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bond/react: allow custom update of charges near template edges

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also, fixes a bug introduced in PR #1189, when not using stabilization
This commit is contained in:
jrgissing
2018-11-06 19:59:22 -07:00
parent cc0d685e8e
commit 84fcf01bed
3 changed files with 82 additions and 21 deletions
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67
src/USER-MISC/fix_bond_react.cpp
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@ -255,7 +255,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
} 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;
if (strcmp(arg[iarg+1],"none") == 0) update_edges_flag[rxn] = 0;
else if (strcmp(arg[iarg+1],"charges") == 0) update_edges_flag[rxn] = 1;
else if (strcmp(arg[iarg+1],"custom") == 0) update_edges_flag[rxn] = 2;
else error->all(FLERR,"Illegal value for 'update_edges' keyword'");
iarg += 2;
} else error->all(FLERR,"Illegal fix bond/react command: unknown keyword");
}
@ -271,11 +274,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv");
memory->create(edge,max_natoms,nreacts,"bond/react:edge");
memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
for (int j = 0; j < nreacts; j++)
for (int i = 0; i < max_natoms; i++) edge[i][j] = 0;
for (int i = 0; i < max_natoms; i++) {
edge[i][j] = 0;
if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
else custom_edges[i][j] = 0;
}
// read all superimpose files afterward
// read all map files afterward
for (int i = 0; i < nreacts; i++) {
open(files[i]);
onemol = atom->molecules[unreacted_mol[i]];
@ -384,6 +392,7 @@ FixBondReact::~FixBondReact()
memory->destroy(edge);
memory->destroy(equivalences);
memory->destroy(reverse_equiv);
memory->destroy(custom_edges);
memory->destroy(nevery);
memory->destroy(cutsq);
@ -1854,8 +1863,11 @@ void FixBondReact::limit_bond(int limit_bond_mode)
int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
int index2 = atom->find_custom(statted_id,flag);
int *i_statted_tags = atom->ivector[index2];
int *i_statted_tags;
if (stabilization_flag == 1) {
int index2 = atom->find_custom(statted_id,flag);
i_statted_tags = atom->ivector[index2];
}
int index3 = atom->find_custom("react_tags",flag);
int *i_react_tags = atom->ivector[index3];
@ -1863,7 +1875,7 @@ void FixBondReact::limit_bond(int limit_bond_mode)
for (int i = 0; i < temp_limit_num; i++) {
// update->ntimestep could be 0. so add 1 throughout
i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1;
i_statted_tags[atom->map(temp_limit_glove[i])] = 0;
if (stabilization_flag == 1) i_statted_tags[atom->map(temp_limit_glove[i])] = 0;
i_react_tags[atom->map(temp_limit_glove[i])] = rxnID;
}
@ -1884,8 +1896,11 @@ void FixBondReact::unlimit_bond()
int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
int index2 = atom->find_custom(statted_id,flag);
int *i_statted_tags = atom->ivector[index2];
int *i_statted_tags;
if (stabilization_flag == 1) {
int index2 = atom->find_custom(statted_id,flag);
i_statted_tags = atom->ivector[index2];
}
int index3 = atom->find_custom("react_tags",flag);
int *i_react_tags = atom->ivector[index3];
@ -1895,7 +1910,7 @@ void FixBondReact::unlimit_bond()
// first '1': indexing offset, second '1': for next step
if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) { // + 1
i_limit_tags[i] = 0;
i_statted_tags[i] = 1;
if (stabilization_flag == 1) i_statted_tags[i] = 1;
i_react_tags[i] = 0;
}
}
@ -2077,7 +2092,7 @@ void FixBondReact::update_everything()
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 || update_edges_flag[rxnID] == 1) &&
if ((landlocked_atoms[j][rxnID] == 1 || custom_edges[jj][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];
@ -2520,6 +2535,7 @@ void FixBondReact::read(int myrxn)
if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
else break;
}
@ -2532,7 +2548,7 @@ void FixBondReact::read(int myrxn)
// loop over sections of superimpose file
int equivflag = 0, edgeflag = 0, bondflag = 0;
int equivflag = 0, edgeflag = 0, bondflag = 0, customedgesflag = 0;
while (strlen(keyword)) {
if (strcmp(keyword,"BondingIDs") == 0) {
bondflag = 1;
@ -2546,6 +2562,9 @@ void FixBondReact::read(int myrxn)
} else if (strcmp(keyword,"Equivalences") == 0) {
equivflag = 1;
Equivalences(line, myrxn);
} else if (strcmp(keyword,"Custom Edges") == 0) {
customedgesflag = 1;
CustomEdges(line, myrxn);
} else error->one(FLERR,"Unknown section in superimpose file");
parse_keyword(1,line,keyword);
@ -2555,6 +2574,12 @@ void FixBondReact::read(int myrxn)
// error check
if (bondflag == 0 || equivflag == 0)
error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n");
if (update_edges_flag[myrxn] == 2 && customedgesflag == 0)
error->all(FLERR,"Map file must have a Custom Edges section when using 'update_edges custom'\n");
if (update_edges_flag[myrxn] != 2 && customedgesflag == 1)
error->all(FLERR,"Specify 'update_edges custom' to include Custom Edges section in map file\n");
}
void FixBondReact::EdgeIDs(char *line, int myrxn)
@ -2585,6 +2610,26 @@ void FixBondReact::Equivalences(char *line, int myrxn)
}
}
void FixBondReact::CustomEdges(char *line, int myrxn)
{
// 0 for 'none', 1 for 'charges'
int tmp;
int n = MAX(strlen("none"),strlen("charges")) + 1;
char *edgemode = new char[n];
for (int i = 0; i < ncustom; i++) {
readline(line);
sscanf(line,"%d %s",&tmp,edgemode);
if (strcmp(edgemode,"none") == 0)
custom_edges[tmp-1][myrxn] = 0;
else if (strcmp(edgemode,"charges") == 0)
custom_edges[tmp-1][myrxn] = 1;
else
error->one(FLERR,"Illegal value in 'Custom Edges' section of map file");
}
delete [] edgemode;
}
void FixBondReact::open(char *file)
{
fp = fopen(file,"r");