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initialize 'created atoms' mol ID to zero

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can control using molmap option
This commit is contained in:
Jacob Gissinger
2025-01-21 20:15:50 -05:00
parent c353c3c6c6
commit ee3e113339
1 changed files with 5 additions and 21 deletions
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26
src/REACTION/fix_bond_react.cpp
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@ -3819,6 +3819,10 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate)
double *newcoord;
double t,delx,dely,delz,rsq;
double **x = atom->x;
int nlocal = atom->nlocal;
int dimension = domain->dimension;
memory->create(coords,twomol->natoms,3,"bond/react:coords");
memory->create(imageflags,twomol->natoms,"bond/react:imageflags");
@ -3831,17 +3835,6 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate)
subhi = domain->subhi_lamda;
}
// find current max atom and molecule IDs
double **x = atom->x;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint maxmol_all = 0;
for (int i = 0; i < nlocal; i++) maxmol_all = MAX(maxmol_all,molecule[i]);
MPI_Allreduce(MPI_IN_PLACE,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
int dimension = domain->dimension;
// only proc that owns reacting atom (use ibonding),
// fits post-reaction template to reaction site, for creating atoms
int n2superpose = 0;
@ -4019,18 +4012,9 @@ int FixBondReact::insert_atoms_setup(tagint **my_update_mega_glove, int iupdate)
// locally update mega_glove
my_update_mega_glove[preID][iupdate] = myaddatom.tag;
// !! could do better job choosing mol ID for added atoms
// skip if using molmap option? actually, need to never add to maxmol_all here... cause messes up maxmol calculation for molmap later
if (atom->molecule_flag) {
if (twomol->moleculeflag) {
myaddatom.molecule = maxmol_all + twomol->molecule[m];
} else {
myaddatom.molecule = maxmol_all + 1;
}
}
myaddatom.mask = 1 | groupbit;
myaddatom.image = imageflags[m];
if (atom->molecule_flag) myaddatom.molecule = 0;
// guess a somewhat reasonable initial velocity based on reaction site
// further control is possible using bond_react_MASTER_group