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Merge pull request #2504 from jrgissing/bond/react-add-logic-to-constraints

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Bond/react: add logic to constraints
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Axel Kohlmeyer
2020-12-23 15:39:30 -05:00
committed by GitHub
parent 06d7e5ab02 a7fa4739f5
commit 41d6648ac9
3 changed files with 262 additions and 189 deletions
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21
doc/src/fix_bond_react.rst
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@ -457,6 +457,23 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
By default, all constraints must be satisfied for the reaction to
occur. In other words, constraints are evaluated as a series of
logical values using the logical AND operator "&&". More complex logic
can be achieved by explicitly adding the logical AND operator "&&" or
the logical OR operator "||" after a given constraint command. If a
logical operator is specified after a constraint, it must be placed
after all constraint parameters, on the same line as the constraint
(one per line). Similarly, parentheses can be used to group
constraints. The expression that results from concatenating all
constraints should be a valid logical expression that can be read by
the :doc:`variable <variable>` command after converting each
constraint to a logical value. Because exactly one constraint is
allowed per line, having a valid logical expression implies that left
parentheses "(" should only appear before a constraint, and right
parentheses ")" should only appear after a constraint and before any
logical operator.
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
@ -599,8 +616,8 @@ reset_mol_ids = yes, custom_charges = no, molecule = off
.. _Gissinger:
**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
.. _Gissinger2020:
**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules (2020, in press).
**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953–9961 (2020).