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Finish first version of compute reaxff/atom docs

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This commit is contained in:
Richard Berger
2023-12-11 14:05:42 -07:00
parent b72c34d497
commit e241f08cfe
2 changed files with 34 additions and 5 deletions
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1
doc/src/compute.rst
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@ -280,6 +280,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
* :doc:`reaxff/atom <compute_reaxff_atom>` - extract ReaxFF bond information
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
* :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region

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doc/src/compute_reaxff_atom.rst
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@ -1,8 +1,8 @@
.. index:: fix reaxff/atom
.. index:: fix reaxff/atom/kk
.. index:: compute reaxff/atom
.. index:: compute reaxff/atom/kk
fix reaxff/atom command
=======================
compute reaxff/atom command
===========================
Accelerator Variants: *reaxff/atom/kk*
@ -40,7 +40,35 @@ Examples
Description
"""""""""""
TODO
Define a computation that extracts bond information computed by the ReaxFF
potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
By default, it produces per-atom data that includes the following columns:
* abo = atom bond order (sum of all bonds)
* nlp = number of lone pairs
* nb = number of bonds
Bonds will only be included if its atoms are in the group.
In addition, if ``bonds`` is set to ``yes``, the compute will also produce a
local array of all bonds on the current processor whose atoms are in the group.
The columns of each entry of this local array are:
* id_i = atom i id of bond
* id_j = atom j id of bond
* bo = bond order of bond
Output info
"""""""""""
This compute calculates a per-atom array and local array depending on the
number of keywords. The number of rows in the local array is the number of
bonds as described above. Both per-atom and local array have 3 columns.
The arrays can be accessed by any command that uses local and per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` page for
an overview of LAMMPS output options.
----------