def test_serialization(self):
BaTiO3_se_fpath = os.path.join(
self.TEST_FILES_DIR,
"chemenv",
"structure_environments_files",
"se_mp-5020.json",
)
with open(BaTiO3_se_fpath) as f:
dd = json.load(f)
se = StructureEnvironments.from_dict(dd)
lse = LightStructureEnvironments.from_structure_environments(
strategy=SimplestChemenvStrategy(), structure_environments=se
)
cf = ConnectivityFinder()
sc = cf.get_structure_connectivity(light_structure_environments=lse)
sc_from_dict = StructureConnectivity.from_dict(sc.as_dict())
assert sc.light_structure_environments == sc_from_dict.light_structure_environments
assert set(sc._graph.nodes()) == set(sc_from_dict._graph.nodes())
assert set(sc._graph.edges()) == set(sc_from_dict._graph.edges())
sc_from_json = StructureConnectivity.from_dict(json.loads(json.dumps(sc.as_dict())))
assert sc.light_structure_environments == sc_from_json.light_structure_environments
assert set(sc._graph.nodes()) == set(sc_from_json._graph.nodes())
assert set(sc._graph.edges()) == set(sc_from_json._graph.edges())
if bson is not None:
bson_data = bson.BSON.encode(sc.as_dict())
sc_from_bson = StructureConnectivity.from_dict(bson_data.decode())
assert sc.light_structure_environments == sc_from_bson.light_structure_environments
assert set(sc._graph.nodes()) == set(sc_from_bson._graph.nodes())
assert set(sc._graph.edges()) == set(sc_from_bson._graph.edges())
def get_structure_connectivity(self, light_structure_environments):
"""
Get the structure connectivity from the coordination environments provided
as an input.
:param light_structure_environments: LightStructureEnvironments with the
relevant coordination environments in the structure
:return: a StructureConnectivity object describing the connectivity of
the environments in the structure
"""
logging.info("Setup of structure connectivity graph")
structure_connectivity = StructureConnectivity(
light_structure_environments)
structure_connectivity.add_sites()
for isite, site in enumerate(light_structure_environments.structure):
site_neighbors_sets = light_structure_environments.neighbors_sets[
isite]
if site_neighbors_sets is None:
continue
if len(site_neighbors_sets) > 1:
if self.multiple_environments_choice is None:
raise ValueError(
"Local environment of site {:d} is a mix and "
"nothing is asked about it".format(isite))
elif self.multiple_environments_choice == "TAKE_HIGHEST_FRACTION":
imax = np.argmax([
ee["ce_fraction"]
for ee in light_structure_environments.
coordination_environments[isite]
])
print("IMAX {:d}".format(imax))
site_neighbors_set = site_neighbors_sets[imax]
else:
raise RuntimeError("Should not be here")
else:
site_neighbors_set = site_neighbors_sets[0]
structure_connectivity.add_bonds(isite, site_neighbors_set)
return structure_connectivity