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add option to update all atoms' atomic charges

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option to update all atomic charges, even when edge atoms are defined
This commit is contained in:
jrgissing
2018-10-30 22:11:52 -06:00
parent e992bf935b
commit 3faecc4d28
3 changed files with 33 additions and 5 deletions
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12
src/USER-MISC/fix_bond_react.cpp
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@ -163,6 +163,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(seed,nreacts,"bond/react:seed");
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag");
memory->create(iatomtype,nreacts,"bond/react:iatomtype");
memory->create(jatomtype,nreacts,"bond/react:jatomtype");
memory->create(ibonding,nreacts,"bond/react:ibonding");
@ -178,6 +179,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
fraction[i] = 1;
seed[i] = 12345;
stabilize_steps_flag[i] = 0;
update_edges_flag[i] = 0;
// set default limit duration to 60 timesteps
limit_duration[i] = 60;
reaction_count[i] = 0;
@ -249,6 +251,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
limit_duration[rxn] = force->numeric(FLERR,arg[iarg+1]);
stabilize_steps_flag[rxn] = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"update_edges") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'update_edges' has too few arguments");
if (strcmp(arg[iarg+1],"charges") == 0) update_edges_flag[rxn] = 1;
iarg += 2;
} else error->all(FLERR,"Illegal fix bond/react command: unknown keyword");
}
}
@ -379,6 +386,7 @@ FixBondReact::~FixBondReact()
memory->destroy(seed);
memory->destroy(limit_duration);
memory->destroy(stabilize_steps_flag);
memory->destroy(update_edges_flag);
memory->destroy(iatomtype);
memory->destroy(jatomtype);
@ -2022,13 +2030,13 @@ void FixBondReact::update_everything()
}
// update charges and types of landlocked atoms
// here, add check for charge instead of requiring it
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
twomol = atom->molecules[reacted_mol[rxnID]];
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
if (landlocked_atoms[j][rxnID] == 1 && atom->map(update_mega_glove[jj+1][i]) >= 0 &&
if ((landlocked_atoms[j][rxnID] == 1 || update_edges_flag[rxnID] == 1) &&
atom->map(update_mega_glove[jj+1][i]) >= 0 &&
atom->map(update_mega_glove[jj+1][i]) < nlocal) {
type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j];
if (twomol->qflag && atom->q_flag) {