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fix molecule add for MESH and remove 'not compatible' error message

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alphataubio
2024-08-21 16:19:09 -04:00
parent 3aadd8bd84
commit c968787c41
1 changed files with 14 additions and 8 deletions
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22
src/create_atoms.cpp
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@ -303,7 +303,7 @@ void CreateAtoms::command(int narg, char **arg)
if (onemol->xflag == 0) error->all(FLERR, "Create_atoms molecule must have coordinates"); if (onemol->xflag == 0) error->all(FLERR, "Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0) error->all(FLERR, "Create_atoms molecule must have atom types"); 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"); error->all(FLERR, "Invalid atom type {} in create_atoms mol command (onemol->ntypes {} atom->ntypes {})", ntype, onemol->ntypes, atom->ntypes);
if (onemol->tag_require && !atom->tag_enable) if (onemol->tag_require && !atom->tag_enable)
error->all(FLERR, "Create_atoms molecule has atom IDs, but system does not"); error->all(FLERR, "Create_atoms molecule has atom IDs, but system does not");
if (atom->molecular == Atom::TEMPLATE && onemol != atom->avec->onemols[0]) if (atom->molecular == Atom::TEMPLATE && onemol != atom->avec->onemols[0])
@ -319,11 +319,7 @@ void CreateAtoms::command(int narg, char **arg)
memory->create(xmol, onemol->natoms, 3, "create_atoms:xmol"); memory->create(xmol, onemol->natoms, 3, "create_atoms:xmol");
} }
if (style == MESH) { if (style == MESH && scaleflag) error->all(FLERR, "Create_atoms mesh must use 'units box' option");
if (mode == MOLECULE)
error->all(FLERR, "Create_atoms mesh is not compatible with the 'mol' option");
if (scaleflag) error->all(FLERR, "Create_atoms mesh must use 'units box' option");
}
ranlatt = nullptr; ranlatt = nullptr;
if (subsetflag != NONE) ranlatt = new RanMars(lmp, subsetseed + comm->me); if (subsetflag != NONE) ranlatt = new RanMars(lmp, subsetseed + comm->me);
@ -968,7 +964,12 @@ int CreateAtoms::add_bisection(const double vert[3][3], tagint molid)
if ((center[0] >= sublo[0]) && (center[0] < subhi[0]) && (center[1] >= sublo[1]) && if ((center[0] >= sublo[0]) && (center[0] < subhi[0]) && (center[1] >= sublo[1]) &&
(center[1] < subhi[1]) && (center[2] >= sublo[2]) && (center[2] < subhi[2])) { (center[1] < subhi[1]) && (center[2] >= sublo[2]) && (center[2] < subhi[2])) {
atom->avec->create_atom(ntype, center); if (mode == ATOM) atom->avec->create_atom(ntype, center);
else {
get_xmol(center);
add_molecule();
}
int idx = atom->nlocal - 1; int idx = atom->nlocal - 1;
if (atom->radius_flag) atom->radius[idx] = ravg * radscale; if (atom->radius_flag) atom->radius[idx] = ravg * radscale;
if (atom->molecule_flag) atom->molecule[idx] = molid; if (atom->molecule_flag) atom->molecule[idx] = molid;
@ -1050,7 +1051,12 @@ int CreateAtoms::add_quasirandom(const double vert[3][3], tagint molid)
if ((point[0] >= sublo[0]) && (point[0] < subhi[0]) && (point[1] >= sublo[1]) && if ((point[0] >= sublo[0]) && (point[0] < subhi[0]) && (point[1] >= sublo[1]) &&
(point[1] < subhi[1]) && (point[2] >= sublo[2]) && (point[2] < subhi[2])) { (point[1] < subhi[1]) && (point[2] >= sublo[2]) && (point[2] < subhi[2])) {
atom->avec->create_atom(ntype, point); if (mode == ATOM) atom->avec->create_atom(ntype, point);
else {
get_xmol(point);
add_molecule();
}
int idx = atom->nlocal - 1; int idx = atom->nlocal - 1;
if (atom->molecule_flag) atom->molecule[idx] = molid; if (atom->molecule_flag) atom->molecule[idx] = molid;
if (atom->radius_flag) atom->radius[idx] = rad * radscale; if (atom->radius_flag) atom->radius[idx] = rad * radscale;