def get_inequivalent_sites(sub_lattice, lattice): """Given a sub lattice, returns symmetry unique sites for substitutions. Args: sub_lattice (list of lists): array containing Cartesian coordinates of the sub-lattice of interest lattice (ASE crystal): the total lattice Returns: List of sites """ sg = get_sg(lattice) inequivalent_sites = [] for site in sub_lattice: new_site = True # Check against the existing members of the list of inequivalent sites if len(inequivalent_sites) > 0: for inequiv_site in inequivalent_sites: if smact.are_eq(site, inequiv_site) == True: new_site = False # Check against symmetry related members of the list of inequivalent sites equiv_inequiv_sites, _ = sg.equivalent_sites(inequiv_site) for equiv_inequiv_site in equiv_inequiv_sites: if smact.are_eq(site, equiv_inequiv_site) == True: new_site = False if new_site == True: inequivalent_sites.append(site) return inequivalent_sites
def test_are_eq(self): self.assertTrue( smact.are_eq([1.00, 2.00, 3.00], [1.001, 1.999, 3.00], tolerance=1e-2)) self.assertFalse( smact.are_eq([1.00, 2.00, 3.00], [1.001, 1.999, 3.00]))
def make_substitution(lattice,site,new_species): """Change atomic species on lattice site to new_species. Args: lattice (ASE crystal): Input lattice site (list): Cartesian coordinates of the substitution site new_species (str): New species Returns: lattice """ i = 0 # NBNBNBNB It is necessary to use deepcopy for objects, otherwise changes applied to a clone # will also apply to the parent object. new_lattice = copy.deepcopy(lattice) lattice_sites = new_lattice.get_scaled_positions() for lattice_site in lattice_sites: if smact.are_eq(lattice_site, site): new_lattice[i].symbol = new_species i = i + 1 return new_lattice