Examples:
-write_data data.polymer +write_data data.polymer +write_data data.*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 +command to begin a simulation. The read_data command +also describes their format.
-During a long simulation, the restart 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 files, the data filename can contain a "*" +wild-card character. The "*" is replaced with the current timestep +value.
-Similar to dump 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. +
IMPORTANT NOTE: The write-data command is not yet fully implemented in +two respects. First, most pair, bond, angle, dihedral, improper +styles do not yet write their coefficient information into the data +file. This means you will need to specify that information in your +input script that reads the data file, e.g. with the +pair_coeff command. Second, a few of the atom +styles (body, ellipsoid, line, tri) that store +auxiliary "bonus" information about aspherical particles, do not yet +write the bonus info into the data file. Both these functionalities +will be added to the write_data command later.
-Restart files can be read by a read_restart -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. +
Because a data file is in text format, if you use a data file written +out by this command to restart a simulation, the initial state of the +new run will be slightly different than the final state of the old run +(when the file was written) which was represented internally by LAMMPS +in binary format. A new simulation which reads the data file will +thus typically diverge from a simulation that continued in the +original input script.
-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 command for information about what is -stored in a restart file. +
If you want to do more exact restarts, using binary files, see the +restart, write_restart, and +read_restart commands. You can also convert +binary restart files to text data files, after a simulation has run, +using the restart2data tool in the +tools directory. When the write_data command is fully implemented +(see NOTE above), the restart2data command will be obsolete and will +be removed from the LAMMPS distribution. +
+IMPORTANT NOTE: Only limited information about a simulation is stored +in a data file. For example, no information about atom +groups and fixes are stored. Binary restart +files store more information. +
+Bond interactions (angle, etc) that have been turned off by the fix +shake or delete_bonds 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:
diff --git a/doc/write_data.txt b/doc/write_data.txt index 77a84bbcfa..0134e993c8 100644 --- a/doc/write_data.txt +++ b/doc/write_data.txt @@ -16,48 +16,62 @@ file = name of data file to write out :ul [Examples:] -write_data data.polymer :pre +write_data data.polymer +write_data data.* :pre [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 -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 data filename can contain a "*" +wild-card character. The "*" is replaced with the current timestep +value. -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. +IMPORTANT NOTE: The write-data command is not yet fully implemented in +two respects. First, most pair, bond, angle, dihedral, improper +styles do not yet write their coefficient information into the data +file. This means you will need to specify that information in your +input script that reads the data file, e.g. with the +"pair_coeff"_pair_coeff.html command. Second, a few of the "atom +styles"_atom_style.html (body, ellipsoid, line, tri) that store +auxiliary "bonus" information about aspherical particles, do not yet +write the bonus info into the data file. Both these functionalities +will be added to the write_data command later. -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. +Because a data file is in text format, if you use a data file written +out by this command to restart a simulation, the initial state of the +new run will be slightly different than the final state of the old run +(when the file was written) which was represented internally by LAMMPS +in binary format. A new simulation which reads the data file will +thus typically diverge from a simulation that continued in the +original input script. -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. +If you want to do more exact restarts, using binary files, see the +"restart"_restart.html, "write_restart"_write_restart.html, and +"read_restart"_read_restart.html commands. You can also convert +binary restart files to text data files, after a simulation has run, +using the "restart2data"_Section_tools.html#restart2data tool in the +tools directory. When the write_data command is fully implemented +(see NOTE above), the restart2data command will be obsolete and will +be removed from the LAMMPS distribution. + +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:]