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allocate the temporary special array on the heap and not the stack (it may get too big quickly) and clear the array before use.

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This commit is contained in:
Axel Kohlmeyer
2017-08-18 14:23:48 -04:00
parent 9e85b3178a
commit bf7cff73d4
1 changed files with 22 additions and 17 deletions
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33
src/molecule.cpp
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@ -1113,8 +1113,11 @@ void Molecule::special_generate()
tagint atom1,atom2; tagint atom1,atom2;
int count[natoms]; int count[natoms];
// temporary special array // temporary array for special atoms
tagint spec_temp[natoms][atom->maxspecial];
tagint **tmpspecial;
memory->create(tmpspecial,natoms,atom->maxspecial,"molecule:tmpspecial");
memset(&tmpspecial[0][0],0,sizeof(tagint)*natoms*atom->maxspecial);
for (int i = 0; i < natoms; i++) count[i] = 0; for (int i = 0; i < natoms; i++) count[i] = 0;
@ -1129,8 +1132,8 @@ void Molecule::special_generate()
nspecial[atom2][0]++; nspecial[atom2][0]++;
if (count[i] >= atom->maxspecial || count[atom2] >= atom->maxspecial) if (count[i] >= atom->maxspecial || count[atom2] >= atom->maxspecial)
error->one(FLERR,"Molecule auto special bond generation overflow"); error->one(FLERR,"Molecule auto special bond generation overflow");
spec_temp[i][count[i]++] = atom2 + 1; tmpspecial[i][count[i]++] = atom2 + 1;
spec_temp[atom2][count[atom2]++] = i + 1; tmpspecial[atom2][count[atom2]++] = i + 1;
} }
} }
} else { } else {
@ -1141,7 +1144,7 @@ void Molecule::special_generate()
atom2 = bond_atom[i][j]; atom2 = bond_atom[i][j];
if (count[atom1] >= atom->maxspecial) if (count[atom1] >= atom->maxspecial)
error->one(FLERR,"Molecule auto special bond generation overflow"); error->one(FLERR,"Molecule auto special bond generation overflow");
spec_temp[i][count[atom1]++] = atom2; tmpspecial[i][count[atom1]++] = atom2;
} }
} }
} }
@ -1153,18 +1156,18 @@ void Molecule::special_generate()
int dedup; int dedup;
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
for (int m = 0; m < nspecial[i][0]; m++) { for (int m = 0; m < nspecial[i][0]; m++) {
for (int j = 0; j < nspecial[spec_temp[i][m]-1][0]; j++) { for (int j = 0; j < nspecial[tmpspecial[i][m]-1][0]; j++) {
dedup = 0; dedup = 0;
for (int k =0; k < count[i]; k++) { for (int k =0; k < count[i]; k++) {
if (spec_temp[spec_temp[i][m]-1][j] == spec_temp[i][k] || if (tmpspecial[tmpspecial[i][m]-1][j] == tmpspecial[i][k] ||
spec_temp[spec_temp[i][m]-1][j] == i+1) { tmpspecial[tmpspecial[i][m]-1][j] == i+1) {
dedup = 1; dedup = 1;
} }
} }
if (!dedup) { if (!dedup) {
if (count[i] >= atom->maxspecial) if (count[i] >= atom->maxspecial)
error->one(FLERR,"Molecule auto special bond generation overflow"); error->one(FLERR,"Molecule auto special bond generation overflow");
spec_temp[i][count[i]++] = spec_temp[spec_temp[i][m]-1][j]; tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
nspecial[i][1]++; nspecial[i][1]++;
} }
} }
@ -1177,18 +1180,18 @@ void Molecule::special_generate()
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
for (int m = nspecial[i][0]; m < nspecial[i][1]; m++) { for (int m = nspecial[i][0]; m < nspecial[i][1]; m++) {
for (int j = 0; j < nspecial[spec_temp[i][m]-1][0]; j++) { for (int j = 0; j < nspecial[tmpspecial[i][m]-1][0]; j++) {
dedup = 0; dedup = 0;
for (int k =0; k < count[i]; k++) { for (int k =0; k < count[i]; k++) {
if (spec_temp[spec_temp[i][m]-1][j] == spec_temp[i][k] || if (tmpspecial[tmpspecial[i][m]-1][j] == tmpspecial[i][k] ||
spec_temp[spec_temp[i][m]-1][j] == i+1) { tmpspecial[tmpspecial[i][m]-1][j] == i+1) {
dedup = 1; dedup = 1;
} }
} }
if (!dedup) { if (!dedup) {
if (count[i] >= atom->maxspecial) if (count[i] >= atom->maxspecial)
error->one(FLERR,"Molecule auto special bond generation overflow"); error->one(FLERR,"Molecule auto special bond generation overflow");
spec_temp[i][count[i]++] = spec_temp[spec_temp[i][m]-1][j]; tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
nspecial[i][2]++; nspecial[i][2]++;
} }
} }
@ -1202,7 +1205,9 @@ void Molecule::special_generate()
memory->create(special,natoms,maxspecial,"molecule:special"); memory->create(special,natoms,maxspecial,"molecule:special");
for (int i = 0; i < natoms; i++) for (int i = 0; i < natoms; i++)
for (int j = 0; j < nspecial[i][2]; j++) for (int j = 0; j < nspecial[i][2]; j++)
special[i][j] = spec_temp[i][j]; special[i][j] = tmpspecial[i][j];
memory->destroy(tmpspecial);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------