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 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 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 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 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 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 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 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()})
