def check(base_structure, num_type, indices, species, name):
for index in indices:
se = StructureEnumerator(
base_structure,
index,
num_type,
species,
color_exchange=True,
leave_superperiodic=False,
)
list_ds = se.generate()
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_ds)
assert len(grouped) == len(list_ds)
def test_lexicographic_with_composition(benchmark):
setting = get_common_settings()
setting["method"] = "lexicographic"
setting["composition_constraints"] = [1, 3, 2]
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate, iterations=1)
def test_site_constraints(method, benchmark):
setting = {
"base_structure":
get_rutile_structure(),
"index":
4,
"num_types":
3,
"base_site_constraints": [
[2], # 2a
[2], # 2a
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
],
"remove_incomplete":
True,
"remove_superperiodic":
True,
}
if method == "direct":
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate,
kwargs={"output": "poscar"},
iterations=1)
else:
zse = ZddStructureEnumerator(**setting)
if method == "zdd":
benchmark.pedantic(zse.generate,
kwargs={"output": "poscar"},
iterations=1)
elif method == "zdd_count":
benchmark.pedantic(zse.count, iterations=1)
def test_basic_structure(kind, index):
base_structure = get_lattice(kind)
num_type = 2
species = ["Cu", "Au"]
se = StructureEnumerator(
base_structure,
index,
num_type,
species,
color_exchange=True,
remove_superperiodic=True,
)
list_ds = se.generate()
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_ds)
assert len(grouped) == len(list_ds)
def test_poscar_string(kind):
base_structure = get_lattice(kind)
num_type = 2
index = 4
species = [Element("Cu"), Element("Au")]
se = StructureEnumerator(
base_structure,
index,
num_type,
species,
color_exchange=True,
remove_superperiodic=True,
)
list_ds_mg = se.generate(output="pymatgen")
list_ds_pc = se.generate(output="poscar")
assert len(list_ds_mg) == len(list_ds_pc)
for expect, poscar_str in zip(list_ds_mg, list_ds_pc):
actual = Poscar.from_string(poscar_str).structure
assert expect == actual
def test_lexicographic_with_site(benchmark):
setting = get_common_settings()
setting["method"] = "lexicographic"
setting["base_site_constraints"] = [
[2], # 2a
[2], # 2a
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
]
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate, iterations=1)
def test_direct_with_composition_and_site(benchmark):
setting = get_common_settings()
setting["method"] = "direct"
setting["composition_constraints"] = [1, 3, 2]
setting["base_site_constraints"] = [
[2], # 2a
[2], # 2a
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
]
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate, iterations=1)
def test_coloring_with_fixed_species():
lattice = Lattice(3.945 * np.eye(3))
species = ["Sr", "Ti", "O", "O", "O"]
frac_coords = np.array([[0, 0, 0], [0.5, 0.5, 0.5], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
aristo = Structure(lattice, species, frac_coords)
base_structure = aristo.copy()
base_structure.remove_species(["Sr", "Ti"])
additional_species = species[:2]
additional_frac_coords = frac_coords[:2]
mapping_color_species = [DummySpecie("X"), "O"]
num_types = len(mapping_color_species)
index = 2
se = StructureEnumerator(
base_structure,
index,
num_types,
mapping_color_species=mapping_color_species,
color_exchange=False,
leave_superperiodic=False,
use_all_colors=False,
)
list_dstructs = se.generate(additional_species=additional_species,
additional_frac_coords=additional_frac_coords)
# with base_site_constraints
mapping_color_species2 = [DummySpecie("X"), "O", "Sr", "Ti"]
num_types2 = len(mapping_color_species2)
base_site_constraints = [
[2], # Sr site
[3], # Cu site
[0, 1], # O or V
[0, 1], # O or V
[0, 1], # O or V
]
se2 = StructureEnumerator(
aristo,
index,
num_types2,
mapping_color_species=mapping_color_species2,
base_site_constraints=base_site_constraints,
color_exchange=False,
leave_superperiodic=False,
use_all_colors=False,
)
list_dstructs2 = se2.generate()
# check uniqueness by StructureMatcher
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_dstructs + list_dstructs2)
assert len(grouped) == len(list_dstructs)
assert all([(len(matched) == 2) for matched in grouped])
def test_coloring_with_fixed_species(sto_perovskite: Structure):
base_structure = sto_perovskite.copy()
base_structure.remove_species(["Sr", "Ti"])
additional_species = sto_perovskite.species[:2]
additional_frac_coords = sto_perovskite.frac_coords[:2]
mapping_color_species = [DummySpecie("X"), "O"]
num_types = len(mapping_color_species)
index = 2
se = StructureEnumerator(
base_structure,
index,
num_types,
mapping_color_species=mapping_color_species,
color_exchange=False,
remove_superperiodic=True,
remove_incomplete=False,
)
list_dstructs = se.generate(additional_species=additional_species,
additional_frac_coords=additional_frac_coords)
# with base_site_constraints
mapping_color_species2 = [DummySpecie("X"), "O", "Sr", "Ti"]
num_types2 = len(mapping_color_species2)
base_site_constraints = [
[2], # Sr site
[3], # Cu site
[0, 1], # O or V
[0, 1], # O or V
[0, 1], # O or V
]
se2 = StructureEnumerator(
sto_perovskite,
index,
num_types2,
mapping_color_species=mapping_color_species2,
base_site_constraints=base_site_constraints,
color_exchange=False,
remove_superperiodic=True,
remove_incomplete=False,
)
list_dstructs2 = se2.generate()
# check uniqueness by StructureMatcher
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_dstructs +
list_dstructs2) # type: ignore
assert len(grouped) == len(list_dstructs)
assert all([(len(matched) == 2) for matched in grouped])
def test_basic_ternary(method, benchmark):
setting = {
"base_structure": get_lattice("fcc"),
"index": 10,
"num_types": 3,
"remove_incomplete": True,
"remove_superperiodic": True,
}
if method == "direct":
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate,
kwargs={"output": "poscar"},
iterations=1)
else:
zse = ZddStructureEnumerator(**setting)
if method == "zdd":
benchmark.pedantic(zse.generate,
kwargs={"output": "poscar"},
iterations=1)
elif method == "zdd_count":
benchmark.pedantic(zse.count, iterations=1)
def test_lexicographic(benchmark):
setting = get_common_settings()
setting["method"] = "lexicographic"
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate, iterations=1)
def test_direct(benchmark):
setting = get_common_settings()
setting["method"] = "direct"
se = StructureEnumerator(**setting)
benchmark.pedantic(se.generate, iterations=1)
[0, 1], # 4f
[0, 1], # 4f
[0, 1], # 4f
]
# fmt: on
dirname = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"SnO1-x")
os.makedirs(dirname, exist_ok=True)
for index in range(1, max_index + 1):
se = StructureEnumerator(
rutile,
index,
num_types,
mapping_color_species=mapping_color_species,
composition_constraints=composition_constraints,
base_site_constraints=base_site_constraints,
color_exchange=False,
leave_superperiodic=False,
use_all_colors=False,
)
list_dstructs = se.generate()
for i, dstruct in enumerate(list_dstructs):
# remove void
dstruct.remove_species([mapping_color_species[0]])
filename = os.path.join(dirname, f"SnO1-x_{index}_{i}.cif")
write_cif(filename, dstruct, refine_cell=True)
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
aristo = Structure(lattice, species, frac_coords)
base_structure = aristo.copy()
base_structure.remove_species(["Sr", "Ti"])
additional_species = species[:2]
additional_frac_coords = frac_coords[:2]
mapping_color_species = [DummySpecie("X"), "O"]
num_types = len(mapping_color_species)
index = 2
se = StructureEnumerator(
base_structure,
index,
num_types,
mapping_color_species=mapping_color_species,
color_exchange=False,
leave_superperiodic=False,
use_all_colors=False,
)
list_dstructs = se.generate(additional_species=additional_species,
additional_frac_coords=additional_frac_coords)
# leave only SrTiO_{3-x} (0 <= x <= 1)
num_oxygen_lb = index * 2
num_oxygen_ub = index * 3
structures = []
for ds in list_dstructs:
num_oxygen = sum([(str(sp) == "O") for sp in ds.species])
if num_oxygen_lb <= num_oxygen and num_oxygen <= num_oxygen_ub:
structures.append(ds)