forked from lijiext/lammps
143 lines
5.0 KiB
Plaintext
143 lines
5.0 KiB
Plaintext
.. index:: write_data
|
|
|
|
write_data command
|
|
==================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
write_data file keyword value ...
|
|
|
|
* file = name of data file to write out
|
|
* zero or more keyword/value pairs may be appended
|
|
* keyword = *pair* or *nocoeff*
|
|
.. parsed-literal::
|
|
|
|
*nocoeff* = do not write out force field info
|
|
*pair* value = *ii* or *ij*
|
|
*ii* = write one line of pair coefficient info per atom type
|
|
*ij* = write one line of pair coefficient info per IJ atom type pair
|
|
|
|
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
write_data data.polymer
|
|
write_data data.*
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
Write a data file in text format of the current state of the
|
|
simulation. Data files can be read by the :doc:`read data <read_data>`
|
|
command to begin a simulation. The :doc:`read_data <read_data>` command
|
|
also describes their format.
|
|
|
|
Similar to :doc:`dump <dump>` files, the data filename can contain a "*"
|
|
wild-card character. The "*" is replaced with the current timestep
|
|
value.
|
|
|
|
.. note::
|
|
|
|
The write-data command is not yet fully implemented in two
|
|
respects. First, most pair 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, via
|
|
the :doc:`pair_coeff <pair_coeff>` command. Second, a few of the :doc:`atom styles <atom_style>` (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.
|
|
|
|
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.
|
|
|
|
If you want to do more exact restarts, using binary files, see the
|
|
:doc:`restart <restart>`, :doc:`write_restart <write_restart>`, and
|
|
:doc:`read_restart <read_restart>` commands. You can also convert
|
|
binary restart files to text data files, after a simulation has run,
|
|
using the :ref:`-r command-line switch <start_7>`.
|
|
|
|
.. note::
|
|
|
|
Only limited information about a simulation is stored in a data
|
|
file. For example, no information about atom :doc:`groups <group>` and
|
|
:doc:`fixes <fix>` are stored. :doc:`Binary restart files <read_restart>`
|
|
store more information.
|
|
|
|
Bond interactions (angle, etc) that have been turned off by the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <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.
|
|
|
|
|
|
----------
|
|
|
|
|
|
The *nocoeff* keyword requests that no force field parameters should
|
|
be written to the data file. This can be very helpful, if one wants
|
|
to make significant changes to the force field or if the parameters
|
|
are read in separately anyway, e.g. from an include file.
|
|
|
|
The *pair* keyword lets you specify in what format the pair
|
|
coefficient information is written into the data file. If the value
|
|
is specified as *ii*, then one line per atom type is written, to
|
|
specify the coefficients for each of the I=J interactions. This means
|
|
that no cross-interactions for I != J will be specified in the data
|
|
file and the pair style will apply its mixing rule, as documented on
|
|
individual :doc:`pair_style <pair_style>` doc pages. Of course this
|
|
behavior can be overridden in the input script after reading the data
|
|
file, by specifying additional :doc:`pair_coeff <pair_coeff>` commands
|
|
for any desired I,J pairs.
|
|
|
|
If the value is specified as *ij*, then one line of coefficients is
|
|
written for all I,J pairs where I <= J. These coefficients will
|
|
include any specific settings made in the input script up to that
|
|
point. The presence of these I != J coefficients in the data file
|
|
will effectively turn off the default mixing rule for the pair style.
|
|
Again, the coefficient values in the data file can can be overridden
|
|
in the input script after reading the data file, by specifying
|
|
additional :doc:`pair_coeff <pair_coeff>` commands for any desired I,J
|
|
pairs.
|
|
|
|
|
|
----------
|
|
|
|
|
|
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
|
|
""""""""""""""""
|
|
|
|
:doc:`read_data <read_data>`, :doc:`write_restart <write_restart>`
|
|
|
|
Default
|
|
"""""""
|
|
|
|
The option defaults are pair = ii.
|
|
|
|
|
|
.. _lws: http://lammps.sandia.gov
|
|
.. _ld: Manual.html
|
|
.. _lc: Section_commands.html#comm
|