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bond/react doc tweaks 2

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This commit is contained in:
jrgissing
2018-12-06 21:32:10 -07:00
parent cf3aee9083
commit afaaf442d3
3 changed files with 4 additions and 3 deletions
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2
doc/src/fix_bond_react.txt
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@ -318,7 +318,7 @@ unwanted by-products. Therefore, bond/react provides the option to
delete a user-specified set of atoms. These pre-reaction atoms are
identified in the map file. A deleted atom must still be included in
the post-reaction molecule template, in which it cannot be bonded to
an undeleted atom. In addition to deleting unwanted reaction
an atom that is not deleted. In addition to deleting unwanted reaction
by-products, this feature can be used to remove specific topologies,
such as small rings, that may be otherwise indistinguishable.

1
doc/utils/sphinx-config/false_positives.txt
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@ -507,6 +507,7 @@ deepskyblue
defgrad
deformable
del
deleteIDs
Dellago
delocalization
delocalized

4
src/USER-MISC/fix_bond_react.cpp
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@ -1653,13 +1653,13 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
}
}
// additionally, if a deleted atom is bonded to a undeleted atom, bad
// additionally, if a deleted atom is bonded to an atom that is not deleted, bad
for (int i = 0; i < onemol->natoms; i++) {
if (delete_atoms[i][myrxn] == 1) {
int ii = reverse_equiv[i][1][myrxn] - 1;
for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
error->one(FLERR,"A deleted atom cannot be bonded to an undeleted atom");
error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
}
}
}