parallel machines that support parallel
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I/O.
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IMPORTANT NOTE: The write-data command is not yet fully implemented in
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two respects. First, most pair, bond, angle, dihedral, improper
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styles do not yet write their coefficient information into the data
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file. This means you will need to specify that information in your
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input script that reads the data file, e.g. with the
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"pair_coeff"_pair_coeff.html command. Second, a few of the "atom
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styles"_atom_style.html (body, ellipsoid, line, tri) that store
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auxiliary "bonus" information about aspherical particles, do not yet
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write the bonus info into the data file. Both these functionalities
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will be added to the write_data command later.
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Restart files can be read by a "read_restart"_read_restart.html
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command to restart a simulation from a particular state. Because the
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file is binary (to enable exact restarts), it may not be readable on
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another machine. In this case, the restart2data program in the tools
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directory can be used to convert a restart file to an ASCII data file.
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Both the read_restart command and restart2data tool can read in a
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restart file that was written with the "%" character so that multiple
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files were created.
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Because a data file is in text format, if you use a data file written
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out by this command to restart a simulation, the initial state of the
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new run will be slightly different than the final state of the old run
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(when the file was written) which was represented internally by LAMMPS
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in binary format. A new simulation which reads the data file will
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thus typically diverge from a simulation that continued in the
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original input script.
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IMPORTANT NOTE: Although the purpose of restart files is to enable
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restarting a simulation from where it left off, not all information
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about a simulation is stored in the file. For example, the list of
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fixes that were specified during the initial run is not stored, which
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means the new input script must specify any fixes you want to use.
|
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Even when restart information is stored in the file, as it is for some
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fixes, commands may need to be re-specified in the new input script,
|
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in order to re-use that information. See the
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"read_restart"_read_restart.html command for information about what is
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stored in a restart file.
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If you want to do more exact restarts, using binary files, see the
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"restart"_restart.html, "write_restart"_write_restart.html, and
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"read_restart"_read_restart.html commands. You can also convert
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binary restart files to text data files, after a simulation has run,
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using the "restart2data"_Section_tools.html#restart2data tool in the
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tools directory. When the write_data command is fully implemented
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(see NOTE above), the restart2data command will be obsolete and will
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be removed from the LAMMPS distribution.
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IMPORTANT NOTE: Only limited information about a simulation is stored
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in a data file. For example, no information about atom
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"groups"_group.html and "fixes"_fix.html are stored. "Binary restart
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files"_read_restart.html store more information.
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Bond interactions (angle, etc) that have been turned off by the "fix
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shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will
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be written to a data file as if they are turned on. This means they
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will need to be turned off again in a new run after the data file is
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read.
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Bonds that are broken (e.g. by a bond-breaking potential) are not
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written to the data file. Thus these bonds will not exist when the
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data file is read.
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[Restrictions:]
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|
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