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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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This commit is contained in:
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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28
src/MISC/fix_deposit.cpp
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@ -301,6 +301,13 @@ void FixDeposit::pre_exchange()
if (next_reneighbor != update->ntimestep) return;
// clear ghost count and any ghost bonus data internal to AtomVec
// same logic as beginning of Comm::exchange()
// do it now b/c inserting atoms will overwrite ghost atoms
atom->nghost = 0;
atom->avec->clear_bonus();
// compute current offset = bottom of insertion volume
double offset = 0.0;
@ -524,8 +531,10 @@ void FixDeposit::pre_exchange()
atom->v[n][0] = vnew[0];
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
if (mode == MOLECULE)
if (mode == MOLECULE) {
onemols[imol]->quat_external = quat;
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
}
modify->create_attribute(n);
}
}
@ -559,7 +568,8 @@ void FixDeposit::pre_exchange()
// reset global natoms,nbonds,etc
// increment maxtag_all and maxmol_all if necessary
// if global map exists, reset it now instead of waiting for comm
// since adding atoms messes up ghosts
// since other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
if (success) {
atom->natoms += natom;
@ -576,7 +586,6 @@ void FixDeposit::pre_exchange()
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
@ -811,23 +820,24 @@ void *FixDeposit::extract(const char *str, int &itype)
} else {
// find a molecule in template with matching type
// loop over onemols molecules
// skip a molecule with no atoms as large as itype
oneradius = 0.0;
for (int i = 0; i < nmol; i++) {
if (itype-ntype > onemols[i]->ntypes) continue;
if (itype > ntype+onemols[i]->ntypes) continue;
double *radius = onemols[i]->radius;
int *type = onemols[i]->type;
int natoms = onemols[i]->natoms;
// check radii of matching types in Molecule
// check radii of atoms in Molecule with matching types
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked in pre_exchange()
oneradius = 0.0;
for (int i = 0; i < natoms; i++)
if (type[i] == itype-ntype) {
if (type[i]+ntype == itype) {
if (radius) oneradius = MAX(oneradius,radius[i]);
else oneradius = 0.5;
else oneradius = MAX(oneradius,0.5);
}
}
}