ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

additional check/warning for valid templates

Browse Source
This commit is contained in:
Jacob Gissinger
2024-01-03 20:31:22 -05:00
parent 600eaf837b
commit a6b00a60b2
2 changed files with 32 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

35
src/REACTION/fix_bond_react.cpp
View File

@ -2681,16 +2681,43 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
}
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
int warnflag = 0;
if (comm->me == 0)
for (int i = 0; i < twomol->natoms; i++) {
if ((create_atoms[i][myrxn] == 0) &&
(twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) &&
(landlocked_atoms[i][myrxn] == 0))
error->warning(FLERR, "Fix bond/react: Atom affected by reaction {} is too close "
"to template edge",rxn_name[myrxn]);
break;
(landlocked_atoms[i][myrxn] == 0)) {
warnflag = 1;
break;
}
}
// also, if an atom changes any of its bonds, but is not landlocked, that could be bad
int thereflag;
if (comm->me == 0)
for (int i = 0; i < twomol->natoms; i++) {
if (landlocked_atoms[i][myrxn] == 1) continue;
for (int j = 0; j < twomol_nxspecial[i][0]; j++) {
int oneneighID = equivalences[twomol_xspecial[i][j]-1][1][myrxn];
int ii = equivalences[i][1][myrxn] - 1;
thereflag = 0;
for (int k = 0; k < onemol_nxspecial[ii][0]; k++) {
if (oneneighID == onemol_xspecial[ii][k]) {
thereflag = 1;
break;
}
}
if (thereflag == 0) {
warnflag = 1;
break;
}
}
if (warnflag == 1) break;
}
if (comm->me == 0 && warnflag == 1) error->warning(FLERR, "Fix bond/react: Atom affected "
"by reaction {} is too close to template edge",rxn_name[myrxn]);
// finally, if a created atom is not landlocked, bad!
for (int i = 0; i < twomol->natoms; i++) {
if (create_atoms[i][myrxn] == 1 && landlocked_atoms[i][myrxn] == 0) {

2
src/REACTION/fix_bond_react.h
View File

@ -139,7 +139,7 @@ class FixBondReact : public Fix {
int avail_guesses; // num of restore points available
int *guess_branch; // used when there is more than two choices when guessing
int **restore_pt; // contains info about restore points
tagint **restore; // contaings info about restore points
tagint **restore; // contains info about restore points
int *pioneer_count; // counts pioneers
int **edge; // atoms in molecule templates with incorrect valences