96 lines
2.7 KiB
ReStructuredText
96 lines
2.7 KiB
ReStructuredText
.. index:: fix reax/c/bonds
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.. index:: fix reax/c/bonds/kk
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fix reax/c/bonds command
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========================
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Accelerator Variants: *reax/c/bonds/kk*
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID reaxc/bonds Nevery filename
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* reax/bonds = style name of this fix command
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* Nevery = output interval in timesteps
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* filename = name of output file
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all reax/c/bonds 100 bonds.reaxc
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Description
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"""""""""""
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Write out the bond information computed by the ReaxFF potential specified
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by :doc:`pair_style reax/c <pair_reaxc>` in the exact same format as the
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original stand-alone ReaxFF code of Adri van Duin. The bond information
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is written to *filename* on timesteps that are multiples of *Nevery*\ ,
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including timestep 0. For time-averaged chemical species analysis,
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please see the :doc:`fix reaxc/c/species <fix_reaxc_species>` command.
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The specified group-ID is ignored by this fix.
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The format of the output file should be reasonably self-explanatory.
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The meaning of the column header abbreviations is as follows:
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* id = atom id
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* type = atom type
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* nb = number of bonds
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* id_1 = atom id of first bond
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* id_nb = atom id of Nth bond
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* mol = molecule id
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* bo_1 = bond order of first bond
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* bo_nb = bond order of Nth bond
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* abo = atom bond order (sum of all bonds)
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* nlp = number of lone pairs
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* q = atomic charge
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If the filename ends with ".gz", the output file is written in gzipped
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format. A gzipped dump file will be about 3x smaller than the text
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version, but will also take longer to write.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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----------
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.. include:: accel_styles.rst
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----------
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Restrictions
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""""""""""""
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The fix reax/c/bonds command requires that the :doc:`pair_style reax/c <pair_reaxc>` is invoked. This fix is part of the
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USER-REAXC package. It is only enabled if LAMMPS was built with that
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package. See the :doc:`Build package <Build_package>` doc page for more
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info.
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To write gzipped bond files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option.
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Related commands
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""""""""""""""""
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:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/species <fix_reaxc_species>`
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Default
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"""""""
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none
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