Source code for matador.utils.ase_utils

# coding: utf-8
# Distributed under the terms of the MIT License.

""" This file implements some light wrappers to
the Atomic Simulation Environment (ASE).


import copy
from typing import Union
from matador.utils.chem_utils import get_stoich
from matador.utils.cell_utils import get_spacegroup_spg
from matador.crystal import Crystal

__all__ = ["ase2dict", "doc2ase"]

[docs]def ase2dict(atoms, as_model=False) -> Union[dict, Crystal]: """Return a matador document (dictionary or :obj:`Crystal`) from an `ase.Atoms` object. Parameters: atoms (ase.Atoms): input structure. Keyword arguments: as_model (bool): if `True`, return a Crystal instead of a dictionary. Returns: Union[dict, Crystal]: matador output. """ from matador.utils.cell_utils import cart2abc doc = {} # sort atoms, then their positions doc["atom_types"] = atoms.get_chemical_symbols() inds = [i[0] for i in sorted(enumerate(doc["atom_types"]), key=lambda x: x[1])] doc["positions_frac"] = atoms.get_scaled_positions().tolist() doc["positions_frac"] = [doc["positions_frac"][ind] for ind in inds] doc["atom_types"] = [doc["atom_types"][ind] for ind in inds] try: doc["lattice_cart"] = atoms.get_cell().tolist() except AttributeError: doc["lattice_cart"] = atoms.get_cell().array.tolist() doc["lattice_abc"] = cart2abc(doc["lattice_cart"]) doc["num_atoms"] = len(doc["atom_types"]) doc["stoichiometry"] = get_stoich(doc["atom_types"]) doc["cell_volume"] = atoms.get_volume() doc["elems"] = {atom for atom in doc["atom_types"]} doc["num_fu"] = doc["num_atoms"] / int( sum(doc["stoichiometry"][i][1] for i in range(len(doc["stoichiometry"]))) ) doc["space_group"] = get_spacegroup_spg(doc, symprec=0.001) if hasattr(atoms, "info"): doc["ase_info"] = copy.deepcopy( if as_model: doc = Crystal(doc) return doc
[docs]def doc2ase(doc: Union[dict, Crystal], add_keys_to_info=True): """Convert matador document to simple ASE object. Parameters: doc (dict/:obj:`Crystal`): matador document or `Crystal` containing the structure. Keyword arguments: add_keys_to_info (bool): whether or not to add the keys from the matador document to the info section of the Atoms object. """ from ase import Atoms atoms = Atoms( symbols=doc["atom_types"], scaled_positions=doc["positions_frac"], cell=doc["lattice_cart"], pbc=True, ) if add_keys_to_info: if isinstance(doc, Crystal):["matador"] = doc._data else:["matador"] = copy.deepcopy(doc) if "_id" in["matador"]:["matador"]["_id"] = str(["matador"]["_id"]) return atoms