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Merge branch 'feature-create-atoms-exclude' of https://github.com/erozic/lammps into feature-create-atoms-exclude

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This commit is contained in:
Eugen Rožić
2022-05-06 01:48:37 +02:00
parent ae230a33f5 484a7c5db0
commit 46d638af0c
1 changed files with 13 additions and 6 deletions
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19
src/create_atoms.cpp
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@ -750,8 +750,11 @@ void CreateAtoms::add_random()
coord = xone;
}
// check for overlap of new atom with all others including prior insertions
// minimum_image() required to account for distances across PBC
// 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;
@ -1023,13 +1026,15 @@ void CreateAtoms::loop_lattice(int action)
/* ----------------------------------------------------------------------
add a molecule with its center at center
if quat_user set use quatone, else generate a random quaternion
------------------------------------------------------------------------- */
void CreateAtoms::add_molecule(double *center)
{
double r[3], rotmat[3][3];
// use quatone as-is if user set it
// else generate random quaternion in quatone
if (!quat_user) {
if (domain->dimension == 3) {
r[0] = ranmol->uniform() - 0.5;
@ -1045,12 +1050,14 @@ void CreateAtoms::add_molecule(double *center)
}
MathExtra::quat_to_mat(quatone, rotmat);
onemol->quat_external = quatone;
// create atoms in molecule with atom ID = 0 and mol ID = 0
// reset in caller after all molecules created by all procs
// 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
// max tag of atoms in previous molecules at this point
// onemol->quat_external is used by atom->add_moleclue_atom()
onemol->quat_external = quatone;
int n, natoms = onemol->natoms;
double xnew[3];