def setUp(self):
struct = Structure.from_file(f"{dir_path}/full_path_files/MnO2_full_Li.vasp")
self.fpm_li = MigrationGraph.with_distance(structure=struct, migrating_specie="Li", max_distance=4)
# Particularity difficult pathfinding since both the starting and ending positions are outside the unit cell
struct = Structure.from_file(f"{dir_path}/full_path_files/Mg_2atom.vasp")
self.fpm_mg = MigrationGraph.with_distance(structure=struct, migrating_specie="Mg", max_distance=2)
def test_m_graph_from_entries_failed(self):
# only base
s_list = MigrationGraph.get_structure_from_entries(
entries=[self.test_ents_MOF["ent_base"]],
migrating_ion_entry=self.li_ent,
)
self.assertEqual(len(s_list), 0)
s_list = MigrationGraph.get_structure_from_entries(
entries=self.test_ents_MOF["one_cation"],
migrating_ion_entry=self.li_ent,
)
self.assertEqual(len(s_list), 0)
def setUp(self):
self.test_ents_MOF = loadfn(f"{dir_path}/full_path_files/Mn6O5F7_cat_migration.json")
self.aeccar_MOF = Chgcar.from_file(f"{dir_path}/full_path_files/AECCAR_Mn6O5F7.vasp")
self.li_ent = loadfn(f"{dir_path}/full_path_files/li_ent.json")["li_ent"]
self.full_struct = MigrationGraph.get_structure_from_entries(
base_entries=[self.test_ents_MOF["ent_base"]],
inserted_entries=self.test_ents_MOF["one_cation"],
migrating_ion_entry=self.li_ent,
)[0]
def add_edge_data_from_sc(
mg: MigrationGraph,
i_sc: Structure,
e_sc: Structure,
data_array: list,
key: str = "custom_key",
use_host_sg: bool = True,
) -> None:
"""
Add a data entry and key to edges within FullPathMapper object with the same hop_label.
These hops are equivalent by symmetry to the 2 positions given in the supercell structures.
Args:
i_sc: Supercell structure containing working ion at initial position
e_sc: Supercell structure containing working ion at ending position
data_array: The data to be added to the edges
key: Key of the edge attribute to be added
use_host_sg: Flag t whether or not to use the host structure's spacegroup to initiate MigrationHop
Returns:
None
"""
wi = list(mg.m_graph.graph.edges(data=True))[0][2]["hop"].isite.specie.name
i_wi = [x for x in i_sc.sites if x.species_string == wi]
e_wi = [x for x in e_sc.sites if x.species_string == wi]
if len(i_wi) != 1 or len(e_wi) != 1:
raise ValueError(
"The number of working ions in each supercell structure should be one"
)
isite, esite = i_wi[0], e_wi[0]
uhop_index, mh_from_sc = get_unique_hop(mg, i_sc, isite, esite,
use_host_sg)
add_dict = {key: data_array}
mg.add_data_to_similar_edges(target_label=uhop_index,
data=add_dict,
m_hop=mh_from_sc)
def setUp(self):
self.lifepo = self.get_structure("LiFePO4")
migration_graph = MigrationGraph.with_distance(self.lifepo,
max_distance=4.0,
migrating_specie="Li")
gen = iter(migration_graph.migration_graph.graph.edges(data=True))
u, v, d = next(gen)
i_site = PeriodicSite("Li",
coords=d["ipos"],
lattice=self.lifepo.lattice)
e_site = PeriodicSite("Li",
coords=d["epos"],
lattice=self.lifepo.lattice)
a = SpacegroupAnalyzer(self.lifepo)
symm_structure = a.get_symmetrized_structure()
self.m_hop = MigrationHop(i_site, e_site, symm_structure)
def test_m_graph_construction(self):
self.assertEqual(self.full_struct.composition["Li"], 8)
mg = MigrationGraph.with_distance(self.full_struct,
migrating_specie="Li",
max_distance=4.0)
self.assertEqual(len(mg.m_graph.structure), 8)
def setUp(self):
struct = Structure.from_file(
f"{dir_path}/full_path_files/MnO2_full_Li.vasp")
self.fpm = MigrationGraph.with_distance(structure=struct,
migrating_specie="Li",
max_distance=4)
def test_not_matching_first(self):
structure = Structure.from_file(
f"{dir_path}/pathfinder_files/Li6MnO4.json")
fpm_lmo = MigrationGraph.with_distance(structure, "Li", max_distance=4)
for u, v, d in fpm_lmo.m_graph.graph.edges(data=True):
self.assertIn(d["hop"].eindex, {0, 1})
test_dir = os.path.dirname(os.path.realpath(__file__))
__author__ = "Haoming Li"
__version__ = "1.0"
__date__ = "February 17, 2021"
uc_full_sites = Structure.from_file(f"{test_dir}/test_files/Li4Sr3Fe2O7_uc.vasp")
input_struct_i = Structure.from_file(f"{test_dir}/test_files/Sr3Fe2O7_sc_i.vasp")
input_struct_e = Structure.from_file(f"{test_dir}/test_files/Sr3Fe2O7_sc_e.vasp")
mg_uc_full_sites = Structure.from_file(f"{test_dir}/test_files/Mg3VOPO4_uc.vasp")
mg_input_struct_i = Structure.from_file(f"{test_dir}/test_files/Mg3VOPO4_sc_i.vasp")
mg_input_struct_e = Structure.from_file(f"{test_dir}/test_files/Mg3VOPO4_sc_e.vasp")
mg_Li = MigrationGraph.with_distance(structure=uc_full_sites, migrating_specie="Li", max_distance=5)
mg_Mg = MigrationGraph.with_distance(structure=mg_uc_full_sites, migrating_specie="Mg", max_distance=4)
def test_add_edge_data_from_sc():
errors = []
test_key = "test_key"
test_array = [0, 1, 2, 3, 4]
add_edge_data_from_sc(
mg_Li,
i_sc=input_struct_i,
e_sc=input_struct_e,
data_array=test_array,
key=test_key,
)