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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14421 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-01-11 22:00:29 +00:00
parent e24ed78dd1
commit e72cef0c3a
3 changed files with 43 additions and 24 deletions
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35
src/create_atoms.cpp
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@ -347,6 +347,13 @@ void CreateAtoms::command(int narg, char **arg)
}
}
// clear ghost count and any ghost bonus data internal to AtomVec
// same logic as beginning of Comm::exchange()
// do it now b/c creating atoms will overwrite ghost atoms
atom->nghost = 0;
atom->avec->clear_bonus();
// add atoms/molecules in one of 3 ways
bigint natoms_previous = atom->natoms;
@ -400,11 +407,10 @@ void CreateAtoms::command(int narg, char **arg)
if (atom->tag_enable) atom->tag_extend();
atom->tag_check();
// create global mapping of atoms
// zero nghost in case are adding new atoms to existing atoms
// if global map exists, reset it
// invoke map_init() b/c atom count has grown
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
@ -595,7 +601,7 @@ void CreateAtoms::add_single()
if (mode == ATOM) atom->avec->create_atom(ntype,xone);
else if (quatone[0] == 0.0 && quatone[1] == 0.0 && quatone[2] == 0.0)
add_molecule(xone);
else add_molecule(xone,&quatone[0]);
else add_molecule(xone,quatone);
}
}
@ -807,24 +813,25 @@ void CreateAtoms::add_molecule(double *center, double *quat_user)
int n;
double r[3],rotmat[3][3],quat[4],xnew[3];
if (domain->dimension == 3) {
r[0] = ranmol->uniform() - 0.5;
r[1] = ranmol->uniform() - 0.5;
r[2] = ranmol->uniform() - 0.5;
} else {
r[0] = r[1] = 0.0;
r[2] = 1.0;
}
if (quat_user) {
quat[0] = quat_user[0]; quat[1] = quat_user[1];
quat[2] = quat_user[2]; quat[3] = quat_user[3];
} else {
double theta = ranmol->uniform() * MY_2PI;
if (domain->dimension == 3) {
r[0] = ranmol->uniform() - 0.5;
r[1] = ranmol->uniform() - 0.5;
r[2] = ranmol->uniform() - 0.5;
} else {
r[0] = r[1] = 0.0;
r[2] = 1.0;
}
MathExtra::norm3(r);
double theta = ranmol->uniform() * MY_2PI;
MathExtra::axisangle_to_quat(r,theta,quat);
}
MathExtra::quat_to_mat(quat,rotmat);
onemol->quat_external = quat;
// create atoms in molecule with atom ID = 0 and mol ID = 0
// reset in caller after all moleclues created by all procs