def to_berny_geom(mol, include_ghost=INCLUDE_GHOST):
atom_charges = mol.atom_charges()
if include_ghost:
# Symbol Ghost is not supported in current version of pyberny
#species = [mol.atom_symbol(i) if z != 0 else 'Ghost'
# for i,z in enumerate(atom_charges)]
species = [mol.atom_symbol(i) if z != 0 else 'H'
for i,z in enumerate(atom_charges)]
coords = mol.atom_coords() * lib.param.BOHR
else:
atmlst = numpy.where(atom_charges != 0)[0] # Exclude ghost atoms
species = [mol.atom_symbol(i) for i in atmlst]
coords = mol.atom_coords()[atmlst] * lib.param.BOHR
return geomlib.Molecule(species, coords)
def to_berny_geom(mol, include_ghost=INCLUDE_GHOST):
atom_charges = mol.atom_charges()
if include_ghost:
# Symbol Ghost is not supported in current version of pyberny
#species = [mol.atom_symbol(i) if z != 0 else 'Ghost'
# for i,z in enumerate(atom_charges)]
species = [mol.atom_symbol(i) if z != 0 else 'H'
for i,z in enumerate(atom_charges)]
coords = mol.atom_coords() * lib.param.BOHR
else:
atmlst = numpy.where(atom_charges != 0)[0] # Exclude ghost atoms
species = [mol.atom_symbol(i) for i in atmlst]
coords = mol.atom_coords()[atmlst] * lib.param.BOHR
# geomlib.Geometry is available in the new version of pyberny solver. (issue #212)
if getattr(geomlib, 'Geometry', None):
return geomlib.Geometry(species, coords)
else:
return geomlib.Molecule(species, coords)
def to_berny_geom(mol):
species = [mol.atom_symbol(i) for i in range(mol.natm)]
coords = mol.atom_coords() * lib.param.BOHR
return geomlib.Molecule(species, coords)
