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Logic fix in random-overlap and comment implemented

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This commit is contained in:
Eugen Rožić
2022-05-05 23:35:11 +02:00
parent 6b47d6246b
commit 93c0f09c31
2 changed files with 22 additions and 46 deletions
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67
src/create_atoms.cpp
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@ -259,7 +259,7 @@ void CreateAtoms::command(int narg, char **arg)
error->all(FLERR, "Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR, "Create_atoms molecule must have atom types");
if (ntype+onemol->ntypes <= 0 || ntype+onemol->ntypes > atom->ntypes)
if (ntype + onemol->ntypes <= 0 || ntype + onemol->ntypes > atom->ntypes)
error->all(FLERR, "Invalid atom type in create_atoms mol command");
if (onemol->tag_require && !atom->tag_enable)
error->all(FLERR, "Create_atoms molecule has atom IDs, but system does not");
@ -268,11 +268,9 @@ void CreateAtoms::command(int narg, char **arg)
// use geometric center of molecule for insertion
// molecule random number generator, different for each proc
// molecule_coords = memory for atom coords in the molecule
onemol->compute_center();
ranmol = new RanMars(lmp, molseed + comm->me);
memory->create(molecule_coords, onemol->natoms, 3, "create_atoms:molecule_coords");
}
ranlatt = nullptr;
@ -581,7 +579,6 @@ void CreateAtoms::command(int narg, char **arg)
// clean up
if (mode == MOLECULE) memory->destroy(molecule_coords);
delete ranmol;
delete ranlatt;
@ -653,8 +650,7 @@ void CreateAtoms::add_single()
if (mode == ATOM) {
atom->avec->create_atom(ntype, xone);
} else {
generate_molecule(xone);
add_molecule();
add_molecule(xone);
}
}
}
@ -753,8 +749,6 @@ void CreateAtoms::add_random()
coord = xone;
}
if (mode == MOLECULE) generate_molecule(xone);
// check for overlap of new atom with all others including prior insertions
// minimum_image() required to account for distances across PBC
@ -764,16 +758,14 @@ void CreateAtoms::add_random()
int reject = 0;
for (int i = 0; i < nlocal; i++) {
if (mode == ATOM) {
delx = xone[0] - x[i][0];
dely = xone[1] - x[i][1];
delz = xone[2] - x[i][2];
domain->minimum_image(delx,dely,delz);
distsq = delx*delx + dely*dely + delz*delz;
if (distsq < odistsq) {
reject = 1;
break;
}
delx = xone[0] - x[i][0];
dely = xone[1] - x[i][1];
delz = xone[2] - x[i][2];
domain->minimum_image(delx, dely, delz);
distsq = delx*delx + dely*dely + delz*delz;
if (distsq < odistsq) {
reject = 1;
break;
}
}
int reject_any;
@ -802,7 +794,7 @@ void CreateAtoms::add_random()
if (mode == ATOM) {
atom->avec->create_atom(ntype, xone);
} else {
add_molecule();
add_molecule(xone);
}
}
}
@ -810,7 +802,7 @@ void CreateAtoms::add_random()
// warn if did not successfully insert Nrandom atoms/molecules
if (ninsert < nrandom && comm->me == 0)
error->warning(FLERR,"Only inserted {} particles out of {}",ninsert,nrandom);
error->warning(FLERR, "Only inserted {} particles out of {}", ninsert, nrandom);
// clean-up
@ -1009,8 +1001,7 @@ void CreateAtoms::loop_lattice(int action)
if (mode == ATOM) {
atom->avec->create_atom(basistype[m], x);
} else {
generate_molecule(x);
add_molecule();
add_molecule(x);
}
} else if (action == COUNT) {
if (nlatt == MAXSMALLINT) nlatt_overflow = 1;
@ -1018,8 +1009,7 @@ void CreateAtoms::loop_lattice(int action)
if (mode == ATOM) {
atom->avec->create_atom(basistype[m], x);
} else {
generate_molecule(x);
add_molecule();
add_molecule(x);
}
}
@ -1031,12 +1021,11 @@ void CreateAtoms::loop_lattice(int action)
}
/* ----------------------------------------------------------------------
generate molecule atom coordinates for a given center and rotation
if quat_user set use it, else generate a random quaternion
result is stored in temp_mol_coords and onemol->quat_external
add a molecule with its center at center
if quat_user set use quatone, else generate a random quaternion
------------------------------------------------------------------------- */
void CreateAtoms::generate_molecule(double *center)
void CreateAtoms::add_molecule(double *center)
{
double r[3], rotmat[3][3];
@ -1055,31 +1044,19 @@ void CreateAtoms::generate_molecule(double *center)
}
MathExtra::quat_to_mat(quatone, rotmat);
onemol->quat_external = quatone;
int natoms = onemol->natoms;
for (int m = 0; m < natoms; m++) {
MathExtra::matvec(rotmat, onemol->dx[m], molecule_coords[m]);
MathExtra::add3(molecule_coords[m], center, molecule_coords[m]);
}
}
/* ----------------------------------------------------------------------
add molecule to system
generated coords are in molecule_coords
------------------------------------------------------------------------- */
void CreateAtoms::add_molecule()
{
// create atoms in molecule with atom ID = 0 and mol ID = 0
// reset in caller after all molecules created by all procs
// pass add_molecule_atom an offset of 0 since don't know
// max tag of atoms in previous molecules at this point
onemol->quat_external = quatone;
int n, natoms = onemol->natoms;
double xnew[3];
for (int m = 0; m < natoms; m++) {
atom->avec->create_atom(ntype+onemol->type[m], molecule_coords[m]);
MathExtra::matvec(rotmat, onemol->dx[m], xnew);
MathExtra::add3(xnew, center, xnew);
atom->avec->create_atom(ntype + onemol->type[m], xnew);
n = atom->nlocal - 1;
atom->add_molecule_atom(onemol, m, n, 0);
}

1
src/create_atoms.h
View File

@ -58,7 +58,6 @@ class CreateAtoms : public Command {
class Molecule *onemol;
class RanMars *ranmol;
class RanMars *ranlatt;
double **molecule_coords;
int triclinic;
double sublo[3], subhi[3]; // epsilon-extended proc sub-box for adding atoms