Merge pull request #619 from jrgissing/molecule_maxspecial (c4b37039) · Commits · 郑智淋 / lammps

src/molecule.cpp

+44 −29

Original line number	Diff line number	Diff line
		@@ -615,14 +615,12 @@ void Molecule::read(int flag)
		}

		// auto-generate special bonds if needed and not in file
		// set maxspecial on first pass, so allocate() has a size

		if (bondflag && specialflag == 0) {
		if (domain->box_exist == 0)
		error->all(FLERR,"Cannot auto-generate special bonds before "
		"simulation box is defined");

		maxspecial = atom->maxspecial;
		if (flag) {
		special_generate();
		specialflag = 1;
		@@ -1115,6 +1113,12 @@ void Molecule::special_generate()
		tagint atom1,atom2;
		int count[natoms];

		// 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;

		// 1-2 neighbors
		@@ -1126,10 +1130,10 @@ void Molecule::special_generate()
		atom2 = bond_atom[i][j]-1;
		nspecial[i][0]++;
		nspecial[atom2][0]++;
		if (count[i] >= maxspecial \|\| count[atom2] >= maxspecial)
		if (count[i] >= atom->maxspecial \|\| count[atom2] >= atom->maxspecial)
		error->one(FLERR,"Molecule auto special bond generation overflow");
		special[i][count[i]++] = atom2 + 1;
		special[atom2][count[atom2]++] = i + 1;
		tmpspecial[i][count[i]++] = atom2 + 1;
		tmpspecial[atom2][count[atom2]++] = i + 1;
		}
		}
		} else {
		@@ -1138,9 +1142,9 @@ void Molecule::special_generate()
		for (int j = 0; j < num_bond[i]; j++) {
		atom1 = i;
		atom2 = bond_atom[i][j];
		if (count[atom1] >= maxspecial)
		if (count[atom1] >= atom->maxspecial)
		error->one(FLERR,"Molecule auto special bond generation overflow");
		special[i][count[atom1]++] = atom2;
		tmpspecial[i][count[atom1]++] = atom2;
		}
		}
		}
		@@ -1152,18 +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[special[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 (special[special[i][m]-1][j] == special[i][k] \|\|
		special[special[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] >= maxspecial)
		if (count[i] >= atom->maxspecial)
		error->one(FLERR,"Molecule auto special bond generation overflow");
		special[i][count[i]++] = special[special[i][m]-1][j];
		tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
		nspecial[i][1]++;
		}
		}
		@@ -1176,23 +1180,34 @@ 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[special[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 (special[special[i][m]-1][j] == special[i][k] \|\|
		special[special[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] >= maxspecial)
		if (count[i] >= atom->maxspecial)
		error->one(FLERR,"Molecule auto special bond generation overflow");
		special[i][count[i]++] = special[special[i][m]-1][j];
		tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
		nspecial[i][2]++;
		}
		}
		}
		}

		maxspecial = 0;
		for (int i = 0; i < natoms; i++)
		maxspecial = MAX(maxspecial,nspecial[i][2]);

		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] = tmpspecial[i][j];

		memory->destroy(tmpspecial);
		}

		/* ----------------------------------------------------------------------
		@@ -1473,7 +1488,7 @@ void Molecule::allocate()
		if (radiusflag) memory->create(radius,natoms,"molecule:radius");
		if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");

		// always allocate num_bond,num_angle,etc and special+nspecial
		// always allocate num_bond,num_angle,etc and nspecial
		// even if not in molecule file, initialize to 0
		// this is so methods that use these arrays don't have to check they exist

		@@ -1485,13 +1500,13 @@ void Molecule::allocate()
		for (int i = 0; i < natoms; i++) num_dihedral[i] = 0;
		memory->create(num_improper,natoms,"molecule:num_improper");
		for (int i = 0; i < natoms; i++) num_improper[i] = 0;

		memory->create(special,natoms,maxspecial,"molecule:special");

		memory->create(nspecial,natoms,3,"molecule:nspecial");
		for (int i = 0; i < natoms; i++)
		nspecial[i][0] = nspecial[i][1] = nspecial[i][2] = 0;

		if (specialflag)
		memory->create(special,natoms,maxspecial,"molecule:special");

		if (bondflag) {
		memory->create(bond_type,natoms,bond_per_atom,
		"molecule:bond_type");

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