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