def test_distances_mapped_atom_idx(ortho_conventional):
distances = Distances(ortho_conventional, center_coord=[0.0, 0.0, 0.49])
assert distances.atom_idx_at_center(specie="He") == 4
distances = Distances(ortho_conventional, center_coord=[0.251, 0.25, 0.25])
assert distances.atom_idx_at_center(specie="H") is None
distances = Distances(ortho_conventional, center_coord=[0.0, 0.0, 0.5])
assert distances.atom_idx_at_center(specie="Li") == None
def make_d_to_p(self):
result = []
for site in self._defect_structure:
distances = Distances(self._perfect_structure, site.frac_coords,
self.same_distance_criterion)
result.append(distances.atom_idx_at_center(specie=site.specie))
return result
def _atom_projection(self, structure_from, structure_to, specie=True):
result = []
for site in structure_from:
distances = Distances(structure_to, site.frac_coords,
self.dist_tol)
specie = site.specie if specie else None
result.append(distances.atom_idx_at_center(specie=specie))
return result
def make_p_to_d(self):
result = []
for site in self._perfect_structure:
distances = Distances(self._defective_structure, site.frac_coords)
result.append(distances.atom_idx_at_center(specie=site.specie))
return result