574e4067dc
This is the first step for moving the documentation format from *.txt to the *.rst format. In the last years we've been automatically converting txt files from Steve's markup into RST to generate the documentation pages via Sphinx. The decision has now been made to fully migrate to RST and avoid the conversion in the future. This will enable us to fully use RST and Sphinx to improve the documentation. For the intermediate period, while there are still pending PRs with documentation changes, we will keep both source files and update the RST files accordingly.
153 lines
5.4 KiB
ReStructuredText
153 lines
5.4 KiB
ReStructuredText
.. 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
|
|
*nofix* = do not write out extra sections read by fixes
|
|
*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 :doc:`-r command-line switch <Run_options>`.
|
|
|
|
.. 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 *nofix* keyword requests that no extra sections read by fixes
|
|
should be written to the data file (see the *fix* option of the
|
|
:doc:`read\_data <read_data>` command for details). For example, this
|
|
option excludes sections for user-created per-atom properties
|
|
from :doc:`fix property/atom <fix_property_atom>`.
|
|
|
|
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 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: Commands_all.html
|