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make edge atoms optional

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jrgissing
2018-06-26 09:35:38 -06:00
parent f94cdf856c
commit ebe622ff7d
1 changed files with 5 additions and 3 deletions
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8
src/USER-MISC/fix_bond_react.cpp
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@ -264,6 +264,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(edge,max_natoms,nreacts,"bond/react:edge");
memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
for (int j = 0; j < nreacts; j++)
for (int i = 0; i < onemol->natoms; i++) edge[i][j] = 0;
// read all superimpose files afterward
for (int i = 0; i < nreacts; i++) {
open(files[i]);
@ -2445,7 +2448,6 @@ void FixBondReact::read(int myrxn)
sscanf(line,"%d",&jbonding[myrxn]);
} else if (strcmp(keyword,"EdgeIDs") == 0) {
edgeflag = 1;
for (int i = 0; i < onemol->natoms; i++) edge[i][myrxn] = 0;
EdgeIDs(line, myrxn);
} else if (strcmp(keyword,"Equivalences") == 0) {
equivflag = 1;
@ -2457,8 +2459,8 @@ void FixBondReact::read(int myrxn)
}
// error check
if (bondflag == 0 || equivflag == 0 || edgeflag == 0)
error->all(FLERR,"Superimpose file missing BondingIDs, EdgeIDs, or Equivalences section\n");
if (bondflag == 0 || equivflag == 0)
error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n");
}
void FixBondReact::EdgeIDs(char *line, int myrxn)