From afaaf442d3d4d3debc5bbcbf82971f696acf3fba Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Thu, 6 Dec 2018 21:32:10 -0700
Subject: [PATCH] bond/react doc tweaks 2
---
doc/src/fix_bond_react.txt | 2 +-
doc/utils/sphinx-config/false_positives.txt | 1 +
src/USER-MISC/fix_bond_react.cpp | 4 ++--
3 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 5d6349a426..8f71cd14ec 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -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.
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index de60206304..aab1dc12f8 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -507,6 +507,7 @@ deepskyblue
defgrad
deformable
del
+deleteIDs
Dellago
delocalization
delocalized
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 50efca8d09..600bb6a540 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -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");
}
}
}
--
GitLab