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type reassignment bugfix for edge atoms

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This commit is contained in:
jrgissing
2018-05-09 23:55:04 -06:00
parent 662535865f
commit 863a85353a
1 changed files with 8 additions and 4 deletions
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12
src/USER-MISC/fix_bond_react.cpp
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@ -410,14 +410,14 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group
void FixBondReact::post_constructor()
{
// let's add the limit_tags per-atom property fix
int len = strlen("per_atom_props") + 1;
int len = strlen("bond_react_props_internal") + 1;
id_fix2 = new char[len];
strcpy(id_fix2,"per_atom_props");
strcpy(id_fix2,"bond_react_props_internal");
int ifix = modify->find_fix(id_fix2);
if (ifix == -1) {
char **newarg = new char*[8];
newarg[0] = (char *) "per_atom_props";
newarg[0] = (char *) "bond_react_props_internal";
newarg[1] = (char *) "all"; // group ID is ignored
newarg[2] = (char *) "property/atom";
newarg[3] = (char *) "i_limit_tags";
@ -2022,6 +2022,7 @@ void FixBondReact::update_everything()
int nn = equivalences[n][1][rxnID]-1;
if (n!=j && bond_atom[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] && landlocked_atoms[n][rxnID] == 1) {
for (int m = p; m < num_bond[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
bond_type[atom->map(update_mega_glove[jj+1][i])][m] = bond_type[atom->map(update_mega_glove[jj+1][i])][m+1];
bond_atom[atom->map(update_mega_glove[jj+1][i])][m] = bond_atom[atom->map(update_mega_glove[jj+1][i])][m+1];
}
num_bond[atom->map(update_mega_glove[jj+1][i])]--;
@ -2059,6 +2060,7 @@ void FixBondReact::update_everything()
}
}
// Angles! First let's delete all angle info:
if (force->angle && twomol->angleflag) {
int *num_angle = atom->num_angle;
int **angle_type = atom->angle_type;
@ -2069,7 +2071,6 @@ void FixBondReact::update_everything()
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
twomol = atom->molecules[reacted_mol[rxnID]];
// Angles! First let's delete all angle info:
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
@ -2086,6 +2087,7 @@ void FixBondReact::update_everything()
angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
for (int m = p; m < num_angle[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
angle_type[atom->map(update_mega_glove[jj+1][i])][m] = angle_type[atom->map(update_mega_glove[jj+1][i])][m+1];
angle_atom1[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
angle_atom2[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
angle_atom3[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
@ -2162,6 +2164,7 @@ void FixBondReact::update_everything()
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
for (int m = p; m < num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
dihedral_type[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_type[atom->map(update_mega_glove[jj+1][i])][m+1];
dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
@ -2242,6 +2245,7 @@ void FixBondReact::update_everything()
improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
for (int m = p; m < num_improper[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
improper_type[atom->map(update_mega_glove[jj+1][i])][m] = improper_type[atom->map(update_mega_glove[jj+1][i])][m+1];
improper_atom1[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
improper_atom2[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
improper_atom3[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];