From 95d462e5d3dc456cce8ab14198d1a0010e7d1527 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Tue, 21 Aug 2018 02:28:53 -0600
Subject: [PATCH] bond/react: better template validity check
now always throws error if a bond type changes, but both of of the involved atoms are too close to edge of template
---
doc/src/fix_bond_react.txt | 8 +++----
src/USER-MISC/fix_bond_react.cpp | 40 ++++++++++++++++++++++++++++++--
2 files changed, 42 insertions(+), 6 deletions(-)
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 7317dd26bb..327088cb99 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between {Rmin} and
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atomi and atomj have each other as their
+chosen. Then, if both an atom I and atom J have each other as their
nearest bonding partners, these two atoms are identified as the
bonding atom pair of the reaction site. Once this unique bonding atom
pair is identified for each reaction, there could two or more
@@ -323,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
[Default:]
-The option defaults are stabilization = no, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
:line
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index c72a1b027b..d529848e39 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -1063,8 +1063,8 @@ void FixBondReact::superimpose_algorithm()
hang_catch++;
// let's go ahead and catch the simplest of hangs
//if (hang_catch > onemol->natoms*4)
- if (hang_catch > atom->nlocal*3) {
- error->all(FLERR,"Excessive iteration of superimpose algorithm");
+ if (hang_catch > atom->nlocal*30) {
+ error->one(FLERR,"Excessive iteration of superimpose algorithm");
}
}
}
@@ -1554,6 +1554,42 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
error->one(FLERR,"Atom affected by reaction too close to template edge");
}
+ // additionally, if a bond changes type, but neither involved atom is landlocked, bad
+ // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (landlocked_atoms[i][myrxn] == 0) {
+ int twomol_atomi = i+1;
+ for (int j = 0; j < twomol->num_bond[i]; j++) {
+ int twomol_atomj = twomol->bond_atom[i][j];
+ if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
+ int onemol_atomi = equivalences[i][1][myrxn];
+ int onemol_batom;
+ for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
+ if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
+ printf("%d and %d for rxn %d\n",twomol_atomi,twomol_atomj,myrxn);
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ if (newton_bond) {
+ int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
+ for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
+ if (onemol_batom == equivalences[i][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
+ printf("%d and %d for rxn %d\n",twomol_atomi,twomol_atomj,myrxn);
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
if (me == 0)
for (int i = 0; i < twomol->natoms; i++) {
--
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