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create_atoms:overlap_keyword_w_atomic_molecules

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This commit is contained in:
Jacob Gissinger
2023-06-07 22:04:28 -04:00
parent 5fdba37492
commit 0e07089de6
2 changed files with 81 additions and 27 deletions
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103
src/create_atoms.cpp
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@ -308,6 +308,7 @@ void CreateAtoms::command(int narg, char **arg)
onemol->compute_center();
ranmol = new RanMars(lmp, molseed + comm->me);
memory->create(xmol, onemol->natoms, 3, "create_atoms:xmol");
}
if (style == MESH) {
@ -634,6 +635,7 @@ void CreateAtoms::command(int narg, char **arg)
delete[] xstr;
delete[] ystr;
delete[] zstr;
if (mode == MOLECULE) memory->destroy(xmol);
// for MOLECULE mode:
// create special bond lists for molecular systems,
@ -697,7 +699,8 @@ void CreateAtoms::add_single()
if (mode == ATOM) {
atom->avec->create_atom(ntype, xone);
} else {
add_molecule(xone);
get_xmol(xone);
add_molecule();
}
}
}
@ -708,15 +711,17 @@ void CreateAtoms::add_single()
void CreateAtoms::add_random()
{
int incr;
double xlo, ylo, zlo, xhi, yhi, zhi, zmid;
double delx, dely, delz, distsq, odistsq;
double lamda[3], *coord;
double *boxlo, *boxhi;
double *boxlo, *boxhi, *xmolbuf;
if (overlapflag) {
double odist = overlap;
if (mode == MOLECULE) odist += onemol->molradius;
odistsq = odist * odist;
if (mode == MOLECULE)
memory->create(xmolbuf, onemol->natoms*3, "create_atoms:xmolbuf");
}
// random number generator, same for all procs
@ -799,25 +804,54 @@ void CreateAtoms::add_random()
// check for overlap of new atom/mol with all other atoms
// including prior insertions
// minimum_image() needed to account for distances across PBC
// new molecule only checks its center pt against others
// odistsq is expanded for mode=MOLECULE to account for molecule size
if (overlapflag) {
double **x = atom->x;
int nlocal = atom->nlocal;
int reject = 0;
for (int i = 0; i < nlocal; i++) {
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;
if (mode == ATOM) {
for (int i = 0; i < nlocal; i++) {
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;
}
}
} else {
int incr;
if (comm->me == 0) {
get_xmol(xone);
incr = 0;
for (int i = 0; i < onemol->natoms; i++)
for (int j = 0; j < 3; j++)
xmolbuf[incr++] = xmol[i][j];
}
MPI_Bcast(xmolbuf, onemol->natoms*3, MPI_DOUBLE, 0, world);
incr = 0;
for (int i = 0; i < onemol->natoms; i++)
for (int j = 0; j < 3; j++)
xmol[i][j] = xmolbuf[incr++];
for (int i = 0; i < nlocal; i++) {
for (int j = 0; j < onemol->natoms; j++) {
delx = xmol[j][0] - x[i][0];
dely = xmol[j][1] - x[i][1];
delz = xmol[j][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;
MPI_Allreduce(&reject, &reject_any, 1, MPI_INT, MPI_MAX, world);
if (reject_any) continue;
@ -844,7 +878,11 @@ void CreateAtoms::add_random()
if (mode == ATOM) {
atom->avec->create_atom(ntype, xone);
} else {
add_molecule(xone);
// atomic coordinates calculated above for overlap check
if (!overlapflag) get_xmol(xone);
add_molecule();
}
}
}
@ -857,6 +895,7 @@ void CreateAtoms::add_random()
// clean-up
delete random;
if (overlapflag && mode == MOLECULE) memory->destroy(xmolbuf);
}
/* ----------------------------------------------------------------------
@ -1346,7 +1385,8 @@ void CreateAtoms::loop_lattice(int action)
if (mode == ATOM) {
atom->avec->create_atom(basistype[m], x);
} else {
add_molecule(x);
get_xmol(x);
add_molecule();
}
} else if (action == COUNT) {
if (nlatt == MAXSMALLINT) nlatt_overflow = 1;
@ -1354,7 +1394,8 @@ void CreateAtoms::loop_lattice(int action)
if (mode == ATOM) {
atom->avec->create_atom(basistype[m], x);
} else {
add_molecule(x);
get_xmol(x);
add_molecule();
}
}
@ -1369,7 +1410,7 @@ void CreateAtoms::loop_lattice(int action)
add a molecule with its center at center
------------------------------------------------------------------------- */
void CreateAtoms::add_molecule(double *center)
void CreateAtoms::get_xmol(double *center)
{
double r[3], rotmat[3][3];
@ -1392,10 +1433,6 @@ void CreateAtoms::add_molecule(double *center)
MathExtra::quat_to_mat(quatone, rotmat);
// create atoms in molecule with atom ID = 0 and mol ID = 0
// IDs are 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 is used by atom->add_moleclue_atom()
onemol->quat_external = quatone;
@ -1405,9 +1442,25 @@ void CreateAtoms::add_molecule(double *center)
for (int m = 0; m < natoms; 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);
for (int i = 0; i < 3; i++)
xmol[m][i] = xnew[i];
}
}
/* ----------------------------------------------------------------------
add a molecule with atom coordinates from xmol
------------------------------------------------------------------------- */
void CreateAtoms::add_molecule()
{
// create atoms in molecule with atom ID = 0 and mol ID = 0
// IDs are 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
for (int m = 0; m < onemol->natoms; m++) {
atom->avec->create_atom(ntype + onemol->type[m], xmol[m]);
atom->add_molecule_atom(onemol, m, atom->nlocal - 1, 0);
}
}