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bond/react docs tweak: address a common mistake

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no atom of a small molecule should be specified as an edge atom
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jrgissing
2019-09-05 23:50:57 -06:00
parent 50af20d194
commit 49b5825e8d
1 changed files with 16 additions and 13 deletions
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doc/src/fix_bond_react.txt
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@ -186,19 +186,22 @@ reacting atoms.
Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that would connect to the
rest of a long polymer chain. These are referred to as edge atoms, and
are also specified in the map file. When the pre-reaction template
contains edge atoms, not all atoms, bonds, charges, etc. specified in
the reaction templates will be updated. Specifically, topology that
involves only atoms that are 'too near' to template edges will not be
updated. The definition of 'too near the edge' depends on which
interactions are defined in the simulation. If the simulation has
defined dihedrals, atoms within two bonds of edge atoms are considered
'too near the edge.' If the simulation defines angles, but not
dihedrals, atoms within one bond of edge atoms are considered 'too
near the edge.' If just bonds are defined, only edge atoms are
considered 'too near the edge.'
pre-reacted template may contain an atom that, in the simulation, is
currently connected to the rest of a long polymer chain. These are
referred to as edge atoms, and are also specified in the map file.
When the pre-reaction template contains edge atoms, not all atoms,
bonds, charges, etc. specified in the reaction templates will be
updated. Specifically, topology that involves only atoms that are 'too
near' to template edges will not be updated. The definition of 'too
near the edge' depends on which interactions are defined in the
simulation. If the simulation has defined dihedrals, atoms within two
bonds of edge atoms are considered 'too near the edge.' If the
simulation defines angles, but not dihedrals, atoms within one bond of
edge atoms are considered 'too near the edge.' If just bonds are
defined, only edge atoms are considered 'too near the edge.'
NOTE: Small molecules, i.e. ones that have all their atoms contained
within the reaction templates, never have edge atoms.
Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template