def apply_transformation(self, structure): editor = StructureEditor(structure) for i, sp in enumerate(self._species): editor.insert_site(i, sp, self._coords[i], coords_are_cartesian=self._cartesian, validate_proximity=self._validate_proximity) return editor.modified_structure.get_sorted_structure()
def _get_host(structure, species_to_remove): if species_to_remove: editor = StructureEditor(structure) editor.remove_species(species_to_remove) return editor.modified_structure else: return structure
def complete_ordering(self, structure, num_remove_dict): self.logger.debug("Performing complete ordering...") all_structures = [] from pymatgen.symmetry.finder import SymmetryFinder symprec = 0.2 s = SymmetryFinder(structure, symprec=symprec) self.logger.debug("Symmetry of structure is determined to be {}." .format(s.get_spacegroup_symbol())) sg = s.get_spacegroup() tested_sites = [] starttime = time.time() self.logger.debug("Performing initial ewald sum...") ewaldsum = EwaldSummation(structure) self.logger.debug("Ewald sum took {} seconds." .format(time.time() - starttime)) starttime = time.time() allcombis = [] for ind, num in num_remove_dict.items(): allcombis.append(itertools.combinations(ind, num)) count = 0 for allindices in itertools.product(*allcombis): sites_to_remove = [] indices_list = [] for indices in allindices: sites_to_remove.extend([structure[i] for i in indices]) indices_list.extend(indices) mod = StructureEditor(structure) mod.delete_sites(indices_list) s_new = mod.modified_structure energy = ewaldsum.compute_partial_energy(indices_list) already_tested = False for i, tsites in enumerate(tested_sites): tenergy = all_structures[i]["energy"] if abs((energy - tenergy) / len(s_new)) < 1e-5 and \ sg.are_symmetrically_equivalent(sites_to_remove, tsites, symm_prec=symprec): already_tested = True if not already_tested: tested_sites.append(sites_to_remove) all_structures.append({"structure": s_new, "energy": energy}) count += 1 if count % 10 == 0: timenow = time.time() self.logger.debug("{} structures, {:.2f} seconds." .format(count, timenow - starttime)) self.logger.debug("Average time per combi = {} seconds" .format((timenow - starttime) / count)) self.logger.debug("{} symmetrically distinct structures found." .format(len(all_structures))) self.logger.debug("Total symmetrically distinct structures found = {}" .format(len(all_structures))) all_structures = sorted(all_structures, key=lambda s: s["energy"]) return all_structures
def apply_transformation(self, structure): species_map = {} for k, v in self._species_map.items(): if isinstance(v, dict): value = {smart_element_or_specie(x): y for x, y in v.items()} else: value = smart_element_or_specie(v) species_map[smart_element_or_specie(k)] = value editor = StructureEditor(structure) editor.replace_species(species_map) return editor.modified_structure
def test_add_site_property(self): self.modifier.add_site_property("charge", [4.1, 5]) s = self.modifier.modified_structure self.assertEqual(s[0].charge, 4.1) self.assertEqual(s[1].charge, 5) #test adding multiple properties. mod2 = StructureEditor(s) mod2.add_site_property("magmom", [3, 2]) s = mod2.modified_structure self.assertEqual(s[0].charge, 4.1) self.assertEqual(s[0].magmom, 3)
def setUp(self): p = Poscar.from_file(os.path.join(test_dir, 'POSCAR')) self.structure = p.struct self.sg = SymmetryFinder(self.structure, 0.001) parser = CifParser(os.path.join(test_dir, 'Li10GeP2S12.cif')) self.disordered_structure = parser.get_structures()[0] self.disordered_sg = SymmetryFinder(self.disordered_structure, 0.001) s = p.struct editor = StructureEditor(p.struct) site = s[0] editor.delete_site(0) editor.append_site(site.species_and_occu, site.frac_coords) self.sg3 = SymmetryFinder(editor.modified_structure, 0.001)
def fast_ordering(self, structure, num_remove_dict, num_to_return=1): """ This method uses the matrix form of ewaldsum to calculate the ewald sums of the potential structures. This is on the order of 4 orders of magnitude faster when there are large numbers of permutations to consider. There are further optimizations possible (doing a smarter search of permutations for example), but this wont make a difference until the number of permutations is on the order of 30,000. """ self.logger.debug("Performing fast ordering") starttime = time.time() self.logger.debug("Performing initial ewald sum...") ewaldmatrix = EwaldSummation(structure).total_energy_matrix self.logger.debug("Ewald sum took {} seconds." .format(time.time() - starttime)) starttime = time.time() m_list = [] for indices, num in num_remove_dict.items(): m_list.append([0, num, list(indices), None]) self.logger.debug("Calling EwaldMinimizer...") minimizer = EwaldMinimizer(ewaldmatrix, m_list, num_to_return, PartialRemoveSitesTransformation.ALGO_FAST) self.logger.debug("Minimizing Ewald took {} seconds." .format(time.time() - starttime)) all_structures = [] lowest_energy = minimizer.output_lists[0][0] num_atoms = sum(structure.composition.values()) for output in minimizer.output_lists: se = StructureEditor(structure) del_indices = [] for manipulation in output[1]: if manipulation[1] is None: del_indices.append(manipulation[0]) else: se.replace_site(manipulation[0], manipulation[1]) se.delete_sites(del_indices) struct = se.modified_structure.get_sorted_structure() all_structures.append({"energy": output[0], "energy_above_minimum": (output[0] - lowest_energy) / num_atoms, "structure": struct}) return all_structures
def test_init(self): fitter = StructureFitter(self.b, self.a) self.assertTrue(fitter.mapping_op != None, "No fit found!") #Now to try with rotated structure op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False, np.array([0, 0, 1])) editor = StructureEditor(self.a) editor.apply_operation(op) fitter = StructureFitter(self.b, editor.modified_structure) self.assertTrue(fitter.mapping_op != None, "No fit found!") #test with a supercell mod = SupercellMaker(self.a, scaling_matrix=[[2, 0, 0], [0, 1, 0], [0, 0, 1]]) a_super = mod.modified_structure fitter = StructureFitter(self.b, a_super) self.assertTrue(fitter.mapping_op != None, "No fit found!") # Test with a structure with a translated point editor = StructureEditor(self.a) site = self.a[0] editor.delete_site(0) trans = np.random.randint(0, 1000, 3) editor.insert_site(0, site.species_and_occu, site.frac_coords + trans, False, False) fitter = StructureFitter(self.b, editor.modified_structure) self.assertTrue(fitter.mapping_op != None, "No fit found for translation {}!".format(trans)) parser = CifParser(os.path.join(test_dir, "FePO4a.cif")) a = parser.get_structures()[0] parser = CifParser(os.path.join(test_dir, "FePO4b.cif")) b = parser.get_structures()[0] fitter = StructureFitter(b, a) self.assertTrue(fitter.mapping_op != None, "No fit found!")
def enumerate_ordering(self, structure): # Generate the disordered structure first. editor = StructureEditor(structure) for indices, fraction in zip(self._indices, self._fractions): for ind in indices: new_sp = {sp: occu * fraction for sp, occu in structure[ind].species_and_occu.items()} editor.replace_site(ind, new_sp) mod_s = editor.modified_structure # Perform enumeration from pymatgen.transformations.advanced_transformations import \ EnumerateStructureTransformation trans = EnumerateStructureTransformation() return trans.apply_transformation(mod_s, 10000)
def test_remove_oxidation_states(self): co_elem = Element("Co") o_elem = Element("O") co_specie = Specie("Co", 2) o_specie = Specie("O", -2) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice.cubic(10) s_elem = Structure(lattice, [co_elem, o_elem], coords) s_specie = Structure(lattice, [co_specie, o_specie], coords) mod = StructureEditor(s_specie) mod.remove_oxidation_states() mod_s = mod.modified_structure self.assertEqual(s_elem, mod_s, "Oxidation state remover failed")
def test_fit(self): """ Take two known matched structures 1) Ensure match 2) Ensure match after translation and rotations 3) Ensure no-match after large site translation 4) Ensure match after site shuffling """ sm = StructureMatcher() self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1])) # Test rotational/translational invariance op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False, np.array([0.4, 0.7, 0.9])) editor = StructureEditor(self.struct_list[1]) editor.apply_operation(op) self.assertTrue(sm.fit(self.struct_list[0], editor.modified_structure)) #Test failure under large atomic translation editor.translate_sites([0], [.4, .4, .2], frac_coords=True) self.assertFalse(sm.fit(self.struct_list[0], editor.modified_structure)) editor.translate_sites([0], [-.4, -.4, -.2], frac_coords=True) # random.shuffle(editor._sites) self.assertTrue(sm.fit(self.struct_list[0], editor.modified_structure)) #Test FrameworkComporator sm2 = StructureMatcher(comparator=FrameworkComparator()) lfp = read_structure(os.path.join(test_dir, "LiFePO4.cif")) nfp = read_structure(os.path.join(test_dir, "NaFePO4.cif")) self.assertTrue(sm2.fit(lfp, nfp)) self.assertFalse(sm.fit(lfp, nfp)) #Test anonymous fit. self.assertEqual(sm.fit_anonymous(lfp, nfp), {Composition("Li"): Composition("Na")}) self.assertAlmostEqual(sm.get_minimax_rms_anonymous(lfp, nfp)[0], 0.096084154118549828) #Test partial occupancies. s1 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]], [{"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]]) s2 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]], [{"Fe": 0.25}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.75}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]]) self.assertFalse(sm.fit(s1, s2)) self.assertFalse(sm.fit(s2, s1)) s2 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]], [{"Fe": 0.25}, {"Fe": 0.25}, {"Fe": 0.25}, {"Fe": 0.25}], [[0, 0, 0], [0.25, 0.25, 0.25], [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]]) self.assertEqual(sm.fit_anonymous(s1, s2), {Composition("Fe0.5"): Composition("Fe0.25")}) self.assertAlmostEqual(sm.get_minimax_rms_anonymous(s1, s2)[0], 0)
def get_oxi_state_decorated_structure(self, structure): """ Get an oxidation state decorated structure. This currently works only for ordered structures only. Args: structure: Structure to analyze Returns: A modified structure that is oxidation state decorated. Raises: A ValueError is the valences cannot be determined. """ valences = self.get_valences(structure) editor = StructureEditor(structure) editor.add_oxidation_state_by_site(valences) return editor.modified_structure
def setUp(self): self.si = Element("Si") self.fe = Element("Fe") self.ge = Element("Ge") coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) lattice = Lattice.cubic(10) s = Structure(lattice, ["Si", "Fe"], coords) self.modifier = StructureEditor(s)
def best_first_ordering(self, structure, num_remove_dict): self.logger.debug("Performing best first ordering") starttime = time.time() self.logger.debug("Performing initial ewald sum...") ewaldsum = EwaldSummation(structure) self.logger.debug("Ewald sum took {} seconds." .format(time.time() - starttime)) starttime = time.time() ematrix = ewaldsum.total_energy_matrix to_delete = [] totalremovals = sum(num_remove_dict.values()) removed = {k: 0 for k in num_remove_dict.keys()} for i in xrange(totalremovals): maxindex = None maxe = float("-inf") maxindices = None for indices in num_remove_dict.keys(): if removed[indices] < num_remove_dict[indices]: for ind in indices: if ind not in to_delete: energy = sum(ematrix[:, ind]) + \ sum(ematrix[:, ind]) - ematrix[ind, ind] if energy > maxe: maxindex = ind maxe = energy maxindices = indices removed[maxindices] += 1 to_delete.append(maxindex) ematrix[:, maxindex] = 0 ematrix[maxindex, :] = 0 mod = StructureEditor(structure) mod.delete_sites(to_delete) self.logger.debug("Minimizing Ewald took {} seconds." .format(time.time() - starttime)) return [{"energy": sum(sum(ematrix)), "structure": mod.modified_structure.get_sorted_structure()}]
def test_add_oxidation_states(self): si = Element("Si") fe = Element("Fe") coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice.cubic(10) s = Structure(lattice, [si, fe], coords) oxidation_states = {"Fe": 2, "Si": -4} mod = StructureEditor(s) mod.add_oxidation_state_by_element(oxidation_states) mod_s = mod.modified_structure for site in mod_s: for k in site.species_and_occu.keys(): self.assertEqual(k.oxi_state, oxidation_states[k.symbol], "Wrong oxidation state assigned!") oxidation_states = {"Fe": 2} self.assertRaises(ValueError, mod.add_oxidation_state_by_element, oxidation_states) mod.add_oxidation_state_by_site([2, -4]) mod_s = mod.modified_structure self.assertEqual(mod_s[0].specie.oxi_state, 2) self.assertRaises(ValueError, mod.add_oxidation_state_by_site, [1])
def test_init(self): filepath = os.path.join(test_dir, 'POSCAR') p = Poscar.from_file(filepath) original_s = p.structure modifier = StructureEditor(original_s) modifier.add_oxidation_state_by_element({"Li": 1, "Fe": 2, "P": 5, "O":-2}) s = modifier.modified_structure ham = EwaldSummation(s) self.assertAlmostEqual(ham.real_space_energy, -354.91294268, 4, "Real space energy incorrect!") self.assertAlmostEqual(ham.reciprocal_space_energy, 25.475754801, 4) self.assertAlmostEqual(ham.point_energy, -790.463835033, 4, "Point space energy incorrect!") self.assertAlmostEqual(ham.total_energy, -1119.90102291, 2, "Total space energy incorrect!") self.assertAlmostEqual(ham.forces[0,0], -1.98818620e-01, 4, "Forces incorrect") self.assertAlmostEqual(sum(sum(abs(ham.forces))), 915.925354346, 4, "Forces incorrect") self.assertAlmostEqual(sum(sum(ham.real_space_energy_matrix)), - 354.91294268, 4, "Real space energy matrix incorrect!") self.assertAlmostEqual(sum(sum(ham.reciprocal_space_energy_matrix)), 25.475754801, 4, "Reciprocal space energy matrix incorrect!") self.assertAlmostEqual(sum(ham.point_energy_matrix), -790.463835033, 4, "Point space energy matrix incorrect!") self.assertAlmostEqual(sum(sum(ham.total_energy_matrix)), - 1119.90102291, 2, "Total space energy matrix incorrect!") #note that forces are not individually tested, but should work fine. self.assertRaises(ValueError, EwaldSummation, original_s) #try sites with charge. charges = [] for site in original_s: if site.specie.symbol == "Li": charges.append(1) elif site.specie.symbol == "Fe": charges.append(2) elif site.specie.symbol == "P": charges.append(5) else: charges.append(-2) editor = StructureEditor(original_s) editor.add_site_property('charge', charges) ham2 = EwaldSummation(editor.modified_structure) self.assertAlmostEqual(ham2.real_space_energy, -354.91294268, 4, "Real space energy incorrect!")
def __init__( self, structure_a, structure_b, tolerance_cell_misfit=0.1, tolerance_atomic_misfit=1.0, supercells_allowed=True, anonymized=False, fitting_accuracy=FAST_FIT, use_symmetry=False, ): """ Fits two structures. All fitting parameters have been set with defaults that should work in most cases. To use, initialize the structure fitter with parameters. E.g., fitter = StructureFitter(a, b) print fitter.fit_found Args: structure_a : First structure structure_b : Second structure to try to match with first structure tolerance_cell_misfit : Tolerance for cell misfit. Default = 0.1 tolerance_atomic_misfit : Tolerance for atomic misfit. Default = 1.0. supercells_allowed : Whether supercell structures are allowed. Default = True. anonymized : Whether to attempt matching of different species. Setting this to true will allow any two structures with the same framework, but different species to match to each other. Default = False. fitting_accuracy : An integer setting for the fitting accuracy. Corresponds to the max number of candidate rotations considered. Use the static variables, StructureFitter.FAST_FIT StructureFitter.NORMAL_FIT StructureFitter.ACCURATE_FIT to set the tradeoff between accuracy and speed. The default, FAST_FIT, should work reasonably well in most instances. use_symmetry: Whether to use pymatgen.spacegroup to determine the spacegroup first. Eliminates most non-fits. Defaults to True. """ self._tolerance_cell_misfit = tolerance_cell_misfit self._tolerance_atomic_misfit = tolerance_atomic_misfit self._supercells_allowed = supercells_allowed self._anonymized = anonymized self._max_rotations = fitting_accuracy # Sort structures first so that they have the same arrangement of species self._structure_a = structure_a.get_sorted_structure() self._structure_b = structure_b.get_sorted_structure() if use_symmetry: from pymatgen.symmetry.spglib_adaptor import SymmetryFinder finder_a = SymmetryFinder(self._structure_a, symprec=0.1) finder_b = SymmetryFinder(self._structure_b, symprec=0.1) same_sg = finder_a.get_spacegroup_number() == finder_b.get_spacegroup_number() if not use_symmetry or same_sg: self._mapping_op = None if not self._anonymized: self.fit(self._structure_a, self._structure_b) if self.fit_found: self.el_mapping = {el: el for el in self._structure_a.composition.elements} else: comp_a = structure_a.composition comp_b = structure_b.composition if len(comp_a.elements) == len(comp_b.elements): el_a = comp_a.elements # Create permutations of the specie/elements in structure A for p in itertools.permutations(el_a): # Create mapping of the specie/elements in structure B to that of A. # Then create a modified structure with those elements and try to fit it. el_mapping = dict(zip(comp_b.elements, p)) logger.debug("Using specie mapping " + str(el_mapping)) mod = StructureEditor(self._structure_b) mod.replace_species(el_mapping) self.fit(self._structure_a, mod.modified_structure) if self._mapping_op != None: # Store successful element mapping self.el_mapping = {el_a: el_b for el_b, el_a in el_mapping.items()} break else: logger.debug("No. of elements in structures are unequal.") else: self._mapping_op = None logger.debug("Symmetry is different.")
class StructureEditorTest(unittest.TestCase): def setUp(self): self.si = Element("Si") self.fe = Element("Fe") self.ge = Element("Ge") coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) lattice = Lattice.cubic(10) s = Structure(lattice, [self.si, self.fe], coords) self.modifier = StructureEditor(s) def test_translate_sites(self): self.modifier.translate_sites([0, 1], [0.5, 0.5, 0.5], frac_coords=True) self.assertTrue(np.array_equal(self.modifier.modified_structure.frac_coords[0], np.array([ 0.5, 0.5, 0.5]))) self.modifier.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=False) self.assertTrue(np.array_equal(self.modifier.modified_structure.cart_coords[0], np.array([ 5.5, 5.5, 5.5]))) def test_append_site(self): self.modifier.append_site(self.si, [0, 0.5, 0]) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2", "Wrong formula!") self.assertRaises(ValueError, self.modifier.append_site, self.si, np.array([0, 0.5, 0])) def test_modified_structure(self): self.modifier.insert_site(1, self.si, [0, 0.25, 0]) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2", "Wrong formula!") self.modifier.delete_site(0) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1", "Wrong formula!") self.modifier.replace_site(0, self.ge) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge1", "Wrong formula!") self.modifier.append_site(self.si, [0, 0.75, 0]) self.modifier.replace_species({self.si: self.ge}) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge2", "Wrong formula!") self.modifier.replace_species({self.ge: {self.ge:0.5, self.si:0.5}}) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1 Ge1", "Wrong formula!") #this should change the .5Si .5Ge sites to .75Si .25Ge self.modifier.replace_species({self.ge: {self.ge:0.5, self.si:0.5}}) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1.5 Ge0.5", "Wrong formula!") d = 0.1 pre_perturbation_sites = self.modifier.modified_structure.sites self.modifier.perturb_structure(distance=d) post_perturbation_sites = self.modifier.modified_structure.sites for i, x in enumerate(pre_perturbation_sites): self.assertAlmostEqual(x.distance(post_perturbation_sites[i]), d, 3, "Bad perturbation distance") def test_add_site_property(self): self.modifier.add_site_property("charge", [4.1, 5]) s = self.modifier.modified_structure self.assertEqual(s[0].charge, 4.1) self.assertEqual(s[1].charge, 5) #test adding multiple properties. mod2 = StructureEditor(s) mod2.add_site_property("magmom", [3, 2]) s = mod2.modified_structure self.assertEqual(s[0].charge, 4.1) self.assertEqual(s[0].magmom, 3)
def apply_transformation(self, structure): editor = StructureEditor(structure) editor.delete_sites(self._indices) return editor.modified_structure
class StructureEditorTest(unittest.TestCase): def setUp(self): self.si = Element("Si") self.fe = Element("Fe") self.ge = Element("Ge") coords = list() coords.append(np.array([0, 0, 0])) coords.append(np.array([0.75, 0.5, 0.75])) lattice = Lattice.cubic(10) s = Structure(lattice, ["Si", "Fe"], coords) self.modifier = StructureEditor(s) def test_to_unit_cell(self): self.modifier.append_site(self.fe, [1.75, 0.5, 0.75], validate_proximity=False) self.modifier.to_unit_cell() self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1", "Wrong formula!") def test_to_unit_cell(self): self.modifier.apply_strain(0.01) self.assertEqual(self.modifier.modified_structure.lattice.abc, (10.1, 10.1, 10.1)) def test_translate_sites(self): self.modifier.translate_sites([0, 1], [0.5, 0.5, 0.5], frac_coords=True) self.assertTrue(np.array_equal(self.modifier.modified_structure .frac_coords[0], np.array([0.5, 0.5, 0.5]))) self.modifier.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=False) self.assertTrue(np.array_equal(self.modifier.modified_structure .cart_coords[0], np.array([5.5, 5.5, 5.5]))) def test_append_site(self): self.modifier.append_site(self.si, [0, 0.5, 0]) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2", "Wrong formula!") self.assertRaises(ValueError, self.modifier.append_site, self.si, np.array([0, 0.5, 0])) def test_modified_structure(self): self.modifier.insert_site(1, self.si, [0, 0.25, 0]) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si2", "Wrong formula!") self.modifier.delete_site(0) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1", "Wrong formula!") self.modifier.replace_site(0, self.ge) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge1", "Wrong formula!") self.modifier.append_site(self.si, [0, 0.75, 0]) self.modifier.replace_species({self.si: self.ge}) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Ge2", "Wrong formula!") self.modifier.replace_species({self.ge: {self.ge: 0.5, self.si: 0.5}}) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1 Ge1", "Wrong formula!") #this should change the .5Si .5Ge sites to .75Si .25Ge self.modifier.replace_species({self.ge: {self.ge: 0.5, self.si: 0.5}}) self.assertEqual(self.modifier.modified_structure.formula, "Fe1 Si1.5 Ge0.5", "Wrong formula!") d = 0.1 pre_perturbation_sites = self.modifier.modified_structure.sites self.modifier.perturb_structure(distance=d) post_perturbation_sites = self.modifier.modified_structure.sites for i, x in enumerate(pre_perturbation_sites): self.assertAlmostEqual(x.distance(post_perturbation_sites[i]), d, 3, "Bad perturbation distance") def test_add_site_property(self): self.modifier.add_site_property("charge", [4.1, 5]) s = self.modifier.modified_structure self.assertEqual(s[0].charge, 4.1) self.assertEqual(s[1].charge, 5) #test adding multiple properties. mod2 = StructureEditor(s) mod2.add_site_property("magmom", [3, 2]) s = mod2.modified_structure self.assertEqual(s[0].charge, 4.1) self.assertEqual(s[0].magmom, 3) def test_add_oxidation_states(self): si = Element("Si") fe = Element("Fe") coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice.cubic(10) s = Structure(lattice, [si, fe], coords) oxidation_states = {"Fe": 2, "Si": -4} mod = StructureEditor(s) mod.add_oxidation_state_by_element(oxidation_states) mod_s = mod.modified_structure for site in mod_s: for k in site.species_and_occu.keys(): self.assertEqual(k.oxi_state, oxidation_states[k.symbol], "Wrong oxidation state assigned!") oxidation_states = {"Fe": 2} self.assertRaises(ValueError, mod.add_oxidation_state_by_element, oxidation_states) mod.add_oxidation_state_by_site([2, -4]) mod_s = mod.modified_structure self.assertEqual(mod_s[0].specie.oxi_state, 2) self.assertRaises(ValueError, mod.add_oxidation_state_by_site, [1]) def test_remove_oxidation_states(self): co_elem = Element("Co") o_elem = Element("O") co_specie = Specie("Co", 2) o_specie = Specie("O", -2) coords = list() coords.append([0, 0, 0]) coords.append([0.75, 0.5, 0.75]) lattice = Lattice.cubic(10) s_elem = Structure(lattice, [co_elem, o_elem], coords) s_specie = Structure(lattice, [co_specie, o_specie], coords) mod = StructureEditor(s_specie) mod.remove_oxidation_states() mod_s = mod.modified_structure self.assertEqual(s_elem, mod_s, "Oxidation state remover failed")
def apply_transformation(self, structure): editor = StructureEditor(structure) for i, sp in self._indices_species_map.items(): editor.replace_site(int(i), sp) return editor.modified_structure
def apply_transformation(self, structure): editor = StructureEditor(structure) editor.apply_operation(self._symmop) return editor.modified_structure
def apply_transformation(self, structure): editor = StructureEditor(structure) editor.perturb_structure(self._amp) return editor.modified_structure
def _calc_rms(self, struct1, struct2, break_on_match): """ Calculate RMS displacement between two structures Args: struct1: 1st structure struct2: 2nd structure break_on_match: True or False. Will break if the maximum distance found is less than the provided stol Returns: rms displacement normalized by (Vol / nsites) ** (1/3) and maximum distance found between two paired sites """ stol = self.stol comparator = self._comparator #initial stored rms stored_rms = None if comparator.get_structure_hash(struct1) != \ comparator.get_structure_hash(struct2): return None #primitive cell transformation if self._primitive_cell and struct1.num_sites != struct2.num_sites: struct1 = struct1.get_primitive_structure() struct2 = struct2.get_primitive_structure() # Same number of sites if struct1.num_sites != struct2.num_sites: return None # Get niggli reduced cells. Though technically not necessary, this # minimizes cell lengths and speeds up the matching of skewed # cells considerably. struct1 = struct1.get_reduced_structure(reduction_algo="niggli") struct2 = struct2.get_reduced_structure(reduction_algo="niggli") nl1 = struct1.lattice nl2 = struct2.lattice #rescale lattice to same volume if self._scale: scale_vol = (nl2.volume / nl1.volume) ** (1 / 6) se1 = StructureEditor(struct1) nl1 = Lattice(nl1.matrix * scale_vol) se1.modify_lattice(nl1) struct1 = se1.modified_structure se2 = StructureEditor(struct2) nl2 = Lattice(nl2.matrix / scale_vol) se2.modify_lattice(nl2) struct2 = se2.modified_structure #Volume to determine invalid lattices vol_tol = nl2.volume / 2 #fractional tolerance of atomic positions (2x for initial fitting) frac_tol = \ np.array([stol / ((1 - self.ltol) * np.pi) * i for i in struct1.lattice.reciprocal_lattice.abc]) * \ ((nl1.volume + nl2.volume) / (2 * struct1.num_sites)) ** (1.0 / 3) #generate structure coordinate lists species_list = [] s1 = [] for site in struct1: found = False for i, species in enumerate(species_list): if comparator.are_equal(site.species_and_occu, species): found = True s1[i].append(site.frac_coords) break if not found: s1.append([site.frac_coords]) species_list.append(site.species_and_occu) zipped = sorted(zip(s1, species_list), key=lambda x: len(x[0])) s1 = [x[0] for x in zipped] species_list = [x[1] for x in zipped] s2_cart = [[] for i in s1] for site in struct2: found = False for i, species in enumerate(species_list): if comparator.are_equal(site.species_and_occu, species): found = True s2_cart[i].append(site.coords) break #if no site match found return None if not found: return None #check that sizes of the site groups are identical for f1, c2 in zip(s1, s2_cart): if len(f1) != len(c2): return None #translate s1 s1_translation = s1[0][0] for i in range(len(species_list)): s1[i] = np.mod(s1[i] - s1_translation, 1) #do permutations of vectors, check for equality for nl in self._get_lattices(struct1, struct2, vol_tol): s2 = [nl.get_fractional_coords(c) for c in s2_cart] for coord in s2[0]: t_s2 = [np.mod(coords - coord, 1) for coords in s2] if self._cmp_fractional_struct(s1, t_s2, frac_tol): rms, max_dist = self._cmp_cartesian_struct(s1, t_s2, nl, nl1) if break_on_match and max_dist < stol: return max_dist elif stored_rms is None or rms < stored_rms[0]: stored_rms = rms, max_dist if break_on_match: return None else: return stored_rms
def apply_transformation(self, structure): editor = StructureEditor(structure) editor.remove_oxidation_states() return editor.modified_structure
def apply_transformation(self, structure): editor = StructureEditor(structure) editor.add_oxidation_state_by_element(self.oxi_states) return editor.modified_structure
def apply_operation(structure, symmop): editor = StructureEditor(structure) editor.apply_operation(symmop) return editor.modified_structure
def apply_transformation(self, structure, return_ranked_list=False): """ For this transformation, the apply_transformation method will return only the ordered structure with the lowest Ewald energy, to be consistent with the method signature of the other transformations. However, all structures are stored in the all_structures attribute in the transformation object for easy access. Args: structure: Oxidation state decorated disordered structure to order return_ranked_list: Boolean stating whether or not multiple structures are returned. If return_ranked_list is a number, that number of structures is returned. Returns: Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {'structure' = .... , 'other_arguments'} the key 'transformation' is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class. """ ordered_sites = [] sites_to_order = {} try: num_to_return = int(return_ranked_list) except: num_to_return = 1 num_to_return = max(1, num_to_return) sites = list(structure.sites) for i in range(len(structure)): site = sites[i] if sum(site.species_and_occu.values()) == 1 and len(site.species_and_occu) == 1: ordered_sites.append(site) else: species = tuple([sp for sp, occu in site.species_and_occu.items()]) #group the sites by the list of species on that site for sp, occu in site.species_and_occu.items(): if species not in sites_to_order: sites_to_order[species] = {} if sp not in sites_to_order[species]: sites_to_order[species][sp] = [[occu, i]] else: sites_to_order[species][sp].append([occu, i]) total_occu = sum(site.species_and_occu.values()) #if the total occupancy on a site is less than one, add #a list with None as the species (for removal) if total_occu < 1: if None not in sites_to_order[species]: sites_to_order[species][None] = [[1 - total_occu, i]] else: sites_to_order[species][None].append([1 - total_occu, i]) """ Create a list of [multiplication fraction, number of replacements, [indices], replacement species] """ m_list = [] se = StructureEditor(structure) for species in sites_to_order.values(): initial_sp = None sorted_keys = sorted(species.keys(), key=lambda x: x is not None and -abs(x.oxi_state) or 1000) for sp in sorted_keys: if initial_sp is None: initial_sp = sp for site in species[sp]: se.replace_site(site[1], initial_sp) else: if sp is None: oxi = 0 else: oxi = float(sp.oxi_state) manipulation = [oxi / initial_sp.oxi_state, 0, [], sp] site_list = species[sp] site_list.sort(key=itemgetter(0)) prev_fraction = site_list[0][0] for site in site_list: if site[0] - prev_fraction > .1: """ tolerance for creating a new group of sites. if site occupancies are similar, they will be put in a group where the fraction has to be consistent over the whole. """ manipulation[1] = int(round(manipulation[1])) m_list.append(manipulation) manipulation = [oxi / initial_sp.oxi_state, 0, [], sp] prev_fraction = site[0] manipulation[1] += site[0] manipulation[2].append(site[1]) if abs(manipulation[1] - round(manipulation[1])) > .25: #if the # of atoms to remove isn't within .25 of an integer raise ValueError('Occupancy fractions not consistent with size of unit cell') manipulation[1] = int(round(manipulation[1])) m_list.append(manipulation) structure = se.modified_structure matrix = EwaldSummation(structure).total_energy_matrix ewald_m = EwaldMinimizer(matrix, m_list, num_to_return, self._algo) self._all_structures = [] lowest_energy = ewald_m.output_lists[0][0] num_atoms = sum(structure.composition.values()) for output in ewald_m.output_lists: se = StructureEditor(structure) del_indices = [] #do deletions afterwards because they screw up the indices of the structure for manipulation in output[1]: if manipulation[1] is None: del_indices.append(manipulation[0]) else: se.replace_site(manipulation[0], manipulation[1]) se.delete_sites(del_indices) self._all_structures.append({'energy':output[0], 'energy_above_minimum':(output[0] - lowest_energy) / num_atoms, 'structure': se.modified_structure.get_sorted_structure()}) if return_ranked_list: return self._all_structures else: return self._all_structures[0]['structure']
def apply_transformation(self, structure, return_ranked_list=False): """ For this transformation, the apply_transformation method will return only the ordered structure with the lowest Ewald energy, to be consistent with the method signature of the other transformations. However, all structures are stored in the all_structures attribute in the transformation object for easy access. Args: structure: Oxidation state decorated disordered structure to order return_ranked_list: Boolean stating whether or not multiple structures are returned. If return_ranked_list is a number, that number of structures is returned. Returns: Depending on returned_ranked list, either a transformed structure or a list of dictionaries, where each dictionary is of the form {"structure" = .... , "other_arguments"} the key "transformation" is reserved for the transformation that was actually applied to the structure. This transformation is parsed by the alchemy classes for generating a more specific transformation history. Any other information will be stored in the transformation_parameters dictionary in the transmuted structure class. """ try: num_to_return = int(return_ranked_list) except ValueError: num_to_return = 1 num_to_return = max(1, num_to_return) equivalent_sites = [] exemplars = [] #generate list of equivalent sites to order #equivalency is determined by sp_and_occu and symmetry #if symmetrized structure is true for i, site in enumerate(structure): if site.is_ordered: continue found = False for j, ex in enumerate(exemplars): sp = ex.species_and_occu if not site.species_and_occu.almost_equals(sp): continue if self._symmetrized: sym_equiv = structure.find_equivalent_sites(ex) sym_test = site in sym_equiv else: sym_test = True if sym_test: equivalent_sites[j].append(i) found = True if not found: equivalent_sites.append([i]) exemplars.append(site) #generate the list of manipulations and input structure se = StructureEditor(structure) m_list = [] for g in equivalent_sites: total_occupancy = sum([structure[i].species_and_occu for i in g], Composition()) total_occupancy = dict(total_occupancy.items()) #round total occupancy to possible values for k, v in total_occupancy.items(): if abs(v - round(v)) > 0.25: raise ValueError("Occupancy fractions not consistent " "with size of unit cell") total_occupancy[k] = int(round(v)) #start with an ordered structure initial_sp = max(total_occupancy.keys(), key=lambda x: abs(x.oxi_state)) for i in g: se.replace_site(i, initial_sp) #determine the manipulations for k, v in total_occupancy.items(): if k == initial_sp: continue m = [k.oxi_state / initial_sp.oxi_state, v, list(g), k] m_list.append(m) #determine the number of empty sites empty = len(g) - sum(total_occupancy.values()) if empty > 0.5: m_list.append([0, empty, list(g), None]) structure = se.modified_structure matrix = EwaldSummation(structure).total_energy_matrix ewald_m = EwaldMinimizer(matrix, m_list, num_to_return, self._algo) self._all_structures = [] lowest_energy = ewald_m.output_lists[0][0] num_atoms = sum(structure.composition.values()) for output in ewald_m.output_lists: se = StructureEditor(structure) # do deletions afterwards because they screw up the indices of the # structure del_indices = [] for manipulation in output[1]: if manipulation[1] is None: del_indices.append(manipulation[0]) else: se.replace_site(manipulation[0], manipulation[1]) se.delete_sites(del_indices) self._all_structures.append( {"energy": output[0], "energy_above_minimum": (output[0] - lowest_energy) / num_atoms, "structure": se.modified_structure.get_sorted_structure()}) if return_ranked_list: return self._all_structures else: return self._all_structures[0]["structure"]
def apply_transformation(self, structure): editor = StructureEditor(structure) editor.translate_sites(self._indices, self._vector, self._frac) return editor.modified_structure