def test_converter(transformation, frac_coords):
converter = DerivativeMultiLatticeHash(transformation, frac_coords)
index = converter.index
num_sites = converter.num_sites
all_factors = converter.get_all_factors()
assert len({tuple(f) for f in all_factors}) == index
all_lattice_points = converter.get_lattice_points()
assert len({tuple(f) for f in all_lattice_points}) == index
all_periodic_sites = converter.get_canonical_sites_list()
assert len(set(all_periodic_sites)) == num_sites
all_dsites = converter.get_distinct_derivative_sites_list()
for dsite in all_dsites:
csite, derivative_jimage = converter.hash_derivative_site(dsite, return_image=True)
fcoords1 = converter.get_frac_coords(dsite)
fcoords2 = (
converter.displacement_set[dsite.site_index]
+ np.dot(converter.left_inv, csite.factor)
+ np.dot(converter.hnf, derivative_jimage)
)
assert np.allclose(fcoords1, fcoords2)
for csite in all_periodic_sites:
ind = converter.ravel_canonical_site(csite)
csite2 = converter.unravel_to_canonical_site(ind)
assert csite2 == csite
def test_converter():
list_transformations = [
np.diag((2, 2, 2)),
np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]]),
np.array([[-1, 1, 1], [1, -1, 1], [-1, -1, 1]]), # negative determinat
]
list_frac_coords = [
np.array([[0, 0, 0]]),
np.array([[0, 0, 0], [0.5, 0.5, 0.5]])
]
for transformation in list_transformations:
for frac_coords in list_frac_coords:
converter = DerivativeMultiLatticeHash(transformation, frac_coords)
index = converter.index
num_sites = converter.num_sites
all_factors = converter.get_all_factors()
assert len(set([tuple((f)) for f in all_factors])) == index
all_lattice_points = converter.get_lattice_points()
assert len(set([tuple(f) for f in all_lattice_points])) == index
all_periodic_sites = converter.get_canonical_sites_list()
assert len(set(all_periodic_sites)) == num_sites
all_dsites = converter.get_distinct_derivative_sites_list()
for dsite in all_dsites:
csite, derivative_jimage = converter.hash_derivative_site(
dsite, return_image=True)
fcoords1 = converter.get_frac_coords(dsite)
fcoords2 = (converter.displacement_set[dsite.site_index] +
np.dot(converter.left_inv, csite.factor) +
np.dot(converter.hnf, derivative_jimage))
assert np.allclose(fcoords1, fcoords2)
for csite in all_periodic_sites:
ind = converter.ravel_canonical_site(csite)
csite2 = converter.unravel_to_canonical_site(ind)
assert csite2 == csite
def __init__(
self,
base_structure: Structure,
dshash: DerivativeMultiLatticeHash,
mapping_color_to_species: List[Union[str, Element, Specie,
DummySpecie]],
additional_species=None,
additional_frac_coords=None,
):
"""
Parameters
----------
base_structure:
Structure with only ordering species
dshash:
mapping_color_to_species:
additional_species: list of pymatgen.core.Species, optional
species which are nothing to do with ordering
additional_frac_coords: np.ndarray, optional
fractional coordinates of species which are nothing to do with ordering
"""
self.base_structure = base_structure
self.dshash = dshash
self.mapping_color_to_species = mapping_color_to_species
self.lattice_matrix = np.dot(self.base_matrix.T, self.dshash.hnf).T
# lattice of derivative structure
self.lattice = Lattice(self.lattice_matrix)
self.canonical_derivative_sites = dshash.get_canonical_and_derivative_sites_list(
)
list_coords = []
for _, dsite in self.canonical_derivative_sites:
coords = dshash.get_frac_coords(dsite)
cart_coords = np.dot(coords, self.base_matrix)
list_coords.append(cart_coords)
self.list_coords = list_coords
self.precomputed_psites = [[
PeriodicSite(sp, coords, self.lattice, coords_are_cartesian=True)
for sp in self.mapping_color_to_species
] for coords in self.list_coords]
# additional fixed sites
self.additional_species = additional_species
self.additional_frac_coords = additional_frac_coords
if self.additional_species is not None:
assert len(self.additional_species) == len(
self.additional_frac_coords)
self.additional_psites = []
if self.additional_species is not None:
lattice_points = self.dshash.get_lattice_points()
for sp, disp in zip(self.additional_species,
self.additional_frac_coords):
cart_coords = [
np.dot(np.array(disp) + np.array(lp), self.base_matrix)
for lp in lattice_points
]
self.additional_psites.extend([
PeriodicSite(sp,
coords,
self.lattice,
coords_are_cartesian=True)
for coords in cart_coords
])