def analyse_local_coord_env(atoms=None, ):
"""
"""
#| - analyse_local_coord_env
out_dict = dict()
Ir_indices = []
for i, s in enumerate(atoms.get_chemical_symbols()):
if s == "Ir":
Ir_indices.append(i)
struct = AseAtomsAdaptor.get_structure(atoms)
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(maximum_distance_factor=1.41,
only_cations=False)
strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
isite = 0
cor_env = []
coor_env_dict = dict()
for isite in Ir_indices:
c_env = lse.coordination_environments[isite]
coor_env_dict[isite] = c_env
cor_env += [c_env[0]['ce_symbol']]
out_dict["coor_env_dict"] = coor_env_dict
return (out_dict)
def from_dict(cls, d):
"""
Args:
d ():
Returns:
"""
# Reconstructs the graph with integer as nodes (json's as_dict replaces integer keys with str keys)
cgraph = nx.from_dict_of_dicts(d["connectivity_graph"],
create_using=nx.MultiGraph,
multigraph_input=True)
cgraph = nx.relabel_nodes(
cgraph, int
) # Just relabel the nodes using integer casting (maps str->int)
# Relabel multiedges (removes multiedges with str keys and adds them back with int keys)
edges = set(cgraph.edges())
for n1, n2 in edges:
new_edges = {
int(iedge): edata
for iedge, edata in cgraph[n1][n2].items()
}
cgraph.remove_edges_from([
(n1, n2, iedge) for iedge, edata in cgraph[n1][n2].items()
])
cgraph.add_edges_from([(n1, n2, iedge, edata)
for iedge, edata in new_edges.items()])
return cls(
LightStructureEnvironments.from_dict(
d["light_structure_environments"]),
connectivity_graph=cgraph,
environment_subgraphs=None,
)
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 setUp(self):
with open("mp-7000.json", "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
struct = lse.structure
bva = BVAnalyzer()
valences = bva.get_valences(structure=struct)
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(maximum_distance_factor=1.41, only_cations=False, valences=valences)
strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
self.lse = LightStructureEnvironments.from_structure_environments(strategy=strategy, structure_environments=se)
with open("mp-5634.json", "r") as f:
dict_lse2 = json.load(f)
self.lse2 = LightStructureEnvironments.from_dict(dict_lse2)
def setUp(self):
self.paulingconnetion = PaulingConnection(DISTANCE=8.0)
self.matlist = ["mp-7000.json"]
self.lse_dict = {}
for mat in self.matlist:
with open(mat, "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
self.lse_dict[mat] = lse
def setUp(self):
self.matlist = ["mp-1788.json", "mp-7000.json", "mp-19359.json", "mp-306.json", "mp-886.json", "mp-2605.json"]
self.lse_dict = {}
self.Pauling_dict = {}
for mat in self.matlist:
with open(mat, "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
self.lse_dict[mat] = lse
self.Pauling_dict[mat] = Pauling0(self.lse_dict[mat])
def test_read_structure_environments(self):
f = open("{}/{}".format(json_files_dir, 'test_T--4_FePO4_icsd_4266.json'), 'r')
dd = json.load(f)
f.close()
atom_indices = dd['atom_indices']
struct = Structure.from_dict(dd['structure'])
self.lgf.setup_structure(struct)
se = self.lgf.compute_structure_environments_detailed_voronoi(only_indices=atom_indices,
maximum_distance_factor=2.25)
f = open('tmp_dir/se.json', 'w')
json.dump(se.as_dict(), f)
f.close()
f = open('tmp_dir/se.json', 'r')
dd = json.load(f)
f.close()
se2 = StructureEnvironments.from_dict(dd)
self.assertEqual(se, se2)
_strategy = SimplestChemenvStrategy()
light_se = LightStructureEnvironments(_strategy, se)
f = open('tmp_dir/light_se.json', 'w')
json.dump(light_se.as_dict(), f)
f.close()
f = open('tmp_dir/light_se.json', 'r')
dd = json.load(f)
f.close()
light_se2 = LightStructureEnvironments.from_dict(dd)
self.assertEqual(light_se._strategy, light_se2._strategy)
self.assertEqual(light_se._structure, light_se2._structure)
self.assertEqual(light_se._bva_valences, light_se2._bva_valences)
self.assertEqual(light_se._coordination_environments, light_se2._coordination_environments)
self.assertEqual(light_se._neighbors, light_se2._neighbors)
self.assertEqual(light_se, light_se2)
def test_read_write_structure_environments(self):
f = open(
"{}/{}".format(json_files_dir, "test_T--4_FePO4_icsd_4266.json"),
"r")
dd = json.load(f)
f.close()
atom_indices = dd["atom_indices"]
struct = Structure.from_dict(dd["structure"])
self.lgf.setup_structure(struct)
se = self.lgf.compute_structure_environments(
only_indices=atom_indices,
maximum_distance_factor=2.25,
get_from_hints=True)
f = open("tmp_dir/se.json", "w")
json.dump(se.as_dict(), f)
f.close()
f = open("tmp_dir/se.json", "r")
dd = json.load(f)
f.close()
se2 = StructureEnvironments.from_dict(dd)
self.assertEqual(se, se2)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(
structure_environments=se, strategy=strategy, valences="undefined")
f = open("tmp_dir/lse.json", "w")
json.dump(lse.as_dict(), f)
f.close()
f = open("tmp_dir/lse.json", "r")
dd = json.load(f)
f.close()
lse2 = LightStructureEnvironments.from_dict(dd)
self.assertEqual(lse, lse2)
def setUp(self):
self.matlist = ["mp-7000.json", "mp-19359.json", "mp-1788.json", "mp-12236.json", "mp-5986.json"]
self.lse_dict = {}
self.Pauling_List = {}
for mat in self.matlist:
with open(mat, "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
self.lse_dict[mat] = lse
self.Pauling_List[mat] = Pauling5()
self.Pauling_List[mat].newsetup(lse=lse, save_to_file=False)
def test_read_write_structure_environments(self):
f = open(
"{}/{}".format(json_files_dir, 'test_T--4_FePO4_icsd_4266.json'),
'r')
dd = json.load(f)
f.close()
atom_indices = dd['atom_indices']
struct = Structure.from_dict(dd['structure'])
self.lgf.setup_structure(struct)
se = self.lgf.compute_structure_environments(
only_indices=atom_indices, maximum_distance_factor=2.25)
f = open('tmp_dir/se.json', 'w')
json.dump(se.as_dict(), f)
f.close()
f = open('tmp_dir/se.json', 'r')
dd = json.load(f)
f.close()
se2 = StructureEnvironments.from_dict(dd)
self.assertEqual(se, se2)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(
structure_environments=se, strategy=strategy, valences='undefined')
f = open('tmp_dir/lse.json', 'w')
json.dump(lse.as_dict(), f)
f.close()
f = open('tmp_dir/lse.json', 'r')
dd = json.load(f)
f.close()
lse2 = LightStructureEnvironments.from_dict(dd)
self.assertEqual(lse, lse2)
def setUp(self):
# test it for further candidates -> differing in CN, differing in val
self.matlist = ["mp-7000.json", "mp-19359.json", "mp-1788.json", "mp-5986.json", "mp-19418.json"]
self.lse_dict = {}
self.Pauling_List = {}
for mat in self.matlist:
with open(mat, "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
self.lse_dict[mat] = lse
self.Pauling_List[mat] = Pauling4()
self.Pauling_List[mat].newsetup(lse=lse, save_to_file=False)
def test_read_write_structure_environments(self):
f = open("{}/{}".format(json_files_dir, 'test_T--4_FePO4_icsd_4266.json'), 'r')
dd = json.load(f)
f.close()
atom_indices = dd['atom_indices']
struct = Structure.from_dict(dd['structure'])
self.lgf.setup_structure(struct)
se = self.lgf.compute_structure_environments(only_indices=atom_indices,
maximum_distance_factor=2.25,
get_from_hints=True)
f = open('tmp_dir/se.json', 'w')
json.dump(se.as_dict(), f)
f.close()
f = open('tmp_dir/se.json', 'r')
dd = json.load(f)
f.close()
se2 = StructureEnvironments.from_dict(dd)
self.assertEqual(se, se2)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(structure_environments=se, strategy=strategy,
valences='undefined')
f = open('tmp_dir/lse.json', 'w')
json.dump(lse.as_dict(), f)
f.close()
f = open('tmp_dir/lse.json', 'r')
dd = json.load(f)
f.close()
lse2 = LightStructureEnvironments.from_dict(dd)
self.assertEqual(lse, lse2)
def setUp(self):
self.matlist = ["mp-7000.json", "mp-19418.json"]
self.lse_dict = {}
for mat in self.matlist:
with open(mat, "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
self.lse_dict[mat] = lse
self.pauling3and4_dist1 = Pauling3and4()
self.pauling3and4_dist1.newsetup(self.lse_dict["mp-7000.json"], save_to_file=False, filename=False,
distance=4.5)
self.pauling3and4_dist2 = Pauling3and4()
self.pauling3and4_dist2.newsetup(self.lse_dict["mp-7000.json"], save_to_file=False, filename=False)
self.pauling3and4_dict3 = Pauling3and4()
self.pauling3and4_dict3.newsetup(self.lse_dict["mp-19418.json"], save_to_file=False, filename=False, distance=4)
def setUp(self):
# TODO: initilaize normal pauling as well
self.matlist = ["mp-7000.json", "mp-566090.json", "mp-2605.json", "mp-4056.json"]
self.lse_dict = {}
self.Pauling_dict = {}
self.Pauling_dict_perc1 = {}
self.Pauling_dict_perc02 = {}
self.Pauling_dict_realtwo = {}
for mat in self.matlist:
with open(mat, "r") as f:
dict_lse = json.load(f)
lse = LightStructureEnvironments.from_dict(dict_lse)
self.lse_dict[mat] = lse
self.Pauling_dict[mat] = Pauling2_optimized_environments(self.lse_dict[mat], perc=0.3)
self.Pauling_dict_perc02[mat] = Pauling2_optimized_environments(self.lse_dict[mat], perc=0.2)
self.Pauling_dict_perc1[mat] = Pauling2_optimized_environments(self.lse_dict[mat], perc=1.0)
self.Pauling_dict_realtwo[mat] = Pauling2(self.lse_dict[mat])
def getSimplestChemenvStrategy(struct):
# Setup the local geometry finder
lgf = LocalGeometryFinder()
lgf.setup_parameters(centering_type='centroid',
include_central_site_in_centroid=True)
#you can also save the logging to a file, just remove the comment
# logging.basicConfig(#filename='chemenv_structure_environments.log',
# format='%(levelname)s:%(module)s:%(funcName)s:%(message)s',
# level=logging.DEBUG)
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(maximum_distance_factor=1.41,
only_cations=False)
strategy = SimplestChemenvStrategy(distance_cutoff=1.4, angle_cutoff=0.3)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
return lse.coordination_environments
def run_task(self, fw_spec):
logging.basicConfig(filename='chemenv_light_structure_environments.log',
format='%(levelname)s:%(module)s:%(funcName)s:%(message)s',
level=logging.DEBUG)
identifier = fw_spec['identifier']
criteria = {'identifier': identifier}
# Where to get the full structure environments object
se_database = fw_spec['structure_environments_database']
entry = se_database.collection.find_one(criteria)
if fw_spec['structure_environments_setup'] == 'from_gridfs':
gfs_fileobject = se_database.gridfs.get(entry['structure_environments'])
dd = json.load(gfs_fileobject)
se = StructureEnvironments.from_dict(dd)
elif fw_spec['structure_environments_setup'] == 'from_storedfile':
se_storage_server = fw_spec['se_storage_server']
se_filepath = entry['structure_environments_file']
se_storage_server.get(se_filepath, 'se.json')
f = open('se.json', 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
else:
raise RuntimeError('Wrong structure_environments_setup : '
'"{}" is not allowed'.format(fw_spec['structure_environments_setup']))
# Compute the light structure environments
chemenv_strategy = fw_spec['chemenv_strategy']
if 'valences' in fw_spec:
valences = fw_spec['valences']
valences_origin = fw_spec['valences_origin']
else:
valences = 'undefined'
valences_origin = 'None'
lse = LightStructureEnvironments.from_structure_environments(strategy=chemenv_strategy,
structure_environments=se,
valences=valences,
valences_origin=valences_origin)
# Write to json file
if 'json_file' in fw_spec:
json_file = fw_spec['json_file']
else:
json_file = 'light_structure_environments.json'
f = open(json_file, 'w')
json.dump(lse.as_dict(), f)
f.close()
# Save to database
if 'mongo_database' in fw_spec:
database = fw_spec['mongo_database']
entry = {'identifier': identifier,
'elements': [elmt.symbol for elmt in lse.structure.composition.elements],
'nelements': len(lse.structure.composition.elements),
'pretty_formula': lse.structure.composition.reduced_formula,
'nsites': len(lse.structure),
'chemenv_statistics': lse.get_statistics(statistics_fields='ALL', bson_compatible=True)
}
saving_option = fw_spec['saving_option']
if saving_option == 'gridfs':
gridfs_msonables = {'structure': lse.structure,
'light_structure_environments': lse}
elif saving_option == 'storefile':
gridfs_msonables = None
if 'lse_prefix' in fw_spec:
lse_prefix = fw_spec['lse_prefix']
if not lse_prefix.isalpha():
raise ValueError('Prefix for light_structure_environments file is "{}" '
'while it should be alphabetic'.format(lse_prefix))
else:
lse_prefix = ''
if lse_prefix:
lse_rfilename = '{}_{}.json'.format(lse_prefix, fw_spec['storefile_basename'])
else:
lse_rfilename = '{}.json'.format(fw_spec['storefile_basename'])
lse_rfilepath = '{}/{}'.format(fw_spec['storefile_dirpath'], lse_rfilename)
storage_server = fw_spec['storage_server']
storage_server.put(localpath=json_file, remotepath=lse_rfilepath, overwrite=True, makedirs=False)
entry['light_structure_environments_file'] = lse_rfilepath
else:
raise ValueError('Saving option is "{}" while it should be '
'"gridfs" or "storefile"'.format(saving_option))
criteria = {'identifier': identifier}
if database.collection.find(criteria).count() == 1:
database.update_entry(query=criteria, entry_update=entry,
gridfs_msonables=gridfs_msonables)
else:
database.insert_entry(entry=entry, gridfs_msonables=gridfs_msonables)
def from_dict(cls, d):
return cls(LightStructureEnvironments.from_dict(d['light_structure_environments']),
connectivity_graph=nx.from_dict_of_dicts(d['connectivity_graph'], multigraph_input=True),
environment_subgraphs={env_key: nx.from_dict_of_dicts(subgraph, multigraph_input=True)
for env_key, subgraph in d['environment_subgraphs'].items()})
def test_light_structure_environments(self):
with ScratchDir("."):
with open(f"{se_files_dir}/se_mp-7000.json") as f:
dd = json.load(f)
se = StructureEnvironments.from_dict(dd)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(
structure_environments=se,
strategy=strategy,
valences="undefined")
isite = 6
nb_set = lse.neighbors_sets[isite][0]
neighb_coords = [
np.array([0.2443798, 1.80409653, -1.13218359]),
np.array([1.44020353, 1.11368738, 1.13218359]),
np.array([2.75513098, 2.54465207, -0.70467298]),
np.array([0.82616785, 3.65833945, 0.70467298]),
]
neighb_indices = [0, 3, 5, 1]
neighb_images = [[0, 0, -1], [0, 0, 0], [0, 0, -1], [0, 0, 0]]
np.testing.assert_array_almost_equal(neighb_coords,
nb_set.neighb_coords)
np.testing.assert_array_almost_equal(
neighb_coords, [s.coords for s in nb_set.neighb_sites])
nb_sai = nb_set.neighb_sites_and_indices
np.testing.assert_array_almost_equal(
neighb_coords, [sai["site"].coords for sai in nb_sai])
np.testing.assert_array_almost_equal(
neighb_indices, [sai["index"] for sai in nb_sai])
nb_iai = nb_set.neighb_indices_and_images
np.testing.assert_array_almost_equal(
neighb_indices, [iai["index"] for iai in nb_iai])
np.testing.assert_array_equal(
neighb_images, [iai["image_cell"] for iai in nb_iai])
self.assertEqual(nb_set.__len__(), 4)
self.assertEqual(nb_set.__hash__(), 4)
self.assertFalse(nb_set.__ne__(nb_set))
self.assertEqual(
nb_set.__str__(),
"Neighbors Set for site #6 :\n"
" - Coordination number : 4\n"
" - Neighbors sites indices : 0, 1, 2, 3\n",
)
stats = lse.get_statistics()
neighbors = lse.strategy.get_site_neighbors(
site=lse.structure[isite])
self.assertArrayAlmostEqual(
neighbors[0].coords,
np.array([0.2443798, 1.80409653, -1.13218359]))
self.assertArrayAlmostEqual(
neighbors[1].coords,
np.array([1.44020353, 1.11368738, 1.13218359]))
self.assertArrayAlmostEqual(
neighbors[2].coords,
np.array([2.75513098, 2.54465207, -0.70467298]))
self.assertArrayAlmostEqual(
neighbors[3].coords,
np.array([0.82616785, 3.65833945, 0.70467298]))
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(
neighbors[0])
self.assertEqual(equiv_site_index_and_transform[0], 0)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1],
[0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2],
[0.0, 0.0, -1.0])
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(
neighbors[1])
self.assertEqual(equiv_site_index_and_transform[0], 3)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1],
[0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2],
[0.0, 0.0, 0.0])
self.assertEqual(stats["atom_coordination_environments_present"],
{"Si": {
"T:4": 3.0
}})
self.assertEqual(stats["coordination_environments_atom_present"],
{"T:4": {
"Si": 3.0
}})
self.assertEqual(
stats["fraction_atom_coordination_environments_present"],
{"Si": {
"T:4": 1.0
}},
)
site_info_ce = lse.get_site_info_for_specie_ce(specie=Species(
"Si", 4),
ce_symbol="T:4")
np.testing.assert_array_almost_equal(site_info_ce["fractions"],
[1.0, 1.0, 1.0])
np.testing.assert_array_almost_equal(
site_info_ce["csms"],
[
0.009887784240541068, 0.009887786546730826,
0.009887787384385317
],
)
self.assertEqual(site_info_ce["isites"], [6, 7, 8])
site_info_allces = lse.get_site_info_for_specie_allces(
specie=Species("Si", 4))
self.assertEqual(site_info_allces["T:4"], site_info_ce)
self.assertFalse(lse.contains_only_one_anion("I-"))
self.assertFalse(lse.contains_only_one_anion_atom("I"))
self.assertTrue(
lse.site_contains_environment(isite=isite, ce_symbol="T:4"))
self.assertFalse(
lse.site_contains_environment(isite=isite, ce_symbol="S:4"))
self.assertFalse(
lse.structure_contains_atom_environment(atom_symbol="Si",
ce_symbol="S:4"))
self.assertTrue(
lse.structure_contains_atom_environment(atom_symbol="Si",
ce_symbol="T:4"))
self.assertFalse(
lse.structure_contains_atom_environment(atom_symbol="O",
ce_symbol="T:4"))
self.assertTrue(lse.uniquely_determines_coordination_environments)
self.assertFalse(lse.__ne__(lse))
envs = lse.strategy.get_site_coordination_environments(
lse.structure[6])
self.assertEqual(len(envs), 1)
self.assertEqual(envs[0][0], "T:4")
multi_strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters(
)
lse_multi = LightStructureEnvironments.from_structure_environments(
strategy=multi_strategy,
structure_environments=se,
valences="undefined")
self.assertAlmostEqual(
lse_multi.coordination_environments[isite][0]["csm"],
0.009887784240541068,
)
self.assertAlmostEqual(
lse_multi.coordination_environments[isite][0]["ce_fraction"],
1.0)
self.assertEqual(
lse_multi.coordination_environments[isite][0]["ce_symbol"],
"T:4")
def get_chemenv_analysis(struct, distance_cutoff, angle_cutoff):
if not struct:
raise PreventUpdate
struct = self.from_data(struct)
distance_cutoff = float(distance_cutoff)
angle_cutoff = float(angle_cutoff)
# decide which indices to present to user
sga = SpacegroupAnalyzer(struct)
symm_struct = sga.get_symmetrized_structure()
inequivalent_indices = [
indices[0] for indices in symm_struct.equivalent_indices
]
wyckoffs = symm_struct.wyckoff_symbols
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
maximum_distance_factor=distance_cutoff + 0.01,
only_indices=inequivalent_indices,
)
strategy = SimplestChemenvStrategy(distance_cutoff=distance_cutoff,
angle_cutoff=angle_cutoff)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
all_ce = AllCoordinationGeometries()
envs = []
unknown_sites = []
for index, wyckoff in zip(inequivalent_indices, wyckoffs):
datalist = {
"Site": struct[index].species_string,
"Wyckoff Label": wyckoff,
}
if not lse.neighbors_sets[index]:
unknown_sites.append(
f"{struct[index].species_string} ({wyckoff})")
continue
# represent the local environment as a molecule
mol = Molecule.from_sites(
[struct[index]] +
lse.neighbors_sets[index][0].neighb_sites)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
static=True,
id=
f"{struct.composition.reduced_formula}_site_{index}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
).all_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
env = lse.coordination_environments[index]
co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
name = co.name
if co.alternative_names:
name += f" (also known as {', '.join(co.alternative_names)})"
datalist.update({
"Environment":
name,
"IUPAC Symbol":
co.IUPAC_symbol_str,
get_tooltip(
"CSM",
'"Continuous Symmetry Measure," a measure of how symmetrical a '
"local environment is from most symmetrical at 0% to least "
"symmetrical at 100%",
):
f"{env[0]['csm']:.2f}%",
"Interactive View":
view,
})
envs.append(get_data_list(datalist))
# TODO: switch to tiles?
envs_grouped = [envs[i:i + 2] for i in range(0, len(envs), 2)]
analysis_contents = []
for env_group in envs_grouped:
analysis_contents.append(
Columns([Column(e, size=6) for e in env_group]))
if unknown_sites:
unknown_sites = html.Strong(
f"The following sites were not identified: {', '.join(unknown_sites)}. "
f"Please try changing the distance or angle cut-offs to identify these sites."
)
else:
unknown_sites = html.Span()
return html.Div(
[html.Div(analysis_contents),
html.Br(), unknown_sites])
def test_light_structure_environments(self):
f = open("{}/{}".format(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(structure_environments=se, strategy=strategy,
valences='undefined')
isite = 6
nb_set = lse.neighbors_sets[isite][0]
neighb_coords = [np.array([0.2443798, 1.80409653, -1.13218359]),
np.array([1.44020353, 1.11368738, 1.13218359]),
np.array([2.75513098, 2.54465207, -0.70467298]),
np.array([0.82616785, 3.65833945, 0.70467298])]
neighb_indices = [0, 3, 5, 1]
neighb_images = [[0, 0, -1], [0, 0, 0], [0, 0, -1], [0, 0, 0]]
np.testing.assert_array_almost_equal(neighb_coords, nb_set.neighb_coords)
np.testing.assert_array_almost_equal(neighb_coords, [s.coords for s in nb_set.neighb_sites])
nb_sai = nb_set.neighb_sites_and_indices
np.testing.assert_array_almost_equal(neighb_coords, [sai['site'].coords for sai in nb_sai])
np.testing.assert_array_almost_equal(neighb_indices, [sai['index'] for sai in nb_sai])
nb_iai = nb_set.neighb_indices_and_images
np.testing.assert_array_almost_equal(neighb_indices, [iai['index'] for iai in nb_iai])
np.testing.assert_array_equal(neighb_images, [iai['image_cell'] for iai in nb_iai])
self.assertEqual(nb_set.__len__(), 4)
self.assertEqual(nb_set.__hash__(), 4)
self.assertFalse(nb_set.__ne__(nb_set))
self.assertEqual(nb_set.__str__(), 'Neighbors Set for site #6 :\n'
' - Coordination number : 4\n'
' - Neighbors sites indices : 0, 1, 2, 3\n')
stats = lse.get_statistics()
neighbors = lse.strategy.get_site_neighbors(site=lse.structure[isite])
self.assertArrayAlmostEqual(neighbors[0].coords, np.array([ 0.2443798, 1.80409653, -1.13218359]))
self.assertArrayAlmostEqual(neighbors[1].coords, np.array([ 1.44020353, 1.11368738, 1.13218359]))
self.assertArrayAlmostEqual(neighbors[2].coords, np.array([ 2.75513098, 2.54465207, -0.70467298]))
self.assertArrayAlmostEqual(neighbors[3].coords, np.array([ 0.82616785, 3.65833945, 0.70467298]))
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(neighbors[0])
self.assertEqual(equiv_site_index_and_transform[0], 0)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1], [0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2], [0.0, 0.0, -1.0])
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(neighbors[1])
self.assertEqual(equiv_site_index_and_transform[0], 3)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1], [0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2], [0.0, 0.0, 0.0])
self.assertEqual(stats['atom_coordination_environments_present'], {'Si': {'T:4': 3.0}})
self.assertEqual(stats['coordination_environments_atom_present'], {'T:4': {'Si': 3.0}})
self.assertEqual(stats['fraction_atom_coordination_environments_present'], {'Si': {'T:4': 1.0}})
site_info_ce = lse.get_site_info_for_specie_ce(specie=Specie('Si', 4), ce_symbol='T:4')
np.testing.assert_array_almost_equal(site_info_ce['fractions'], [1.0, 1.0, 1.0])
np.testing.assert_array_almost_equal(site_info_ce['csms'],
[0.009887784240541068, 0.009887786546730826, 0.009887787384385317])
self.assertEqual(site_info_ce['isites'], [6, 7, 8])
site_info_allces = lse.get_site_info_for_specie_allces(specie=Specie('Si', 4))
self.assertEqual(site_info_allces['T:4'], site_info_ce)
self.assertFalse(lse.contains_only_one_anion('I-'))
self.assertFalse(lse.contains_only_one_anion_atom('I'))
self.assertTrue(lse.site_contains_environment(isite=isite, ce_symbol='T:4'))
self.assertFalse(lse.site_contains_environment(isite=isite, ce_symbol='S:4'))
self.assertFalse(lse.structure_contains_atom_environment(atom_symbol='Si', ce_symbol='S:4'))
self.assertTrue(lse.structure_contains_atom_environment(atom_symbol='Si', ce_symbol='T:4'))
self.assertFalse(lse.structure_contains_atom_environment(atom_symbol='O', ce_symbol='T:4'))
self.assertTrue(lse.uniquely_determines_coordination_environments)
self.assertFalse(lse.__ne__(lse))
envs = lse.strategy.get_site_coordination_environments(lse.structure[6])
self.assertEqual(len(envs), 1)
self.assertEqual(envs[0][0], 'T:4')
multi_strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
lse_multi = LightStructureEnvironments.from_structure_environments(strategy=multi_strategy,
structure_environments=se,
valences='undefined')
self.assertAlmostEqual(lse_multi.coordination_environments[isite][0]['csm'], 0.009887784240541068)
self.assertAlmostEqual(lse_multi.coordination_environments[isite][0]['ce_fraction'], 1.0)
self.assertEqual(lse_multi.coordination_environments[isite][0]['ce_symbol'], 'T:4')
Ir_indices = [
i for i, s in enumerate(atoms.get_chemical_symbols()) if s == 'Ir'
]
struct = AseAtomsAdaptor.get_structure(atoms)
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(maximum_distance_factor=1.41,
only_cations=False)
strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters(
)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
isite = 0
cor_env = []
for isite in Ir_indices:
c_env = lse.coordination_environments[isite]
if len(c_env) == 0:
continue
cor_env += [c_env[0]['ce_symbol']]
if len(cor_env) == 0:
continue
uniques, counts = np.unique(cor_env, return_counts=True)
if len(uniques) > 1:
def run_task(self, fw_spec):
logging.basicConfig(
filename='chemenv_light_structure_environments.log',
format='%(levelname)s:%(module)s:%(funcName)s:%(message)s',
level=logging.DEBUG)
identifier = fw_spec['identifier']
criteria = {'identifier': identifier}
# Where to get the full structure environments object
se_database = fw_spec['structure_environments_database']
entry = se_database.collection.find_one(criteria)
if fw_spec['structure_environments_setup'] == 'from_gridfs':
gfs_fileobject = se_database.gridfs.get(
entry['structure_environments'])
dd = json.load(gfs_fileobject)
se = StructureEnvironments.from_dict(dd)
elif fw_spec['structure_environments_setup'] == 'from_storedfile':
se_storage_server = fw_spec['se_storage_server']
se_filepath = entry['structure_environments_file']
se_storage_server.get(se_filepath, 'se.json')
f = open('se.json', 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
else:
raise RuntimeError('Wrong structure_environments_setup : '
'"{}" is not allowed'.format(
fw_spec['structure_environments_setup']))
# Compute the light structure environments
chemenv_strategy = fw_spec['chemenv_strategy']
if 'valences' in fw_spec:
valences = fw_spec['valences']
valences_origin = fw_spec['valences_origin']
else:
valences = 'undefined'
valences_origin = 'None'
lse = LightStructureEnvironments.from_structure_environments(
strategy=chemenv_strategy,
structure_environments=se,
valences=valences,
valences_origin=valences_origin)
# Write to json file
if 'json_file' in fw_spec:
json_file = fw_spec['json_file']
else:
json_file = 'light_structure_environments.json'
f = open(json_file, 'w')
json.dump(lse.as_dict(), f)
f.close()
# Save to database
if 'mongo_database' in fw_spec:
database = fw_spec['mongo_database']
entry = {
'identifier':
identifier,
'elements':
[elmt.symbol for elmt in lse.structure.composition.elements],
'nelements':
len(lse.structure.composition.elements),
'pretty_formula':
lse.structure.composition.reduced_formula,
'nsites':
len(lse.structure),
'chemenv_statistics':
lse.get_statistics(statistics_fields='ALL',
bson_compatible=True)
}
saving_option = fw_spec['saving_option']
if saving_option == 'gridfs':
gridfs_msonables = {
'structure': lse.structure,
'light_structure_environments': lse
}
elif saving_option == 'storefile':
gridfs_msonables = None
if 'lse_prefix' in fw_spec:
lse_prefix = fw_spec['lse_prefix']
if not lse_prefix.isalpha():
raise ValueError(
'Prefix for light_structure_environments file is "{}" '
'while it should be alphabetic'.format(lse_prefix))
else:
lse_prefix = ''
if lse_prefix:
lse_rfilename = '{}_{}.json'.format(
lse_prefix, fw_spec['storefile_basename'])
else:
lse_rfilename = '{}.json'.format(
fw_spec['storefile_basename'])
lse_rfilepath = '{}/{}'.format(fw_spec['storefile_dirpath'],
lse_rfilename)
storage_server = fw_spec['storage_server']
storage_server.put(localpath=json_file,
remotepath=lse_rfilepath,
overwrite=True,
makedirs=False)
entry['light_structure_environments_file'] = lse_rfilepath
else:
raise ValueError(
'Saving option is "{}" while it should be '
'"gridfs" or "storefile"'.format(saving_option))
criteria = {'identifier': identifier}
if database.collection.find(criteria).count() == 1:
database.update_entry(query=criteria,
entry_update=entry,
gridfs_msonables=gridfs_msonables)
else:
database.insert_entry(entry=entry,
gridfs_msonables=gridfs_msonables)
def test_real_systems(self):
# Initialize geometry and connectivity finders
strat = SimplestChemenvStrategy()
lgf = LocalGeometryFinder()
cf = ConnectivityFinder()
# Connectivity of LiFePO4
struct = self.get_structure("LiFePO4")
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(only_atoms=["Li", "Fe", "P"],
maximum_distance_factor=1.2)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strat, structure_environments=se)
# Make sure the initial structure and environments are correct
for isite in range(0, 4):
assert lse.structure[isite].specie.symbol == "Li"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "O:6"
for isite in range(4, 8):
assert lse.structure[isite].specie.symbol == "Fe"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "O:6"
for isite in range(8, 12):
assert lse.structure[isite].specie.symbol == "P"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "T:4"
# Get the connectivity including all environments and check results
sc = cf.get_structure_connectivity(lse)
assert len(sc.environment_subgraphs
) == 0 # Connected component not computed by default
ccs = sc.get_connected_components(
) # by default, will use all the environments (O:6 and T:4 here)
assert list(sc.environment_subgraphs.keys()) == [
"O:6-T:4"
] # Now the default components are there
assert len(sc.environment_subgraphs) == 1
assert len(ccs) == 1
cc = ccs[0]
assert len(cc) == 12
assert cc.periodicity == "3D"
assert (
cc.description() == """Connected component with environment nodes :
Node #0 Li (O:6)
Node #1 Li (O:6)
Node #2 Li (O:6)
Node #3 Li (O:6)
Node #4 Fe (O:6)
Node #5 Fe (O:6)
Node #6 Fe (O:6)
Node #7 Fe (O:6)
Node #8 P (T:4)
Node #9 P (T:4)
Node #10 P (T:4)
Node #11 P (T:4)""")
assert (cc.description(
full=True) == """Connected component with environment nodes :
Node #0 Li (O:6), connected to :
- Node #1 Li (O:6) with delta image cells
(-1 0 1)
(-1 1 1)
- Node #4 Fe (O:6) with delta image cells
(-1 1 1)
(0 1 1)
- Node #5 Fe (O:6) with delta image cells
(0 0 1)
- Node #6 Fe (O:6) with delta image cells
(-1 1 0)
- Node #7 Fe (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #8 P (T:4) with delta image cells
(-1 0 1)
(0 0 1)
- Node #11 P (T:4) with delta image cells
(-1 1 0)
(0 1 0)
Node #1 Li (O:6), connected to :
- Node #0 Li (O:6) with delta image cells
(1 -1 -1)
(1 0 -1)
- Node #4 Fe (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #5 Fe (O:6) with delta image cells
(1 0 0)
- Node #6 Fe (O:6) with delta image cells
(0 0 -1)
- Node #7 Fe (O:6) with delta image cells
(0 0 -1)
(1 0 -1)
- Node #8 P (T:4) with delta image cells
(0 0 0)
(1 0 0)
- Node #11 P (T:4) with delta image cells
(0 0 -1)
(1 0 -1)
Node #2 Li (O:6), connected to :
- Node #3 Li (O:6) with delta image cells
(0 0 0)
(0 1 0)
- Node #4 Fe (O:6) with delta image cells
(0 1 0)
- Node #5 Fe (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #6 Fe (O:6) with delta image cells
(-1 1 0)
(0 1 0)
- Node #7 Fe (O:6) with delta image cells
(0 0 0)
- Node #9 P (T:4) with delta image cells
(0 1 0)
(1 1 0)
- Node #10 P (T:4) with delta image cells
(-1 0 0)
(0 0 0)
Node #3 Li (O:6), connected to :
- Node #2 Li (O:6) with delta image cells
(0 -1 0)
(0 0 0)
- Node #4 Fe (O:6) with delta image cells
(0 0 0)
- Node #5 Fe (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #6 Fe (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #7 Fe (O:6) with delta image cells
(0 0 0)
- Node #9 P (T:4) with delta image cells
(0 0 0)
(1 0 0)
- Node #10 P (T:4) with delta image cells
(-1 0 0)
(0 0 0)
Node #4 Fe (O:6), connected to :
- Node #0 Li (O:6) with delta image cells
(0 -1 -1)
(1 -1 -1)
- Node #1 Li (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #2 Li (O:6) with delta image cells
(0 -1 0)
- Node #3 Li (O:6) with delta image cells
(0 0 0)
- Node #5 Fe (O:6) with delta image cells
(0 -1 0)
(0 0 0)
(1 -1 0)
(1 0 0)
- Node #8 P (T:4) with delta image cells
(0 -1 0)
(0 0 0)
- Node #9 P (T:4) with delta image cells
(0 0 0)
(1 0 0)
- Node #11 P (T:4) with delta image cells
(0 0 -1)
Node #5 Fe (O:6), connected to :
- Node #0 Li (O:6) with delta image cells
(0 0 -1)
- Node #1 Li (O:6) with delta image cells
(-1 0 0)
- Node #2 Li (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #3 Li (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #4 Fe (O:6) with delta image cells
(-1 0 0)
(-1 1 0)
(0 0 0)
(0 1 0)
- Node #8 P (T:4) with delta image cells
(-1 0 0)
(0 0 0)
- Node #9 P (T:4) with delta image cells
(0 0 0)
(0 1 0)
- Node #10 P (T:4) with delta image cells
(-1 0 0)
Node #6 Fe (O:6), connected to :
- Node #0 Li (O:6) with delta image cells
(1 -1 0)
- Node #1 Li (O:6) with delta image cells
(0 0 1)
- Node #2 Li (O:6) with delta image cells
(0 -1 0)
(1 -1 0)
- Node #3 Li (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #7 Fe (O:6) with delta image cells
(0 -1 0)
(0 0 0)
(1 -1 0)
(1 0 0)
- Node #9 P (T:4) with delta image cells
(1 0 0)
- Node #10 P (T:4) with delta image cells
(0 -1 0)
(0 0 0)
- Node #11 P (T:4) with delta image cells
(0 0 0)
(1 0 0)
Node #7 Fe (O:6), connected to :
- Node #0 Li (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #1 Li (O:6) with delta image cells
(-1 0 1)
(0 0 1)
- Node #2 Li (O:6) with delta image cells
(0 0 0)
- Node #3 Li (O:6) with delta image cells
(0 0 0)
- Node #6 Fe (O:6) with delta image cells
(-1 0 0)
(-1 1 0)
(0 0 0)
(0 1 0)
- Node #8 P (T:4) with delta image cells
(0 0 1)
- Node #10 P (T:4) with delta image cells
(-1 0 0)
(0 0 0)
- Node #11 P (T:4) with delta image cells
(0 0 0)
(0 1 0)
Node #8 P (T:4), connected to :
- Node #0 Li (O:6) with delta image cells
(0 0 -1)
(1 0 -1)
- Node #1 Li (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #4 Fe (O:6) with delta image cells
(0 0 0)
(0 1 0)
- Node #5 Fe (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #7 Fe (O:6) with delta image cells
(0 0 -1)
Node #9 P (T:4), connected to :
- Node #2 Li (O:6) with delta image cells
(-1 -1 0)
(0 -1 0)
- Node #3 Li (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #4 Fe (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #5 Fe (O:6) with delta image cells
(0 -1 0)
(0 0 0)
- Node #6 Fe (O:6) with delta image cells
(-1 0 0)
Node #10 P (T:4), connected to :
- Node #2 Li (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #3 Li (O:6) with delta image cells
(0 0 0)
(1 0 0)
- Node #5 Fe (O:6) with delta image cells
(1 0 0)
- Node #6 Fe (O:6) with delta image cells
(0 0 0)
(0 1 0)
- Node #7 Fe (O:6) with delta image cells
(0 0 0)
(1 0 0)
Node #11 P (T:4), connected to :
- Node #0 Li (O:6) with delta image cells
(0 -1 0)
(1 -1 0)
- Node #1 Li (O:6) with delta image cells
(-1 0 1)
(0 0 1)
- Node #4 Fe (O:6) with delta image cells
(0 0 1)
- Node #6 Fe (O:6) with delta image cells
(-1 0 0)
(0 0 0)
- Node #7 Fe (O:6) with delta image cells
(0 -1 0)
(0 0 0)""")
# Get the connectivity for T:4 and O:6 separately and check results
# Only tetrahedral
sc.setup_environment_subgraph(environments_symbols=["T:4"])
assert list(sc.environment_subgraphs.keys()) == ["O:6-T:4", "T:4"]
ccs = sc.get_connected_components()
assert len(ccs) == 4
for cc in ccs:
assert cc.periodicity == "0D"
# Only octahedral
sc.setup_environment_subgraph(environments_symbols=["O:6"])
assert list(
sc.environment_subgraphs.keys()) == ["O:6-T:4", "T:4", "O:6"]
ccs = sc.get_connected_components()
assert len(ccs) == 1
cc = ccs[0]
assert cc.periodicity == "3D"
# Only Manganese octahedral
sc.setup_environment_subgraph(environments_symbols=["O:6"],
only_atoms=["Fe"])
assert list(sc.environment_subgraphs.keys()) == [
"O:6-T:4",
"T:4",
"O:6",
"O:6#Fe",
]
ccs = sc.get_connected_components()
assert len(ccs) == 2
for cc in ccs:
assert cc.periodicity == "2D"
# Connectivity of Li4Fe3Mn1(PO4)4
struct = Structure.from_file(
os.path.join(self.TEST_FILES_DIR, "Li4Fe3Mn1(PO4)4.cif"))
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
only_atoms=["Li", "Fe", "Mn", "P"], maximum_distance_factor=1.2)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strat, structure_environments=se)
# Make sure the initial structure and environments are correct
for isite in range(0, 4):
assert lse.structure[isite].specie.symbol == "Li"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "O:6"
for isite in range(4, 5):
assert lse.structure[isite].specie.symbol == "Mn"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "O:6"
for isite in range(5, 8):
assert lse.structure[isite].specie.symbol == "Fe"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "O:6"
for isite in range(8, 12):
assert lse.structure[isite].specie.symbol == "P"
assert lse.coordination_environments[isite][0][
"ce_symbol"] == "T:4"
# Get the connectivity including all environments and check results
sc = cf.get_structure_connectivity(lse)
assert len(sc.environment_subgraphs
) == 0 # Connected component not computed by default
ccs = sc.get_connected_components(
) # by default, will use all the environments (O:6 and T:4 here)
# Now connected components for the defaults are there :
assert list(sc.environment_subgraphs.keys()) == ["O:6-T:4"]
assert len(sc.environment_subgraphs) == 1
assert len(ccs) == 1
cc = ccs[0]
assert cc.periodicity == "3D"
# Get the connectivity for Li octahedral only
ccs = sc.get_connected_components(environments_symbols=["O:6"],
only_atoms=["Li"])
assert list(sc.environment_subgraphs.keys()) == ["O:6-T:4", "O:6#Li"]
assert len(ccs) == 2
for cc in ccs:
assert cc.periodicity == "1D"
assert len(cc) == 2
# Sort connected components as they might
# come in a different order depending on
# the algorithm used to get them.
sorted_ccs = sorted(ccs, key=lambda x: sorted(x.graph.nodes())[0])
assert (sorted_ccs[0].description(
full=True) == """Connected component with environment nodes :
Node #0 Li (O:6), connected to :
- Node #1 Li (O:6) with delta image cells
(1 -1 1)
(1 0 1)
Node #1 Li (O:6), connected to :
- Node #0 Li (O:6) with delta image cells
(-1 0 -1)
(-1 1 -1)""")
assert (sorted_ccs[1].description(
full=True) == """Connected component with environment nodes :
Node #2 Li (O:6), connected to :
- Node #3 Li (O:6) with delta image cells
(0 -1 0)
(0 0 0)
Node #3 Li (O:6), connected to :
- Node #2 Li (O:6) with delta image cells
(0 0 0)
(0 1 0)""")
# Get the connectivity for Mn octahedral only
ccs = sc.get_connected_components(environments_symbols=["O:6"],
only_atoms=["Mn"])
assert list(sc.environment_subgraphs.keys()) == [
"O:6-T:4", "O:6#Li", "O:6#Mn"
]
assert len(ccs) == 1
assert ccs[0].periodicity == "0D"
# Get the connectivity for Fe octahedral only
ccs = sc.get_connected_components(environments_symbols=["O:6"],
only_atoms=["Fe"])
assert list(sc.environment_subgraphs.keys()) == [
"O:6-T:4",
"O:6#Li",
"O:6#Mn",
"O:6#Fe",
]
assert len(ccs) == 2
ccs_periodicities = set(cc.periodicity for cc in ccs)
assert ccs_periodicities == {"0D", "2D"}
def test_light_structure_environments(self):
with ScratchDir("."):
f = open("{}/{}".format(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
strategy = SimplestChemenvStrategy()
lse = LightStructureEnvironments.from_structure_environments(
structure_environments=se,
strategy=strategy,
valences='undefined')
isite = 6
nb_set = lse.neighbors_sets[isite][0]
neighb_coords = [
np.array([0.2443798, 1.80409653, -1.13218359]),
np.array([1.44020353, 1.11368738, 1.13218359]),
np.array([2.75513098, 2.54465207, -0.70467298]),
np.array([0.82616785, 3.65833945, 0.70467298])
]
neighb_indices = [0, 3, 5, 1]
neighb_images = [[0, 0, -1], [0, 0, 0], [0, 0, -1], [0, 0, 0]]
np.testing.assert_array_almost_equal(neighb_coords,
nb_set.neighb_coords)
np.testing.assert_array_almost_equal(
neighb_coords, [s.coords for s in nb_set.neighb_sites])
nb_sai = nb_set.neighb_sites_and_indices
np.testing.assert_array_almost_equal(
neighb_coords, [sai['site'].coords for sai in nb_sai])
np.testing.assert_array_almost_equal(
neighb_indices, [sai['index'] for sai in nb_sai])
nb_iai = nb_set.neighb_indices_and_images
np.testing.assert_array_almost_equal(
neighb_indices, [iai['index'] for iai in nb_iai])
np.testing.assert_array_equal(
neighb_images, [iai['image_cell'] for iai in nb_iai])
self.assertEqual(nb_set.__len__(), 4)
self.assertEqual(nb_set.__hash__(), 4)
self.assertFalse(nb_set.__ne__(nb_set))
self.assertEqual(
nb_set.__str__(), 'Neighbors Set for site #6 :\n'
' - Coordination number : 4\n'
' - Neighbors sites indices : 0, 1, 2, 3\n')
stats = lse.get_statistics()
neighbors = lse.strategy.get_site_neighbors(
site=lse.structure[isite])
self.assertArrayAlmostEqual(
neighbors[0].coords,
np.array([0.2443798, 1.80409653, -1.13218359]))
self.assertArrayAlmostEqual(
neighbors[1].coords,
np.array([1.44020353, 1.11368738, 1.13218359]))
self.assertArrayAlmostEqual(
neighbors[2].coords,
np.array([2.75513098, 2.54465207, -0.70467298]))
self.assertArrayAlmostEqual(
neighbors[3].coords,
np.array([0.82616785, 3.65833945, 0.70467298]))
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(
neighbors[0])
self.assertEqual(equiv_site_index_and_transform[0], 0)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1],
[0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2],
[0.0, 0.0, -1.0])
equiv_site_index_and_transform = lse.strategy.equivalent_site_index_and_transform(
neighbors[1])
self.assertEqual(equiv_site_index_and_transform[0], 3)
self.assertArrayAlmostEqual(equiv_site_index_and_transform[1],
[0.0, 0.0, 0.0])
self.assertArrayAlmostEqual(equiv_site_index_and_transform[2],
[0.0, 0.0, 0.0])
self.assertEqual(stats['atom_coordination_environments_present'],
{'Si': {
'T:4': 3.0
}})
self.assertEqual(stats['coordination_environments_atom_present'],
{'T:4': {
'Si': 3.0
}})
self.assertEqual(
stats['fraction_atom_coordination_environments_present'],
{'Si': {
'T:4': 1.0
}})
site_info_ce = lse.get_site_info_for_specie_ce(specie=Species(
'Si', 4),
ce_symbol='T:4')
np.testing.assert_array_almost_equal(site_info_ce['fractions'],
[1.0, 1.0, 1.0])
np.testing.assert_array_almost_equal(site_info_ce['csms'], [
0.009887784240541068, 0.009887786546730826,
0.009887787384385317
])
self.assertEqual(site_info_ce['isites'], [6, 7, 8])
site_info_allces = lse.get_site_info_for_specie_allces(
specie=Species('Si', 4))
self.assertEqual(site_info_allces['T:4'], site_info_ce)
self.assertFalse(lse.contains_only_one_anion('I-'))
self.assertFalse(lse.contains_only_one_anion_atom('I'))
self.assertTrue(
lse.site_contains_environment(isite=isite, ce_symbol='T:4'))
self.assertFalse(
lse.site_contains_environment(isite=isite, ce_symbol='S:4'))
self.assertFalse(
lse.structure_contains_atom_environment(atom_symbol='Si',
ce_symbol='S:4'))
self.assertTrue(
lse.structure_contains_atom_environment(atom_symbol='Si',
ce_symbol='T:4'))
self.assertFalse(
lse.structure_contains_atom_environment(atom_symbol='O',
ce_symbol='T:4'))
self.assertTrue(lse.uniquely_determines_coordination_environments)
self.assertFalse(lse.__ne__(lse))
envs = lse.strategy.get_site_coordination_environments(
lse.structure[6])
self.assertEqual(len(envs), 1)
self.assertEqual(envs[0][0], 'T:4')
multi_strategy = MultiWeightsChemenvStrategy.stats_article_weights_parameters(
)
lse_multi = LightStructureEnvironments.from_structure_environments(
strategy=multi_strategy,
structure_environments=se,
valences='undefined')
self.assertAlmostEqual(
lse_multi.coordination_environments[isite][0]['csm'],
0.009887784240541068)
self.assertAlmostEqual(
lse_multi.coordination_environments[isite][0]['ce_fraction'],
1.0)
self.assertEqual(
lse_multi.coordination_environments[isite][0]['ce_symbol'],
'T:4')
def test_coordination_sequences(self):
BaTiO3_se_fpath = os.path.join(
self.TEST_FILES_DIR,
"chemenv",
"structure_environments_files",
"se_mp-5020.json",
)
with open(BaTiO3_se_fpath, "r") 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)
ccs_oct = sc.get_connected_components(environments_symbols=["O:6"])
ccs_all = sc.get_connected_components(
environments_symbols=["O:6", "C:12"])
assert len(ccs_oct) == 1
assert len(ccs_all) == 1
cc_oct = ccs_oct[0]
cc_all = ccs_all[0]
cc_oct_node = list(cc_oct.graph.nodes())[0]
cseq = cc_oct.coordination_sequence(source_node=cc_oct_node,
path_size=6)
assert cseq == {1: 6, 2: 18, 3: 38, 4: 66, 5: 102, 6: 146}
cc_all_oct_node = next(n for n in cc_all.graph.nodes()
if n.coordination_environment == "O:6")
cc_all_cuboct_node = next(n for n in cc_all.graph.nodes()
if n.coordination_environment == "C:12")
cseq = cc_all.coordination_sequence(source_node=cc_all_oct_node,
path_size=6)
assert cseq == {1: 14, 2: 74, 3: 218, 4: 442, 5: 746, 6: 1130}
cseq = cc_all.coordination_sequence(source_node=cc_all_cuboct_node,
path_size=6)
assert cseq == {1: 26, 2: 122, 3: 298, 4: 554, 5: 890, 6: 1306}
cseq = cc_all.coordination_sequence(source_node=cc_all_cuboct_node,
path_size=6,
include_source=True)
assert cseq == {0: 1, 1: 26, 2: 122, 3: 298, 4: 554, 5: 890, 6: 1306}
cseq = cc_all.coordination_sequence(source_node=cc_all_oct_node,
path_size=4,
coordination="env:number")
assert cseq == {
1: {
"O:6": 6,
"C:12": 8
},
2: {
"O:6": 26,
"C:12": 48
},
3: {
"O:6": 90,
"C:12": 128
},
4: {
"O:6": 194,
"C:12": 248
},
}
cseq = cc_all.coordination_sequence(source_node=cc_all_cuboct_node,
path_size=4,
coordination="env:number")
assert cseq == {
1: {
"O:6": 8,
"C:12": 18
},
2: {
"O:6": 48,
"C:12": 74
},
3: {
"O:6": 128,
"C:12": 170
},
4: {
"O:6": 248,
"C:12": 306
},
}
cseq = cc_all.coordination_sequence(
source_node=cc_all_cuboct_node,
path_size=4,
coordination="env:number",
include_source=True,
)
assert cseq == {
0: {
"C:12": 1
},
1: {
"O:6": 8,
"C:12": 18
},
2: {
"O:6": 48,
"C:12": 74
},
3: {
"O:6": 128,
"C:12": 170
},
4: {
"O:6": 248,
"C:12": 306
},
}
def get_chemenv_analysis(struct, distance_cutoff, angle_cutoff):
if not struct:
raise PreventUpdate
struct = self.from_data(struct)
kwargs = self.reconstruct_kwargs_from_state(
callback_context.inputs)
distance_cutoff = kwargs["distance_cutoff"]
angle_cutoff = kwargs["angle_cutoff"]
# TODO: remove these brittle guard statements, figure out more robust way to handle multiple input types
if isinstance(struct, StructureGraph):
struct = struct.structure
def get_valences(struct):
valences = [
getattr(site.specie, "oxi_state", None) for site in struct
]
valences = [v for v in valences if v is not None]
if len(valences) == len(struct):
return valences
else:
return "undefined"
# decide which indices to present to user
sga = SpacegroupAnalyzer(struct)
symm_struct = sga.get_symmetrized_structure()
inequivalent_indices = [
indices[0] for indices in symm_struct.equivalent_indices
]
wyckoffs = symm_struct.wyckoff_symbols
lgf = LocalGeometryFinder()
lgf.setup_structure(structure=struct)
se = lgf.compute_structure_environments(
maximum_distance_factor=distance_cutoff + 0.01,
only_indices=inequivalent_indices,
valences=get_valences(struct),
)
strategy = SimplestChemenvStrategy(distance_cutoff=distance_cutoff,
angle_cutoff=angle_cutoff)
lse = LightStructureEnvironments.from_structure_environments(
strategy=strategy, structure_environments=se)
all_ce = AllCoordinationGeometries()
envs = []
unknown_sites = []
for index, wyckoff in zip(inequivalent_indices, wyckoffs):
datalist = {
"Site": unicodeify_species(struct[index].species_string),
"Wyckoff Label": wyckoff,
}
if not lse.neighbors_sets[index]:
unknown_sites.append(
f"{struct[index].species_string} ({wyckoff})")
continue
# represent the local environment as a molecule
mol = Molecule.from_sites(
[struct[index]] +
lse.neighbors_sets[index][0].neighb_sites)
mol = mol.get_centered_molecule()
mg = MoleculeGraph.with_empty_graph(molecule=mol)
for i in range(1, len(mol)):
mg.add_edge(0, i)
view = html.Div(
[
StructureMoleculeComponent(
struct_or_mol=mg,
disable_callbacks=True,
id=
f"{struct.composition.reduced_formula}_site_{index}",
scene_settings={
"enableZoom": False,
"defaultZoom": 0.6
},
)._sub_layouts["struct"]
],
style={
"width": "300px",
"height": "300px"
},
)
env = lse.coordination_environments[index]
co = all_ce.get_geometry_from_mp_symbol(env[0]["ce_symbol"])
name = co.name
if co.alternative_names:
name += f" (also known as {', '.join(co.alternative_names)})"
datalist.update({
"Environment":
name,
"IUPAC Symbol":
co.IUPAC_symbol_str,
get_tooltip(
"CSM",
"The continuous symmetry measure (CSM) describes the similarity to an "
"ideal coordination environment. It can be understood as a 'distance' to "
"a shape and ranges from 0 to 100 in which 0 corresponds to a "
"coordination environment that is exactly identical to the ideal one. A "
"CSM larger than 5.0 already indicates a relatively strong distortion of "
"the investigated coordination environment.",
):
f"{env[0]['csm']:.2f}",
"Interactive View":
view,
})
envs.append(get_data_list(datalist))
# TODO: switch to tiles?
envs_grouped = [envs[i:i + 2] for i in range(0, len(envs), 2)]
analysis_contents = []
for env_group in envs_grouped:
analysis_contents.append(
Columns([Column(e, size=6) for e in env_group]))
if unknown_sites:
unknown_sites = html.Strong(
f"The following sites were not identified: {', '.join(unknown_sites)}. "
f"Please try changing the distance or angle cut-offs to identify these sites, "
f"or try an alternative algorithm such as LocalEnv.")
else:
unknown_sites = html.Span()
return html.Div(
[html.Div(analysis_contents),
html.Br(), unknown_sites])
def run(self, sn):
"""
Args:
sn (SiteNetwork)
Returns:
``sn``, with type information.
"""
# -- Determine local environments
# Get an ASE structure with a single mobile site that we'll move around
if sn.n_sites == 0:
logger.warning("Site network had no sites.")
return sn
site_struct, site_species = sn[0:1].get_structure_with_sites()
pymat_struct = AseAtomsAdaptor.get_structure(site_struct)
lgf = cgf.LocalGeometryFinder()
site_atom_index = len(site_struct) - 1
coord_envs = []
vertices = []
valences = 'undefined'
if self._guess_ionic_bonds:
sim_struct = AseAtomsAdaptor.get_structure(sn.structure)
valences = np.zeros(shape = len(site_struct), dtype = np.int)
bv = BVAnalyzer()
try:
struct_valences = np.asarray(bv.get_valences(sim_struct))
except ValueError as ve:
logger.warning("Failed to compute bond valences: %s" % ve)
else:
valences = np.zeros(shape = len(site_struct), dtype = np.int)
valences[:site_atom_index] = struct_valences[sn.static_mask]
mob_val = struct_valences[sn.mobile_mask]
if np.any(mob_val != mob_val[0]):
logger.warning("Mobile atom estimated valences (%s) not uniform; arbitrarily taking first." % mob_val)
valences[site_atom_index] = mob_val[0]
finally:
valences = list(valences)
logger.info("Running site coordination environment analysis...")
# Do this once.
# __init__ here defaults to disabling structure refinement, so all this
# method is doing is making a copy of the structure and setting some
# variables to None.
lgf.setup_structure(structure = pymat_struct)
for site in tqdm(range(sn.n_sites), desc = 'Site'):
# Update the position of the site
lgf.structure[site_atom_index].coords = sn.centers[site]
# Compute structure environments for the site
struct_envs = lgf.compute_structure_environments(
only_indices = [site_atom_index],
valences = valences,
additional_conditions = [AdditionalConditions.ONLY_ANION_CATION_BONDS],
**self._kwargs
)
struct_envs = LightStructureEnvironments.from_structure_environments(
strategy = cgf.LocalGeometryFinder.DEFAULT_STRATEGY,
structure_environments = struct_envs
)
# Store the results
# We take the first environment for each site since it's the most likely
this_site_envs = struct_envs.coordination_environments[site_atom_index]
if len(this_site_envs) > 0:
coord_envs.append(this_site_envs[0])
vertices.append(
[n['index'] for n in struct_envs.neighbors_sets[site_atom_index][0].neighb_indices_and_images]
)
else:
coord_envs.append({'ce_symbol' : 'BAD:0', 'ce_fraction' : 0.})
vertices.append([])
del lgf
del struct_envs
# -- Postprocess
# TODO: allow user to ask for full fractional breakdown
str_coord_environments = [env['ce_symbol'] for env in coord_envs]
# The closer to 1 this is, the better
site_type_confidences = np.array([env['ce_fraction'] for env in coord_envs])
coordination_numbers = np.array([int(env['ce_symbol'].split(':')[1]) for env in coord_envs])
assert np.all(coordination_numbers == [len(v) for v in vertices])
typearr = str_coord_environments if self._full_chemenv_site_types else coordination_numbers
unique_envs = list(set(typearr))
site_types = np.array([unique_envs.index(t) for t in typearr])
n_types = len(unique_envs)
logger.info(("Type " + "{:<8}" * n_types).format(*unique_envs))
logger.info(("# of sites " + "{:<8}" * n_types).format(*np.bincount(site_types)))
sn.site_types = site_types
sn.vertices = vertices
sn.add_site_attribute("coordination_environments", str_coord_environments)
sn.add_site_attribute("site_type_confidences", site_type_confidences)
sn.add_site_attribute("coordination_numbers", coordination_numbers)
return sn
