def test_zdd_with_naive(kind, num_types, composition_constraints,
site_constraints):
structure = get_lattice(kind)
for index in range(1, 6 + 1):
if composition_constraints:
ratio_sum = sum(composition_constraints)
if structure.num_sites * index % ratio_sum != 0:
# Incorrect composition ratio
continue
se = StructureEnumerator(
structure,
index,
num_types,
composition_constraints=composition_constraints,
base_site_constraints=site_constraints,
color_exchange=False,
remove_incomplete=False,
remove_superperiodic=False,
)
zse = ZddStructureEnumerator(
structure,
index,
num_types,
composition_constraints=composition_constraints,
base_site_constraints=site_constraints,
remove_superperiodic=False,
remove_incomplete=False,
)
count_naive = len(se.generate())
count_zdd = len(zse.generate())
assert count_zdd == count_naive
def test_fixed_colorings_with_polya(kind, num_types):
structure = get_lattice(kind)
displacement_set = structure.frac_coords
num_sites_base = structure.num_sites
for index in range(num_types, 5):
list_reduced_HNF, rotations, translations = generate_symmetry_distinct_superlattices(
index, structure, return_symops=True)
num_sites = num_sites_base * index
# TODO: test at more color_ratio cases
color_ratio = [1] * (num_types - 1) + [
num_sites - num_types + 1,
]
cl_generator = FixedConcentrationColoringGenerator(
num_sites, num_types, color_ratio)
for hnf in tqdm(list_reduced_HNF):
ds_permutaion = DerivativeStructurePermutation(
hnf, displacement_set, rotations, translations)
sc_enum = SiteColoringEnumerator(
num_types,
ds_permutaion,
cl_generator,
color_exchange=False,
remove_superperiodic=False,
remove_incomplete=False,
)
colorings = sc_enum.unique_colorings()
cnt_polya = polya_fixed_degrees_counting(sc_enum.permutation_group,
num_types, color_ratio)
assert len(colorings) == cnt_polya
def test_hcp():
base_structure = get_lattice("hcp")
num_type = 2
indices = [2, 3, 4]
species = [Specie("Cu"), Specie("Au")]
check(base_structure, num_type, indices, species, "hcp")
def test_sc():
base_structure = get_lattice("sc")
num_type = 2
indices = [2, 3, 4]
species = [Element("Cu"), Element("Au")]
check(base_structure, num_type, indices, species, "sc")
def test_fcc():
base_structure = get_lattice("fcc")
num_type = 2
indices = [2, 3, 4]
species = ["Cu", "Au"]
check(base_structure, num_type, indices, species, "fcc")
def test_reduce_HNF_list_by_parent_lattice_symmetry(kind, list_expected):
# Confirm table 4
structure = get_lattice(kind)
for index, expected in zip(range(1,
len(list_expected) + 1), list_expected):
list_reduced_HNF = generate_symmetry_distinct_superlattices(
index, structure)
assert len(list_reduced_HNF) == expected
def test_permutations(kind):
structure = get_lattice(kind)
frac_coords = structure.frac_coords
for index in range(1, 10 + 1):
list_reduced_HNF, rotations, translations = generate_symmetry_distinct_superlattices(
index, structure, return_symops=True)
for hnf in list_reduced_HNF:
dsperm = DerivativeStructurePermutation(hnf, frac_coords,
rotations, translations)
assert is_permutation_group(dsperm.prm_t)
prm_all = dsperm.get_symmetry_operation_permutations()
assert is_permutation_group(prm_all)
def test_reduce_HNF_list_by_parent_lattice_symmetry():
# confirm table 4
obj = {
"fcc": {
"structure": get_lattice("fcc"),
"num_expected": [1, 2, 3, 7, 5, 10, 7, 20, 14, 18],
},
"bcc": {
"structure": get_lattice("bcc"),
"num_expected": [1, 2, 3, 7, 5, 10, 7, 20, 14, 18],
},
"sc": {"structure": get_lattice("sc"), "num_expected": [1, 3, 3, 9, 5, 13, 7, 24, 14, 23]},
"hex": {
"structure": get_lattice("hex"),
"num_expected": [1, 3, 5, 11, 7, 19, 11, 34, 23, 33],
},
"tetragonal": {
"structure": get_lattice("tet"),
"num_expected": [1, 5, 5, 17, 9, 29, 13, 51, 28, 53],
},
"hcp": {
"structure": get_lattice("hcp"),
"num_expected": [1, 3, 5, 11, 7, 19, 11, 34, 23, 33],
},
}
for name, dct in obj.items():
structure = dct["structure"]
for index, expected in zip(range(1, len(dct["num_expected"]) + 1), dct["num_expected"]):
list_reduced_HNF = generate_symmetry_distinct_superlattices(index, structure)
assert len(list_reduced_HNF) == expected
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_colorings_small(kind, num_types, index_start, num_expected, method):
# Skip too time-consuming cases...
max_index = 7
structure = get_lattice(kind)
index_end = index_start + len(num_expected)
for index, expected in zip(range(index_start, index_end), num_expected):
if index > max_index:
continue
se = StructureEnumerator(
structure,
index,
num_types,
color_exchange=True,
remove_superperiodic=True,
method=method,
)
actual = se.generate()
assert len(actual) == expected
def test_enumerated_structures(kind, num_types, composition_constraints,
site_constraints):
structure = get_lattice(kind)
for index in range(1, 5):
# TODO: when remove_superperiodic = remove_incomplete = False, this test is failed.
zse = ZddStructureEnumerator(
structure,
index,
num_types,
composition_constraints=composition_constraints,
base_site_constraints=site_constraints,
remove_superperiodic=True,
remove_incomplete=True,
)
list_dstructs = zse.generate()
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_dstructs)
assert len(grouped) == len(list_dstructs)
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_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_permutations():
obj = {
"fcc": {
"structure": get_lattice("fcc"),
"num_type": 2,
"indices": range(1, 10 + 1)
},
"bcc": {
"structure": get_lattice("bcc"),
"indices": range(1, 10 + 1)
},
"sc": {
"structure": get_lattice("sc"),
"indices": range(1, 10 + 1)
},
"hex": {
"structure": get_lattice("hex"),
"indices": range(1, 10 + 1)
},
"tetragonal": {
"structure": get_lattice("tet"),
"indices": range(1, 10 + 1)
},
"hcp": {
"structure": get_lattice("hcp"),
"indices": range(1, 10 + 1)
},
}
for name, dct in obj.items():
structure = dct["structure"]
frac_coords = structure.frac_coords
for index in dct["indices"]:
list_reduced_HNF, rotations, translations = generate_symmetry_distinct_superlattices(
index, structure, return_symops=True)
for hnf in list_reduced_HNF:
dsperm = DerivativeStructurePermutation(
hnf, frac_coords, rotations, translations)
assert is_permutation_group(dsperm.prm_t)
prm_all = dsperm.get_symmetry_operation_permutations()
assert is_permutation_group(prm_all)
G = PermutationGroup(gens)
data = {
"index": index,
"hnf": hnf,
"generators": gens,
"group": G,
"order": G.order(),
"orbits": G.orbits(),
}
list_data.append(data)
df = pd.DataFrame(list_data)
sns.swarmplot(x="index", y="order", data=df)
plt.title(output_name)
plt.savefig(output_name + ".png")
return df
if __name__ == "__main__":
Permutation.print_cyclic = False
print("fcc")
base_structure = get_lattice("fcc")
df_fcc = plot_permutation_groups(base_structure, "fcc")
joblib.dump(df_fcc, "fcc.df.joblib")
print("fcc with tetragonal and octhedral sites")
base_structure = get_fcc_with_vacancy()
df_fcc_ot = plot_permutation_groups(base_structure, "fcc_oct_tet")
joblib.dump(df_fcc_ot, "fcc_oct_tet.df.joblib")
def test_reduce_HNF_list_by_parent_lattice_symmetry_fcc_bcc(kind):
# https://oeis.org/A045790
lst_num = [
1,
2,
3,
7,
5,
10,
7,
20,
14,
18,
11,
41,
15,
28,
31,
58,
21,
60,
25,
77,
49,
54,
33,
144,
50,
72,
75,
123,
49,
158,
55,
177,
97,
112,
99,
268,
75,
136,
129,
286,
89,
268,
97,
249,
218,
190,
113,
496,
146,
280,
]
structure = get_lattice(kind)
for index, expected in zip(range(1, len(lst_num) + 1), lst_num):
if index >= 20:
continue
list_reduced_HNF = generate_symmetry_distinct_superlattices(
index, structure)
assert len(list_reduced_HNF) == expected