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add singlezero keyword to compute fragment/atom to give all single non-bonded atoms an ID of 0

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Axel Kohlmeyer
2020-07-07 17:13:43 -04:00
parent 12f62583f9
commit d3853af4be
3 changed files with 46 additions and 25 deletions
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9
doc/src/compute_cluster_atom.rst
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@ -15,12 +15,13 @@ Syntax
.. parsed-literal::
compute ID group-ID cluster/atom cutoff
compute ID group-ID fragment/atom
compute ID group-ID fragment/atom [singlezero]
compute ID group-ID aggregate/atom cutoff
* ID, group-ID are documented in :doc:`compute <compute>` command
* *cluster/atom* or *fragment/atom* or *aggregate/atom* = style name of this compute command
* cutoff = distance within which to label atoms as part of same cluster (distance units)
* *singlezero* = keyword to trigger assigning an ID of 0 to fragments with a single atom (optional)
Examples
""""""""
@ -52,6 +53,12 @@ bond/break <fix_bond_break>`. The cluster ID or fragment ID of every
atom in the cluster will be set to the smallest atom ID of any atom in
the cluster or fragment, respectively.
The *singlezero* keyword turns on a special treatment for fragments,
where all fragments within the compute group that contain only a single
atom will have a fragment ID of 0. This can be useful in cases where
the fragment IDs are used as input for other commands in LAMMPS that
treat such single atoms different.
An aggregate is defined by combining the rules for clusters and
fragments, i.e. a set of atoms, where each of it is within the cutoff
distance from one or more atoms within a fragment that is part of