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< title > write_data command — LAMMPS 15 May 2015 version documentation< / title >
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< li > write_data command< / li >
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< span id = "index-0" > < / span > < h1 > write_data command< a class = "headerlink" href = "#write-data-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > write_data file keyword value ...
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< ul class = "simple" >
< li > file = name of data file to write out< / li >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > pair< / em > or < em > nocoeff< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > nocoeff< / em > = do not write out force field info
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< em > pair< / em > value = < em > ii< / em > or < em > ij< / em >
< em > ii< / em > = write one line of pair coefficient info per atom type
< em > ij< / em > = write one line of pair coefficient info per IJ atom type pair
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > write_data data.polymer
write_data data.*
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< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Write a data file in text format of the current state of the
simulation. Data files can be read by the < a class = "reference internal" href = "read_data.html" > < em > read data< / em > < / a >
command to begin a simulation. The < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command
also describes their format.< / p >
< p > Similar to < a class = "reference internal" href = "dump.html" > < em > dump< / em > < / a > files, the data filename can contain a “ *”
wild-card character. The “ *” is replaced with the current timestep
value.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > The write-data command is not yet fully implemented in
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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
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file, via the < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > command. Second, a few of
the < a class = "reference internal" href = "atom_style.html" > < em > atom styles< / em > < / a > (body, ellipsoid, line, tri) that
store auxiliary “ bonus” information about aspherical particles, do not
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yet write the bonus info into the data file. Both these
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functionalities will be added to the write_data command later.< / p >
< / div >
< 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
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
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original input script.< / p >
< p > If you want to do more exact restarts, using binary files, see the
< a class = "reference internal" href = "restart.html" > < em > restart< / em > < / a > , < a class = "reference internal" href = "write_restart.html" > < em > write_restart< / em > < / a > , and
< a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / 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 class = "reference internal" href = "Section_start.html#start-7" > < span > -r command-line switch< / span > < / a > .< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > 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 class = "reference internal" href = "group.html" > < em > groups< / em > < / a > and < a class = "reference internal" href = "fix.html" > < em > fixes< / em > < / a > are stored. < a class = "reference internal" href = "read_restart.html" > < em > Binary restart files< / em > < / a > store more information.< / p >
< / div >
< p > Bond interactions (angle, etc) that have been turned off by the < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > or < a class = "reference internal" href = "delete_bonds.html" > < em > delete_bonds< / em > < / a > command will
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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
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read.< / p >
< 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.< / p >
< hr class = "docutils" / >
< p > The < em > nocoeff< / em > keyword requests that no force field parameters should
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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
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are read in separately anyway, e.g. from an include file.< / p >
< p > The < em > pair< / em > keyword lets you specify in what format the pair
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coefficient information is written into the data file. If the value
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is specified as < em > ii< / em > , then one line per atom type is written, to
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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
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individual < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / a > doc pages. Of course this
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behavior can be overridden in the input script after reading the data
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file, by specifying additional < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > commands
for any desired I,J pairs.< / p >
< p > If the value is specified as < em > ij< / em > , then one line of coefficients is
written for all I,J pairs where I < = J. These coefficients will
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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
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additional < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > commands for any desired I,J
pairs.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This command requires inter-processor communication to migrate atoms
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before the data file is written. This means that your system must be
ready to perform a simulation before using this command (force fields
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setup, atom masses initialized, etc).< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > , < a class = "reference internal" href = "write_restart.html" > < em > write_restart< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option defaults are pair = ii.< / p >
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