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 test_structure_environments_neighbors_sets(self):
f = open("{}/{}".format(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
isite = 6
nb_set = se.neighbors_sets[isite][4][0]
nb_set_surface_points = np.array([[1.0017922780870239, 0.99301365328679292],
[1.0017922780870239, 0.0],
[2.2237615554448569, 0.0],
[2.2237615554448569, 0.016430233861405744],
[2.25, 0.016430233861405744],
[2.25, 0.99301365328679292]])
self.assertTrue(np.allclose(np.array(nb_set.voronoi_grid_surface_points()), nb_set_surface_points))
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 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)
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 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 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_structure_environments_neighbors_sets(self):
f = open("{}/{}".format(se_files_dir, "se_mp-7000.json"), "r")
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
isite = 6
nb_set = se.neighbors_sets[isite][4][0]
nb_set_surface_points = np.array([
[1.0017922780870239, 0.99301365328679292],
[1.0017922780870239, 0.0],
[2.2237615554448569, 0.0],
[2.2237615554448569, 0.0060837],
[2.25, 0.0060837],
[2.25, 0.99301365328679292],
])
self.assertTrue(
np.allclose(np.array(nb_set.voronoi_grid_surface_points()),
nb_set_surface_points))
neighb_sites = nb_set.neighb_sites
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]),
]
np.testing.assert_array_almost_equal(coords[0], neighb_sites[0].coords)
np.testing.assert_array_almost_equal(coords[1], neighb_sites[1].coords)
np.testing.assert_array_almost_equal(coords[2], neighb_sites[2].coords)
np.testing.assert_array_almost_equal(coords[3], neighb_sites[3].coords)
neighb_coords = nb_set.coords
np.testing.assert_array_almost_equal(coords, neighb_coords[1:])
np.testing.assert_array_almost_equal(
nb_set.structure[nb_set.isite].coords, neighb_coords[0])
normdist = nb_set.normalized_distances
self.assertAlmostEqual(
sorted(normdist),
sorted([
1.0017922783963027, 1.0017922780870239, 1.000000000503177, 1.0
]),
)
normang = nb_set.normalized_angles
self.assertAlmostEqual(
sorted(normang),
sorted([
0.9999999998419052, 1.0, 0.9930136530585189, 0.9930136532867929
]),
)
dist = nb_set.distances
self.assertAlmostEqual(
sorted(dist),
sorted([
1.6284399814843944,
1.6284399809816534,
1.6255265861208676,
1.6255265853029401,
]),
)
ang = nb_set.angles
self.assertAlmostEqual(
sorted(ang),
sorted([
3.117389876236432,
3.117389876729275,
3.095610709498583,
3.0956107102102024,
]),
)
nb_set_info = nb_set.info
self.assertAlmostEqual(nb_set_info["normalized_angles_mean"],
0.996506826547)
self.assertAlmostEqual(nb_set_info["normalized_distances_std"],
0.000896138995037)
self.assertAlmostEqual(nb_set_info["angles_std"], 0.0108895833142)
self.assertAlmostEqual(nb_set_info["distances_std"], 0.00145669776056)
self.assertAlmostEqual(nb_set_info["distances_mean"], 1.62698328347)
self.assertEqual(
nb_set.__str__(),
"Neighbors Set for site #6 :\n"
" - Coordination number : 4\n"
" - Voronoi indices : 1, 4, 5, 6\n",
)
self.assertFalse(nb_set.__ne__(nb_set))
self.assertEqual(nb_set.__hash__(), 4)
def test_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)
isite = 6
csm_and_maps_fig, csm_and_maps_subplot = se.get_csm_and_maps(
isite=isite)
np.testing.assert_array_almost_equal(
csm_and_maps_subplot.lines[0].get_xydata().flatten(),
[0.0, 0.53499332])
np.testing.assert_array_almost_equal(
csm_and_maps_subplot.lines[1].get_xydata().flatten(),
[1.0, 0.47026441])
np.testing.assert_array_almost_equal(
csm_and_maps_subplot.lines[2].get_xydata().flatten(),
[2.0, 0.00988778])
environments_figure, environments_subplot = se.get_environments_figure(
isite=isite)
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[0].get_xy()),
[[1., 1.], [1., 0.99301365], [1.00179228, 0.99301365],
[1.00179228, 1.], [1., 1.]])
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[1].get_xy()),
[[1., 0.99301365], [1., 0.], [1.00179228, 0.],
[1.00179228, 0.99301365], [1., 0.99301365]])
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[2].get_xy()),
[[1.00179228, 1.], [1.00179228, 0.99301365],
[2.25, 0.99301365], [2.25, 1.], [1.00179228, 1.]])
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[3].get_xy()),
[[1.00179228, 0.99301365], [1.00179228, 0.], [2.22376156, 0.],
[2.22376156, 0.0060837], [2.25, 0.0060837],
[2.25, 0.99301365], [1.00179228, 0.99301365]])
np.testing.assert_array_almost_equal(
np.array(environments_subplot.patches[4].get_xy()),
[[2.22376156, 0.0060837], [2.22376156, 0.], [2.25, 0.],
[2.25, 0.0060837], [2.22376156, 0.0060837]])
se.save_environments_figure(isite=isite, imagename='image.png')
self.assertTrue(os.path.exists('image.png'))
self.assertEqual(len(se.differences_wrt(se)), 0)
self.assertFalse(se.__ne__(se))
ce = se.ce_list[isite][4][0]
self.assertTrue(ce.__len__(), 4)
symbol, mingeom = ce.minimum_geometry(
symmetry_measure_type='csm_wocs_ctwocc')
self.assertEqual(symbol, 'T:4')
self.assertAlmostEqual(mingeom['symmetry_measure'],
0.00988778424054)
np.testing.assert_array_almost_equal(
mingeom['other_symmetry_measures']['rotation_matrix_wcs_csc'],
[[
-0.8433079817973094, -0.19705747216466898,
0.5000000005010193
],
[0.4868840909509757, 0.11377118475194581, 0.8660254034951744],
[
-0.22754236927612112, 0.9737681809261427,
1.3979531202869064e-13
]])
self.assertEqual(mingeom['detailed_voronoi_index'], {
'index': 0,
'cn': 4
})
self.assertAlmostEqual(
mingeom['other_symmetry_measures']
['scaling_factor_wocs_ctwocc'], 1.6270605877934026)
ce_string = ce.__str__()
self.assertTrue('csm1 (with central site) : 0.00988' in ce_string)
self.assertTrue(
'csm2 (without central site) : 0.00981' in ce_string)
self.assertTrue('csm1 (with central site) : 12.987' in ce_string)
self.assertTrue(
'csm2 (without central site) : 11.827' in ce_string)
self.assertTrue('csm1 (with central site) : 32.466' in ce_string)
self.assertTrue(
'csm2 (without central site) : 32.466' in ce_string)
self.assertTrue('csm1 (with central site) : 34.644' in ce_string)
self.assertTrue(
'csm2 (without central site) : 32.466' in ce_string)
mingeoms = ce.minimum_geometries(
symmetry_measure_type='csm_wocs_ctwocc', max_csm=12.0)
self.assertEqual(len(mingeoms), 2)
mingeoms = ce.minimum_geometries(
symmetry_measure_type='csm_wocs_ctwcc', max_csm=12.0)
self.assertEqual(len(mingeoms), 1)
mingeoms = ce.minimum_geometries(n=3)
self.assertEqual(len(mingeoms), 3)
ce2 = se.ce_list[7][4][0]
self.assertTrue(ce.is_close_to(ce2, rtol=0.01, atol=1e-4))
self.assertFalse(ce.is_close_to(ce2, rtol=0.0, atol=1e-8))
self.assertFalse(ce.__eq__(ce2))
self.assertTrue(ce.__ne__(ce2))
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_delta_csms_weight(self):
# Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
with open(os.path.join(se_files_dir, "se_mp-743972.json")) as f:
dd = json.load(f)
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(12, 3), (12, 2), (13, 2), (12, 0), (12, 1), (13, 0), (13, 1)]
nbsets = {cn_map: se.neighbors_sets[0][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {
"function": "power2_inverse_decreasing",
"options": {"max_csm": 8.0},
}
weight_estimator = {
"function": "smootherstep",
"options": {"delta_csm_min": 0.5, "delta_csm_max": 3.0},
}
symmetry_measure_type = "csm_wcs_ctwcc"
delta_weight = DeltaCSMNbSetWeight(
effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type,
)
additional_info = {}
cn_map = (12, 3)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 2)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 0)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 1)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (13, 2)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
cn_map = (13, 0)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (13, 1)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
effective_csm_estimator = {
"function": "power2_inverse_decreasing",
"options": {"max_csm": 8.0},
}
weight_estimator = {
"function": "smootherstep",
"options": {"delta_csm_min": -1.0, "delta_csm_max": 3.0},
}
symmetry_measure_type = "csm_wcs_ctwcc"
delta_weight = DeltaCSMNbSetWeight(
effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type,
)
additional_info = {}
cn_map = (12, 3)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.040830741048481355, delta=1e-8)
cn_map = (13, 2)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
cn_map = (13, 0)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.103515625, delta=1e-8)
cn_map = (13, 1)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.103515625, delta=1e-8)
# Get the StructureEnvironments for SiO2 (mp-7000)
with open(os.path.join(se_files_dir, "se_mp-7000.json")) as f:
dd = json.load(f)
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(2, 0), (4, 0)]
nbsets = {cn_map: se.neighbors_sets[6][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {
"function": "power2_inverse_decreasing",
"options": {"max_csm": 8.0},
}
weight_estimator = {
"function": "smootherstep",
"options": {"delta_csm_min": 0.5, "delta_csm_max": 3.0},
}
symmetry_measure_type = "csm_wcs_ctwcc"
delta_weight = DeltaCSMNbSetWeight(
effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type,
)
additional_info = {}
cn_map = (2, 0)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (4, 0)
delta_w = delta_weight.weight(
nb_set=nbsets[cn_map],
structure_environments=se,
cn_map=cn_map,
additional_info=additional_info,
)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
def test_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)
isite = 6
csm_and_maps_fig, csm_and_maps_subplot = se.get_csm_and_maps(isite=isite)
np.testing.assert_array_almost_equal(csm_and_maps_subplot.lines[0].get_xydata().flatten(), [0.0, 0.53499332])
np.testing.assert_array_almost_equal(csm_and_maps_subplot.lines[1].get_xydata().flatten(), [1.0, 0.47026441])
np.testing.assert_array_almost_equal(csm_and_maps_subplot.lines[2].get_xydata().flatten(), [2.0, 0.00988778])
environments_figure, environments_subplot = se.get_environments_figure(isite=isite)
np.testing.assert_array_almost_equal(np.array(environments_subplot.patches[0].get_xy()),
[[1., 1.],
[1., 0.99301365],
[1.00179228, 0.99301365],
[1.00179228, 1.],
[1., 1.]])
np.testing.assert_array_almost_equal(np.array(environments_subplot.patches[1].get_xy()),
[[1., 0.99301365],
[1., 0.],
[1.00179228, 0.],
[1.00179228, 0.99301365],
[1., 0.99301365]])
np.testing.assert_array_almost_equal(np.array(environments_subplot.patches[2].get_xy()),
[[1.00179228, 1.],
[1.00179228, 0.99301365],
[2.25, 0.99301365],
[2.25, 1.],
[1.00179228, 1.]])
np.testing.assert_array_almost_equal(np.array(environments_subplot.patches[3].get_xy()),
[[1.00179228, 0.99301365],
[1.00179228, 0.],
[2.22376156, 0.],
[2.22376156, 0.0060837],
[2.25, 0.0060837],
[2.25, 0.99301365],
[1.00179228, 0.99301365]])
np.testing.assert_array_almost_equal(np.array(environments_subplot.patches[4].get_xy()),
[[2.22376156, 0.0060837],
[2.22376156, 0.],
[2.25, 0.],
[2.25, 0.0060837],
[2.22376156, 0.0060837]])
imgpath = os.path.join('tmp_dir', 'image.png')
se.save_environments_figure(isite=isite, imagename=imgpath)
self.assertTrue(os.path.exists(imgpath))
self.assertEqual(len(se.differences_wrt(se)), 0)
self.assertFalse(se.__ne__(se))
ce = se.ce_list[isite][4][0]
self.assertTrue(ce.__len__(), 4)
symbol, mingeom = ce.minimum_geometry(symmetry_measure_type='csm_wocs_ctwocc')
self.assertEqual(symbol, 'T:4')
self.assertAlmostEqual(mingeom['symmetry_measure'], 0.00988778424054)
np.testing.assert_array_almost_equal(mingeom['other_symmetry_measures']['rotation_matrix_wcs_csc'],
[[-0.8433079817973094, -0.19705747216466898, 0.5000000005010193],
[0.4868840909509757, 0.11377118475194581, 0.8660254034951744],
[-0.22754236927612112, 0.9737681809261427, 1.3979531202869064e-13]])
self.assertEqual(mingeom['detailed_voronoi_index'], {'index': 0, 'cn': 4})
self.assertAlmostEqual(mingeom['other_symmetry_measures']['scaling_factor_wocs_ctwocc'], 1.6270605877934026)
ce_string = ce.__str__()
self.assertTrue('csm1 (with central site) : 0.00988' in ce_string)
self.assertTrue('csm2 (without central site) : 0.00981' in ce_string)
self.assertTrue('csm1 (with central site) : 12.987' in ce_string)
self.assertTrue('csm2 (without central site) : 11.827' in ce_string)
self.assertTrue('csm1 (with central site) : 32.466' in ce_string)
self.assertTrue('csm2 (without central site) : 32.466' in ce_string)
self.assertTrue('csm1 (with central site) : 34.644' in ce_string)
self.assertTrue('csm2 (without central site) : 32.466' in ce_string)
mingeoms = ce.minimum_geometries(symmetry_measure_type='csm_wocs_ctwocc', max_csm=12.0)
self.assertEqual(len(mingeoms), 2)
mingeoms = ce.minimum_geometries(symmetry_measure_type='csm_wocs_ctwcc', max_csm=12.0)
self.assertEqual(len(mingeoms), 1)
mingeoms = ce.minimum_geometries(n=3)
self.assertEqual(len(mingeoms), 3)
ce2 = se.ce_list[7][4][0]
self.assertTrue(ce.is_close_to(ce2, rtol=0.01, atol=1e-4))
self.assertFalse(ce.is_close_to(ce2, rtol=0.0, atol=1e-8))
self.assertFalse(ce.__eq__(ce2))
self.assertTrue(ce.__ne__(ce2))
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')
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 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 test_self_csms_weight(self):
# Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
f = open(os.path.join(se_files_dir, 'se_mp-743972.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(12, 3), (12, 2), (13, 2), (12, 0), (12, 1)]
nbsets = {cn_map: se.neighbors_sets[0][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'power2_decreasing_exp',
'options': {'max_csm': 8.0,
'alpha': 1.0}}
weight_estimator2 = {'function': 'power2_decreasing_exp',
'options': {'max_csm': 8.1,
'alpha': 1.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
self_weight = SelfCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
self_weight2 = SelfCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator2,
symmetry_measure_type=symmetry_measure_type)
self.assertNotEqual(self_weight, self_weight2)
additional_info = {}
cn_map = (12, 3)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.11671945916431022, delta=1e-8)
cn_map = (12, 2)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.0, delta=1e-8)
cn_map = (12, 0)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.0, delta=1e-8)
cn_map = (12, 1)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.0, delta=1e-8)
cn_map = (13, 2)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.14204073172729198, delta=1e-8)
# Get the StructureEnvironments for SiO2 (mp-7000)
f = open(os.path.join(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(2, 0), (4, 0)]
nbsets = {cn_map: se.neighbors_sets[6][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'power2_decreasing_exp',
'options': {'max_csm': 8.0,
'alpha': 1.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
self_weight = SelfCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (2, 0)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.8143992162836029, delta=1e-8)
cn_map = (4, 0)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.99629742352359496, delta=1e-8)
def test_delta_csms_weight(self):
# Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
f = open(os.path.join(se_files_dir, 'se_mp-743972.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(12, 3), (12, 2), (13, 2), (12, 0), (12, 1), (13, 0), (13, 1)]
nbsets = {cn_map: se.neighbors_sets[0][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'smootherstep',
'options': {'delta_csm_min': 0.5,
'delta_csm_max': 3.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
delta_weight = DeltaCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (12, 3)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 2)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 1)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (13, 2)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
cn_map = (13, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (13, 1)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'smootherstep',
'options': {'delta_csm_min': -1.0,
'delta_csm_max': 3.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
delta_weight = DeltaCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (12, 3)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.040830741048481355, delta=1e-8)
cn_map = (13, 2)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
cn_map = (13, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.103515625, delta=1e-8)
cn_map = (13, 1)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.103515625, delta=1e-8)
# Get the StructureEnvironments for SiO2 (mp-7000)
f = open(os.path.join(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(2, 0), (4, 0)]
nbsets = {cn_map: se.neighbors_sets[6][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'smootherstep',
'options': {'delta_csm_min': 0.5,
'delta_csm_max': 3.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
delta_weight = DeltaCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (2, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (4, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
def test_self_csms_weight(self):
# Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
f = open(os.path.join(se_files_dir, 'se_mp-743972.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(12, 3), (12, 2), (13, 2), (12, 0), (12, 1)]
nbsets = {cn_map: se.neighbors_sets[0][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'power2_decreasing_exp',
'options': {'max_csm': 8.0,
'alpha': 1.0}}
weight_estimator2 = {'function': 'power2_decreasing_exp',
'options': {'max_csm': 8.1,
'alpha': 1.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
self_weight = SelfCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
self_weight2 = SelfCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator2,
symmetry_measure_type=symmetry_measure_type)
self.assertNotEqual(self_weight, self_weight2)
additional_info = {}
cn_map = (12, 3)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.11671945916431022, delta=1e-8)
cn_map = (12, 2)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.0, delta=1e-8)
cn_map = (12, 0)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.0, delta=1e-8)
cn_map = (12, 1)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.0, delta=1e-8)
cn_map = (13, 2)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.14204073172729198, delta=1e-8)
# Get the StructureEnvironments for SiO2 (mp-7000)
f = open(os.path.join(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(2, 0), (4, 0)]
nbsets = {cn_map: se.neighbors_sets[6][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'power2_decreasing_exp',
'options': {'max_csm': 8.0,
'alpha': 1.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
self_weight = SelfCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (2, 0)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.8143992162836029, delta=1e-8)
cn_map = (4, 0)
self_w = self_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(self_w, 0.99629742352359496, delta=1e-8)
def test_structure_environments_neighbors_sets(self):
f = open("{}/{}".format(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
isite = 6
nb_set = se.neighbors_sets[isite][4][0]
nb_set_surface_points = np.array([[1.0017922780870239, 0.99301365328679292],
[1.0017922780870239, 0.0],
[2.2237615554448569, 0.0],
[2.2237615554448569, 0.0060837],
[2.25, 0.0060837],
[2.25, 0.99301365328679292]])
self.assertTrue(np.allclose(np.array(nb_set.voronoi_grid_surface_points()), nb_set_surface_points))
neighb_sites = nb_set.neighb_sites
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])]
np.testing.assert_array_almost_equal(coords[0], neighb_sites[0].coords)
np.testing.assert_array_almost_equal(coords[1], neighb_sites[1].coords)
np.testing.assert_array_almost_equal(coords[2], neighb_sites[2].coords)
np.testing.assert_array_almost_equal(coords[3], neighb_sites[3].coords)
neighb_coords = nb_set.coords
np.testing.assert_array_almost_equal(coords, neighb_coords[1:])
np.testing.assert_array_almost_equal(nb_set.structure[nb_set.isite].coords, neighb_coords[0])
normdist = nb_set.normalized_distances
self.assertAlmostEqual(sorted(normdist),
sorted([1.0017922783963027, 1.0017922780870239, 1.000000000503177, 1.0]))
normang = nb_set.normalized_angles
self.assertAlmostEqual(sorted(normang),
sorted([0.9999999998419052, 1.0, 0.9930136530585189, 0.9930136532867929]))
dist = nb_set.distances
self.assertAlmostEqual(sorted(dist),
sorted([1.6284399814843944, 1.6284399809816534, 1.6255265861208676, 1.6255265853029401]))
ang = nb_set.angles
self.assertAlmostEqual(sorted(ang),
sorted([3.117389876236432, 3.117389876729275, 3.095610709498583, 3.0956107102102024]))
nb_set_info = nb_set.info
self.assertAlmostEqual(nb_set_info['normalized_angles_mean'], 0.996506826547)
self.assertAlmostEqual(nb_set_info['normalized_distances_std'], 0.000896138995037)
self.assertAlmostEqual(nb_set_info['angles_std'], 0.0108895833142)
self.assertAlmostEqual(nb_set_info['distances_std'], 0.00145669776056)
self.assertAlmostEqual(nb_set_info['distances_mean'], 1.62698328347)
self.assertEqual(nb_set.__str__(), 'Neighbors Set for site #6 :\n'
' - Coordination number : 4\n'
' - Voronoi indices : 1, 4, 5, 6\n')
self.assertFalse(nb_set.__ne__(nb_set))
self.assertEqual(nb_set.__hash__(), 4)
def test_delta_csms_weight(self):
# Get the StructureEnvironments for K2NaNb2Fe7Si8H4O31 (mp-743972)
f = open(os.path.join(se_files_dir, 'se_mp-743972.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(12, 3), (12, 2), (13, 2), (12, 0), (12, 1), (13, 0), (13, 1)]
nbsets = {cn_map: se.neighbors_sets[0][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'smootherstep',
'options': {'delta_csm_min': 0.5,
'delta_csm_max': 3.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
delta_weight = DeltaCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (12, 3)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 2)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (12, 1)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (13, 2)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
cn_map = (13, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (13, 1)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'smootherstep',
'options': {'delta_csm_min': -1.0,
'delta_csm_max': 3.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
delta_weight = DeltaCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (12, 3)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.040830741048481355, delta=1e-8)
cn_map = (13, 2)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
cn_map = (13, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.103515625, delta=1e-8)
cn_map = (13, 1)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.103515625, delta=1e-8)
# Get the StructureEnvironments for SiO2 (mp-7000)
f = open(os.path.join(se_files_dir, 'se_mp-7000.json'), 'r')
dd = json.load(f)
f.close()
se = StructureEnvironments.from_dict(dd)
# Get neighbors sets for which we get the weights
cn_maps = [(2, 0), (4, 0)]
nbsets = {cn_map: se.neighbors_sets[6][cn_map[0]][cn_map[1]] for cn_map in cn_maps}
effective_csm_estimator = {'function': 'power2_inverse_decreasing',
'options': {'max_csm': 8.0}}
weight_estimator = {'function': 'smootherstep',
'options': {'delta_csm_min': 0.5,
'delta_csm_max': 3.0}}
symmetry_measure_type = 'csm_wcs_ctwcc'
delta_weight = DeltaCSMNbSetWeight(effective_csm_estimator=effective_csm_estimator,
weight_estimator=weight_estimator,
symmetry_measure_type=symmetry_measure_type)
additional_info = {}
cn_map = (2, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 0.0, delta=1e-8)
cn_map = (4, 0)
delta_w = delta_weight.weight(nb_set=nbsets[cn_map], structure_environments=se,
cn_map=cn_map, additional_info=additional_info)
self.assertAlmostEqual(delta_w, 1.0, delta=1e-8)
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)
