allocate the temporary special array on the heap and not the stack (it may get... (bf7cff73) · Commits · 郑智淋 / lammps

src/molecule.cpp

+22 −17

Original line number	Diff line number	Diff line
		@@ -1113,8 +1113,11 @@ void Molecule::special_generate()
		tagint atom1,atom2;
		int count[natoms];

		// temporary special array
		tagint spec_temp[natoms][atom->maxspecial];
		// temporary array for special atoms

		tagint **tmpspecial;
		memory->create(tmpspecial,natoms,atom->maxspecial,"molecule:tmpspecial");
		memset(&tmpspecial[0][0],0,sizeof(tagint)natomsatom->maxspecial);

		for (int i = 0; i < natoms; i++) count[i] = 0;

		@@ -1129,8 +1132,8 @@ void Molecule::special_generate()
		nspecial[atom2][0]++;
		if (count[i] >= atom->maxspecial \|\| count[atom2] >= atom->maxspecial)
		error->one(FLERR,"Molecule auto special bond generation overflow");
		spec_temp[i][count[i]++] = atom2 + 1;
		spec_temp[atom2][count[atom2]++] = i + 1;
		tmpspecial[i][count[i]++] = atom2 + 1;
		tmpspecial[atom2][count[atom2]++] = i + 1;
		}
		}
		} else {
		@@ -1141,7 +1144,7 @@ void Molecule::special_generate()
		atom2 = bond_atom[i][j];
		if (count[atom1] >= atom->maxspecial)
		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;
		for (int i = 0; i < natoms; i++) {
		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;
		for (int k =0; k < count[i]; k++) {
		if (spec_temp[spec_temp[i][m]-1][j] == spec_temp[i][k] \|\|
		spec_temp[spec_temp[i][m]-1][j] == i+1) {
		if (tmpspecial[tmpspecial[i][m]-1][j] == tmpspecial[i][k] \|\|
		tmpspecial[tmpspecial[i][m]-1][j] == i+1) {
		dedup = 1;
		}
		}
		if (!dedup) {
		if (count[i] >= atom->maxspecial)
		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]++;
		}
		}
		@@ -1177,18 +1180,18 @@ void Molecule::special_generate()

		for (int i = 0; i < natoms; i++) {
		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;
		for (int k =0; k < count[i]; k++) {
		if (spec_temp[spec_temp[i][m]-1][j] == spec_temp[i][k] \|\|
		spec_temp[spec_temp[i][m]-1][j] == i+1) {
		if (tmpspecial[tmpspecial[i][m]-1][j] == tmpspecial[i][k] \|\|
		tmpspecial[tmpspecial[i][m]-1][j] == i+1) {
		dedup = 1;
		}
		}
		if (!dedup) {
		if (count[i] >= atom->maxspecial)
		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]++;
		}
		}
		@@ -1202,7 +1205,9 @@ void Molecule::special_generate()
		memory->create(special,natoms,maxspecial,"molecule:special");
		for (int i = 0; i < natoms; i++)
		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);
		}

		/* ----------------------------------------------------------------------

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