def generate_symmetry_distinct_superlattices(
index: int, structure: Structure, return_symops=False
):
"""
generate symmetry distict HNF
Parameters
----------
index: positive integer
structure: pymatgen.core.Structure
return_symops: bool
Returns
-------
list_reduced_HNF: list of matrices, unique by symmetry
(Optional) rotations: array, (# of symmetry operations, 3, 3)
(Optional) translations: array, (# of symmetry operations, 3)
"""
rotations, translations = get_symmetry_operations(structure)
list_HNF = generate_all_superlattices(index)
list_reduced_HNF = reduce_HNF_list_by_parent_lattice_symmetry(list_HNF, rotations)
if return_symops:
return list_reduced_HNF, rotations, translations
else:
return list_reduced_HNF
def plot_permutation_groups(base_structure, output_name):
rotations, translations = get_symmetry_operations(base_structure)
displacement_set = base_structure.frac_coords
list_data = []
for index in range(2, 10 + 1):
for hnf in tqdm(generate_all_superlattices(index)):
dsperm = DerivativeStructurePermutation(hnf, displacement_set,
rotations, translations)
perms = [
Permutation(g)
for g in dsperm.get_symmetry_operation_permutations()
]
gens = get_generators(perms)
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
def remove_symmetry_duplicates_from_generator(
base_structure,
hnf,
num_type,
list_colorings,
color_exchange: bool,
leave_superperiodic: bool,
use_all_colors: bool,
method="direct",
n_jobs=1,
):
displacement_set = base_structure.frac_coords
rotations, translations = get_symmetry_operations(base_structure)
cl_generator = ListBasedColoringGenerator(num_type, list_colorings)
ds_permutation = DerivativeStructurePermutation(hnf, displacement_set,
rotations, translations)
sc_enum = SiteColoringEnumerator(
num_type,
ds_permutation,
cl_generator,
color_exchange,
leave_superperiodic,
use_all_colors,
method=method,
n_jobs=n_jobs,
)
colorings = sc_enum.unique_colorings()
return colorings
def from_structure(cls,
structure: Structure,
transformation: np.ndarray,
symprec: float = 1e-2):
"""
create EquivalentPointClusterGenerator from pymatgen.core.Structure
Parameters
----------
structure: pymatgen.core.Structure, base structure
transformation: transformation matrix of sublattice
symprec: float
"""
frac_coords = structure.frac_coords
rotations, translations = get_symmetry_operations(structure, symprec)
converter = DerivativeMultiLatticeHash(transformation, frac_coords)
return cls(
frac_coords=frac_coords,
rotations=rotations,
translations=translations,
converter=converter,
)