def generate_raspa_mol(ciffile, chargefile, outputfile):
atoms = Atoms.from_cif(ciffile)
# update charges
charges = np.array(
[float(line.strip()) for line in chargefile if line.strip() != ''])
assert len(charges) == len(atoms.positions)
atoms.charges = charges
atoms.to_mol(outputfile)
def cif2lmpdat(ciffile, outputfile, chargefile=None, mic=None):
atoms = Atoms.from_cif(ciffile)
# update charges
if chargefile is not None:
charges = np.array(
[float(line.strip()) for line in chargefile if line.strip() != ''])
assert len(charges) == len(atoms.positions)
atoms.charges = charges
# replicate to meet minimum image convention, if necessary
if mic is not None:
repls = np.array(np.ceil(2 * mic / np.diag(atoms.cell)), dtype=int)
atoms = atoms.replicate(repls)
assign_pair_params_to_structure(atoms)
atoms.to_lammps_data(outputfile)
def functionalize_structure_with_linkers(structure_path,
linker_path,
fnlinkers,
output_dir=Path()):
linker = Atoms.from_cml(Path(linker_path))
structure = Atoms.from_cif(structure_path)
output_dir = Path(output_dir)
assign_pair_params_to_structure(structure)
for fnlinker_path in fnlinkers:
print("reading %s" % fnlinker_path)
fnlinker = Atoms.from_lammps_data(open(fnlinker_path, "r"),
use_comment_for_type_labels=True)
try:
new_structure = replace_pattern_in_structure(
structure, linker, fnlinker)
with open(
output_dir.joinpath(Path(fnlinker_path).stem + ".lmpdat"),
"w") as fd:
new_structure.to_lammps_data(fd)
except Exception as e:
print("ERROR! ", e.args)
