From 677e8dd6810d52f612fa3a37d9a2f98e806a54a3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 30 Mar 2025 23:35:45 -0400 Subject: [PATCH] documentation fixes --- doc/src/fix_bond_react.rst | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 32a146b482..adbfc3f3bd 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -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 ` 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 ` 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):