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Update fix_bond_react.rst

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Jacob Gissinger
2022-11-05 02:03:02 -04:00
parent b2652a4542
commit 3b47afa69f
1 changed files with 15 additions and 1 deletions
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doc/src/fix_bond_react.rst
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@ -42,7 +42,7 @@ Syntax
* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
* zero or more individual keyword/value pairs may be appended to each react argument
* individual_keyword = *prob* or *rate_limit* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
* individual_keyword = *prob* or *rate_limit* or *max_rxn* or *stabilize_steps* or *custom_charges* or *rescale_charges* or *molecule* or *modify_create*
.. parsed-literal::
@ -59,6 +59,9 @@ Syntax
*custom_charges* value = *no* or fragment-ID
*no* = update all atomic charges (default)
fragment-ID = ID of molecule fragment whose charges are updated
*rescale_charges* value = *no* or *yes*
*no* = do not rescale atomic charges (default)
*yes* = rescale charges such that total charge does not change during reaction
*molecule* value = *off* or *inter* or *intra*
*off* = allow both inter- and intramolecular reactions (default)
*inter* = search for reactions between molecules with different IDs
@ -657,6 +660,17 @@ charges are updated to those specified by the post-reaction template
fragment defined in the pre-reaction molecule template. In this case,
only the atomic charges of atoms in the molecule fragment are updated.
The *rescale_charges* keyword can be used to ensure the total charge
of the system does not change as reactions occur. When the argument is
set to *yes*\ , a fixed value is added to the charges of post-reaction
atoms such that their total charge equals that of the pre-reaction
site. If only a subset of atomic charges are updated via the
*custom_charges* keyword, this rescaling is applied to the subset.
This keyword could be useful for systems that contain different
molecules with the same reactive site, if the partial charges on the
reaction site vary from molecule to molecule, or when removing
reaction by-products.
The *molecule* keyword can be used to force the reaction to be
intermolecular, intramolecular or either. When the value is set to
*off*\ , molecule IDs are not considered when searching for reactions