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there is no need to using tagints in molecule templates

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This commit is contained in:
Axel Kohlmeyer
2025-06-21 11:49:55 -04:00
parent eae76faa1f
commit 3eae4066f3
2 changed files with 27 additions and 27 deletions
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40
src/molecule.cpp
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@ -839,7 +839,7 @@ void Molecule::molecules(char *line)
if (iatom < 0 || iatom >= natoms)
error->all(FLERR, "Invalid atom index in Molecules section of molecule file");
count[iatom]++;
molecule[iatom] = values.next_tagint();
molecule[iatom] = values.next_int();
// molecule[iatom] += moffset; // placeholder for possible molecule offset
}
} catch (TokenizerException &e) {
@ -1045,7 +1045,7 @@ void Molecule::bonds(int flag, char *line)
{
const std::string location = "Bonds section of molecule file";
int itype;
tagint m, atom1, atom2;
int m, atom1, atom2;
std::string typestr;
int newton_bond = force->newton_bond;
@ -1131,7 +1131,7 @@ void Molecule::angles(int flag, char *line)
{
const std::string location = "Angles section of molecule file";
int itype;
tagint m, atom1, atom2, atom3;
int m, atom1, atom2, atom3;
std::string typestr;
int newton_bond = force->newton_bond;
@ -1232,7 +1232,7 @@ void Molecule::dihedrals(int flag, char *line)
{
const std::string location = "Dihedrals section of molecule file";
int itype;
tagint m, atom1, atom2, atom3, atom4;
int m, atom1, atom2, atom3, atom4;
std::string typestr;
int newton_bond = force->newton_bond;
@ -1347,7 +1347,7 @@ void Molecule::impropers(int flag, char *line)
{
const std::string location = "Impropers section of molecule file";
int itype;
tagint m, atom1, atom2, atom3, atom4;
int m, atom1, atom2, atom3, atom4;
std::string typestr;
int newton_bond = force->newton_bond;
@ -1544,13 +1544,13 @@ void Molecule::special_read(char *line)
void Molecule::special_generate()
{
int newton_bond = force->newton_bond;
tagint atom1, atom2;
int atom1, atom2;
// temporary array for special atoms
tagint **tmpspecial;
int **tmpspecial;
memory->create(tmpspecial, natoms, atom->maxspecial, "molecule:tmpspecial");
memset(&tmpspecial[0][0], 0, sizeof(tagint) * natoms * atom->maxspecial);
memset(&tmpspecial[0][0], 0, sizeof(int) * natoms * atom->maxspecial);
for (int i = 0; i < natoms; i++) count[i] = 0;
@ -1694,30 +1694,30 @@ void Molecule::shakeatom_read(char *line)
switch (shake_flag[iatom]) {
case 1:
shake_atom[iatom][0] = values.next_tagint();
shake_atom[iatom][1] = values.next_tagint();
shake_atom[iatom][2] = values.next_tagint();
shake_atom[iatom][0] = values.next_int();
shake_atom[iatom][1] = values.next_int();
shake_atom[iatom][2] = values.next_int();
nwant = 4;
break;
case 2:
shake_atom[iatom][0] = values.next_tagint();
shake_atom[iatom][1] = values.next_tagint();
shake_atom[iatom][0] = values.next_int();
shake_atom[iatom][1] = values.next_int();
nwant = 3;
break;
case 3:
shake_atom[iatom][0] = values.next_tagint();
shake_atom[iatom][1] = values.next_tagint();
shake_atom[iatom][2] = values.next_tagint();
shake_atom[iatom][0] = values.next_int();
shake_atom[iatom][1] = values.next_int();
shake_atom[iatom][2] = values.next_int();
nwant = 4;
break;
case 4:
shake_atom[iatom][0] = values.next_tagint();
shake_atom[iatom][1] = values.next_tagint();
shake_atom[iatom][2] = values.next_tagint();
shake_atom[iatom][3] = values.next_tagint();
shake_atom[iatom][0] = values.next_int();
shake_atom[iatom][1] = values.next_int();
shake_atom[iatom][2] = values.next_int();
shake_atom[iatom][3] = values.next_int();
nwant = 5;
break;

14
src/molecule.h
View File

@ -61,7 +61,7 @@ class Molecule : protected Pointers {
double **x; // displacement of each atom from origin
int *type; // type of each atom
tagint *molecule; // molecule of each atom
int *molecule; // molecule-id of each atom
double *q; // charge on each atom
double *radius; // radius of each atom
double *rmass; // mass of each atom
@ -69,25 +69,25 @@ class Molecule : protected Pointers {
int *num_bond; // bonds, angles, dihedrals, impropers for each atom
int **bond_type;
tagint **bond_atom;
int **bond_atom;
int *num_angle;
int **angle_type;
tagint **angle_atom1, **angle_atom2, **angle_atom3;
int **angle_atom1, **angle_atom2, **angle_atom3;
int *num_dihedral;
int **dihedral_type;
tagint **dihedral_atom1, **dihedral_atom2, **dihedral_atom3, **dihedral_atom4;
int **dihedral_atom1, **dihedral_atom2, **dihedral_atom3, **dihedral_atom4;
int *num_improper;
int **improper_type;
tagint **improper_atom1, **improper_atom2, **improper_atom3, **improper_atom4;
int **improper_atom1, **improper_atom2, **improper_atom3, **improper_atom4;
int **nspecial;
tagint **special;
int **special;
int *shake_flag;
tagint **shake_atom;
int **shake_atom;
int **shake_type;
class AtomVecBody *avec_body;