def pmg2dict(pmg: Structure, as_model=False) -> Union[dict, Crystal]:
""" Converts a pymatgen.Structure to a matador document/Crystal.
Parameters:
pmg (pymatgen.Structure): the structure to convert.
Keyword arguments:
as_model (bool): if True, return a Crystal instead of a dict.
Returns:
Union[dict, Crystal]: the converted structure.
"""
from matador.utils.ase_utils import ase2dict
return ase2dict(AseAtomsAdaptor.get_atoms(pmg), as_model=as_model)
def _ase_cif2dict(fname):
""" Read cif file into ASE object,
then convert ASE Atoms into matador document.
Parameters:
fname (str): cif filename
Returns:
(dict, bool): simple matador document with error status.
"""
import ase.io
from matador.utils.ase_utils import ase2dict
fname = fname.replace('.cif', '')
atoms = ase.io.read(fname + '.cif')
doc = ase2dict(atoms)
return doc, True
def test_ase2dict(self):
doc = ase2dict(self.ase_atoms)
self.assertEqual(doc["atom_types"],
sorted(["Si", "O", "Si", "O", "Si", "O", "Si", "O"]))
self.assertListEqual(doc["lattice_cart"][0], [12, 0, 0])
self.assertListEqual(doc["lattice_cart"][1], [0, 12, 0])
self.assertListEqual(doc["lattice_cart"][2], [0, 0, 12])
self.assertListEqual(doc["lattice_abc"][0], [12, 12, 12])
self.assertListEqual(doc["lattice_abc"][1], [90, 90, 90])
self.assertAlmostEqual(doc["cell_volume"], 12**3)
self.assertEqual(len(doc["positions_frac"]), len(doc["atom_types"]))
self.assertListEqual(doc["positions_frac"][0], [0.5, 0.0, 0.0])
self.assertListEqual(doc["positions_frac"][1], [0.5, 0.5, 0.5])
self.assertListEqual(doc["positions_frac"][3], [0.0, 0.5, 0.0])
self.assertEqual(doc["num_atoms"], 8)
self.assertEqual(doc["num_fu"], 4)
self.assertListEqual(doc["stoichiometry"][0], ["O", 1.0])
self.assertListEqual(doc["stoichiometry"][1], ["Si", 1.0])
self.assertListEqual(sorted(list(doc["elems"])), ["O", "Si"])
self.assertEqual(doc["space_group"], "Fm-3m")
self.assertDictEqual(doc["ase_info"], self.ase_atoms.info)
def mp2dict(response):
""" Convert a response from pymatgen.MPRester into a matador document,
via an ASE atoms object. Expects certain properties to be requested
in order to construct a full matador document, e.g. `structure` & `input`.
Parameters:
response (dict): containing one item of the MPRester response.
"""
if 'structure' not in response:
raise RuntimeError('`structure` key missing, nothing to scrape...')
ase_struct = AseAtomsAdaptor.get_atoms(response['structure'])
doc = ase2dict(ase_struct)
doc['source'] = []
if 'material_id' in response:
doc['_mp_id'] = response['material_id']
doc['source'].append('{}'.format(doc['_mp_id']))
if 'pf_ids' in response:
if response['pf_ids']:
doc['_mp_pf_ids'] = response['pf_ids']
for _id in doc['_mp_pf_ids']:
doc['source'].append('pf-{}'.format(_id))
if 'icsd_ids' in response:
if response['icsd_ids']:
doc['icsd'] = response['icsd_ids'][0]
doc['_mp_icsd_ids'] = response['icsd_ids']
if 'formation_energy_per_atom' in response:
doc['formation_energy_per_atom'] = response['formation_energy_per_atom']
doc['enthalpy_per_atom'] = response['formation_energy_per_atom']
doc['enthalpy'] = doc['enthalpy_per_atom'] * doc['num_atoms']
doc['formation_energy'] = doc['formation_energy_per_atom'] * doc['num_atoms']
if 'e_above_hull' in response:
doc['hull_distance'] = response['e_above_hull']
if 'doi' in response:
doc['_mp_doi'] = response['doi']
if 'snl' in response:
doc['_mp_references'] = response['snl'].references
if 'input' in response:
incar = response['input']['incar']
if not isinstance(incar, dict):
incar = incar.as_dict()
doc['cut_off_energy'] = incar['ENCUT']
doc['xc_functional'] = 'PBE'
kpts = response['input']['kpoints']
doc['kpoints_mp_grid'] = kpts.kpts[0]
doc['kpoints_mp_offset'] = kpts.kpts_shift
doc['pressure'] = 0.0
doc['stress'] = 0.0
doc['kpoints_mp_spacing'] = calc_mp_spacing(doc['lattice_cart'], doc['kpoints_mp_grid'])
doc['spin_polarized'] = bool(incar['ISPIN'] - 1)
return doc
def from_ase(cls, atoms):
from matador.utils.ase_utils import ase2dict
return ase2dict(atoms, as_model=True)