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documentation fixes

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This commit is contained in:
Axel Kohlmeyer
2025-03-30 23:35:45 -04:00
parent 6e395424bc
commit 677e8dd681
1 changed files with 12 additions and 8 deletions
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doc/src/fix_bond_react.rst
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@ -28,7 +28,7 @@ Syntax
*no* = no reaction site stabilization (default)
group_prefix = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
xmax = value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
*reset_mol_ids* values = *yes* or *no*
*reset_mol_ids* values = *yes* or *no* or *molmap*
*yes* = update molecule IDs based on new global topology (default)
*no* = do not update molecule IDs
*molmap* = customize how molecule IDs are updated
@ -189,6 +189,10 @@ due to the internal dynamic grouping performed by fix bond/react.
If the group-ID is an existing static group, react-group-IDs
should also be specified as this static group or a subset.
.. versionadded:: TBD
New *molmap* option
If the *reset_mol_ids* keyword is set to *yes* (default), the
:doc:`reset_atoms mol <reset_atoms>` command is invoked after a reaction
occurs, to ensure that molecule IDs are consistent with the new bond
@ -198,17 +202,17 @@ global operation, so it can be slow for very large systems. If the
*reset_mol_ids* keyword is set to *no*, molecule IDs are not updated.
If the *reset_mol_ids* keyword is set to *molmap*, molecule IDs are
updated consistently with the molecule IDs listed in the *Molecules*
section of the pre- and post-reaction templates. If a post-reaction atom
has the same molecule ID as one or more pre-reaction atoms in the
section of the pre- and post-reaction templates. If a post-reaction
atom has the same molecule ID as one or more pre-reaction atoms in the
templates, then the post-reaction simulation atom will be assigned the
same simulation molecule ID that those corresponding pre-reaction
simulation atoms had before the reaction. The *molmap* option is only
guaranteed to work correctly if all the pre-reaction atoms that have
equivalent template molecule IDs also have equivalent molecule IDs in the
simulation. No check is performed to test for this consistency. For
post-reaction atoms that have a template molecule ID that does not exist
in pre-reaction template, they are assigned a new molecule ID that does
not currently exist in the simulation.
equivalent template molecule IDs also have equivalent molecule IDs in
the simulation. No check is performed to test for this consistency.
For post-reaction atoms that have a template molecule ID that does not
exist in pre-reaction template, they are assigned a new molecule ID that
does not currently exist in the simulation.
The following comments pertain to each *react* argument (in other
words, they can be customized for each reaction, or reaction step):