def get_structure(vasp_run, outcar=None, initial_structure=False, additional_info=False): """ Process structure for static calculations from previous run. Args: vasp_run: Vasprun object that contains the final structure from previous run. outcar: Outcar object that contains the magnetization info from previous run. initial_structure: Whether to return the structure from previous run. Default is False. additional_info: Whether to return additional symmetry info related to the structure. If True, return a list of the refined structure ( conventional cell), the conventional standard structure, the symmetry dataset and symmetry operations of the structure (see SymmetryFinder doc for details) Returns: Returns the magmom-decorated structure that can be passed to get Vasp input files, e.g. get_kpoints. """ #TODO: fix magmom for get_*_structures if vasp_run.is_spin: if outcar and outcar.magnetization: magmom = {"magmom": [i['tot'] for i in outcar.magnetization]} else: magmom = { "magmom": vasp_run.to_dict['input']['parameters']['MAGMOM'] } else: magmom = None structure = vasp_run.final_structure if magmom: structure = structure.copy(site_properties=magmom) sym_finder = SymmetryFinder(structure, symprec=0.01) if initial_structure: return structure elif additional_info: info = [ sym_finder.get_refined_structure(), sym_finder.get_conventional_standard_structure(), sym_finder.get_symmetry_dataset(), sym_finder.get_symmetry_operations() ] return [sym_finder.get_primitive_standard_structure(), info] else: return sym_finder.get_primitive_standard_structure()
def get_structure(vasp_run, outcar=None, initial_structure=False, additional_info=False): """ Process structure for static calculations from previous run. Args: vasp_run: Vasprun object that contains the final structure from previous run. outcar: Outcar object that contains the magnetization info from previous run. initial_structure: Whether to return the structure from previous run. Default is False. additional_info: Whether to return additional symmetry info related to the structure. If True, return a list of the refined structure ( conventional cell), the conventional standard structure, the symmetry dataset and symmetry operations of the structure (see SymmetryFinder doc for details) Returns: Returns the magmom-decorated structure that can be passed to get Vasp input files, e.g. get_kpoints. """ #TODO: fix magmom for get_*_structures if vasp_run.is_spin: if outcar and outcar.magnetization: magmom = {"magmom": [i['tot'] for i in outcar.magnetization]} else: magmom = { "magmom": vasp_run.to_dict['input']['parameters'] ['MAGMOM']} else: magmom = None structure = vasp_run.final_structure if magmom: structure = structure.copy(site_properties=magmom) sym_finder = SymmetryFinder(structure, symprec=0.01) if initial_structure: return structure elif additional_info: info = [sym_finder.get_refined_structure(), sym_finder.get_conventional_standard_structure(), sym_finder.get_symmetry_dataset(), sym_finder.get_symmetry_operations()] return [sym_finder.get_primitive_standard_structure(), info] else: return sym_finder.get_primitive_standard_structure()
class SymmetryFinderTest(unittest.TestCase): def setUp(self): p = Poscar.from_file(os.path.join(test_dir, 'POSCAR')) self.structure = p.structure 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.structure.copy() site = s[0] del s[0] s.append(site.species_and_occu, site.frac_coords) self.sg3 = SymmetryFinder(s, 0.001) parser = CifParser(os.path.join(test_dir, 'Graphite.cif')) graphite = parser.get_structures()[0] graphite.add_site_property("magmom", [0.1] * len(graphite)) self.sg4 = SymmetryFinder(graphite, 0.001) def test_get_space_symbol(self): self.assertEqual(self.sg.get_spacegroup_symbol(), "Pnma") self.assertEqual(self.disordered_sg.get_spacegroup_symbol(), "P4_2/nmc") self.assertEqual(self.sg3.get_spacegroup_symbol(), "Pnma") self.assertEqual(self.sg4.get_spacegroup_symbol(), "R-3m") def test_get_space_number(self): self.assertEqual(self.sg.get_spacegroup_number(), 62) self.assertEqual(self.disordered_sg.get_spacegroup_number(), 137) self.assertEqual(self.sg4.get_spacegroup_number(), 166) def test_get_hall(self): self.assertEqual(self.sg.get_hall(), '-P 2ac 2n') self.assertEqual(self.disordered_sg.get_hall(), 'P 4n 2n -1n') def test_get_pointgroup(self): self.assertEqual(self.sg.get_point_group(), 'mmm') self.assertEqual(self.disordered_sg.get_point_group(), '4/mmm') def test_get_symmetry_dataset(self): ds = self.sg.get_symmetry_dataset() self.assertEqual(ds['international'], 'Pnma') def test_get_crystal_system(self): crystal_system = self.sg.get_crystal_system() self.assertEqual('orthorhombic', crystal_system) self.assertEqual('tetragonal', self.disordered_sg.get_crystal_system()) def test_get_symmetry_operations(self): fracsymmops = self.sg.get_symmetry_operations() symmops = self.sg.get_symmetry_operations(True) self.assertEqual(len(symmops), 8) latt = self.structure.lattice for fop, op in zip(fracsymmops, symmops): for site in self.structure: newfrac = fop.operate(site.frac_coords) newcart = op.operate(site.coords) self.assertTrue(np.allclose(latt.get_fractional_coords(newcart), newfrac)) found = False newsite = PeriodicSite(site.species_and_occu, newcart, latt, coords_are_cartesian=True) for testsite in self.structure: if newsite.is_periodic_image(testsite, 1e-3): found = True break self.assertTrue(found) def test_get_refined_structure(self): for a in self.sg.get_refined_structure().lattice.angles: self.assertEqual(a, 90) refined = self.disordered_sg.get_refined_structure() for a in refined.lattice.angles: self.assertEqual(a, 90) self.assertEqual(refined.lattice.a, refined.lattice.b) parser = CifParser(os.path.join(test_dir, 'Li2O.cif')) s = parser.get_structures()[0] sg = SymmetryFinder(s, 0.001) self.assertEqual(sg.get_refined_structure().num_sites, 4 * s.num_sites) def test_get_symmetrized_structure(self): symm_struct = self.sg.get_symmetrized_structure() for a in symm_struct.lattice.angles: self.assertEqual(a, 90) self.assertEqual(len(symm_struct.equivalent_sites), 5) symm_struct = self.disordered_sg.get_symmetrized_structure() self.assertEqual(len(symm_struct.equivalent_sites), 8) self.assertEqual(map(len, symm_struct.equivalent_sites), [16,4,8,4,2,8,8,8]) s1 = symm_struct.equivalent_sites[1][1] s2 = symm_struct[symm_struct.equivalent_indices[1][1]] self.assertEqual(s1, s2) self.assertEqual(self.sg4.get_symmetrized_structure()[0].magmom, 0.1) def test_find_primitive(self): """ F m -3 m Li2O testing of converting to primitive cell """ parser = CifParser(os.path.join(test_dir, 'Li2O.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure) primitive_structure = s.find_primitive() self.assertEqual(primitive_structure.formula, "Li2 O1") # This isn't what is expected. All the angles should be 60 self.assertAlmostEqual(primitive_structure.lattice.alpha, 60) self.assertAlmostEqual(primitive_structure.lattice.beta, 60) self.assertAlmostEqual(primitive_structure.lattice.gamma, 60) self.assertAlmostEqual(primitive_structure.lattice.volume, structure.lattice.volume / 4.0) def test_get_ir_reciprocal_mesh(self): grid=self.sg.get_ir_reciprocal_mesh() self.assertEquals(len(grid), 216) self.assertAlmostEquals(grid[1][0][0], 0.1) self.assertAlmostEquals(grid[1][0][1], 0.0) self.assertAlmostEquals(grid[1][0][2], 0.0) self.assertEquals(grid[1][1], 2) def test_get_conventional_standard_structure(self): parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 9.1980270633769461) self.assertAlmostEqual(conv.lattice.b, 9.1980270633769461) self.assertAlmostEqual(conv.lattice.c, 9.1980270633769461) parser = CifParser(os.path.join(test_dir, 'btet_1915.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 5.0615106678044235) self.assertAlmostEqual(conv.lattice.b, 5.0615106678044235) self.assertAlmostEqual(conv.lattice.c, 4.2327080177761687) parser = CifParser(os.path.join(test_dir, 'orci_1010.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 2.9542233922299999) self.assertAlmostEqual(conv.lattice.b, 4.6330325651443296) self.assertAlmostEqual(conv.lattice.c, 5.373703587040775) parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 4.1430033493799998) self.assertAlmostEqual(conv.lattice.b, 31.437979757624728) self.assertAlmostEqual(conv.lattice.c, 3.99648651) parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 117.53832420192903) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 14.033435583000625) self.assertAlmostEqual(conv.lattice.b, 3.96052850731) self.assertAlmostEqual(conv.lattice.c, 6.8743926325200002) parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 120) self.assertAlmostEqual(conv.lattice.a, 3.699919902005897) self.assertAlmostEqual(conv.lattice.b, 3.699919902005897) self.assertAlmostEqual(conv.lattice.c, 6.9779585500000003) def test_get_primitive_standard_structure(self): parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 109.47122063400001) self.assertAlmostEqual(prim.lattice.beta, 109.47122063400001) self.assertAlmostEqual(prim.lattice.gamma, 109.47122063400001) self.assertAlmostEqual(prim.lattice.a, 7.9657251015812145) self.assertAlmostEqual(prim.lattice.b, 7.9657251015812145) self.assertAlmostEqual(prim.lattice.c, 7.9657251015812145) parser = CifParser(os.path.join(test_dir, 'btet_1915.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 105.015053349) self.assertAlmostEqual(prim.lattice.beta, 105.015053349) self.assertAlmostEqual(prim.lattice.gamma, 118.80658411899999) self.assertAlmostEqual(prim.lattice.a, 4.1579321075608791) self.assertAlmostEqual(prim.lattice.b, 4.1579321075608791) self.assertAlmostEqual(prim.lattice.c, 4.1579321075608791) parser = CifParser(os.path.join(test_dir, 'orci_1010.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 134.78923546600001) self.assertAlmostEqual(prim.lattice.beta, 105.856239333) self.assertAlmostEqual(prim.lattice.gamma, 91.276341676000001) self.assertAlmostEqual(prim.lattice.a, 3.8428217771014852) self.assertAlmostEqual(prim.lattice.b, 3.8428217771014852) self.assertAlmostEqual(prim.lattice.c, 3.8428217771014852) parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 90) self.assertAlmostEqual(prim.lattice.beta, 90) self.assertAlmostEqual(prim.lattice.gamma, 164.985257335) self.assertAlmostEqual(prim.lattice.a, 15.854897098324196) self.assertAlmostEqual(prim.lattice.b, 15.854897098324196) self.assertAlmostEqual(prim.lattice.c, 3.99648651) parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 63.579155761999999) self.assertAlmostEqual(prim.lattice.beta, 116.42084423747779) self.assertAlmostEqual(prim.lattice.gamma, 148.47965136208569) self.assertAlmostEqual(prim.lattice.a, 7.2908007159612325) self.assertAlmostEqual(prim.lattice.b, 7.2908007159612325) self.assertAlmostEqual(prim.lattice.c, 6.8743926325200002) parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 90) self.assertAlmostEqual(prim.lattice.beta, 90) self.assertAlmostEqual(prim.lattice.gamma, 120) self.assertAlmostEqual(prim.lattice.a, 3.699919902005897) self.assertAlmostEqual(prim.lattice.b, 3.699919902005897) self.assertAlmostEqual(prim.lattice.c, 6.9779585500000003)
class SymmetryFinderTest(unittest.TestCase): def setUp(self): p = Poscar.from_file(os.path.join(test_dir, 'POSCAR')) self.structure = p.structure 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.structure.copy() site = s[0] del s[0] s.append(site.species_and_occu, site.frac_coords) self.sg3 = SymmetryFinder(s, 0.001) parser = CifParser(os.path.join(test_dir, 'Graphite.cif')) graphite = parser.get_structures()[0] graphite.add_site_property("magmom", [0.1] * len(graphite)) self.sg4 = SymmetryFinder(graphite, 0.001) def test_get_space_symbol(self): self.assertEqual(self.sg.get_spacegroup_symbol(), "Pnma") self.assertEqual(self.disordered_sg.get_spacegroup_symbol(), "P4_2/nmc") self.assertEqual(self.sg3.get_spacegroup_symbol(), "Pnma") self.assertEqual(self.sg4.get_spacegroup_symbol(), "R-3m") def test_get_space_number(self): self.assertEqual(self.sg.get_spacegroup_number(), 62) self.assertEqual(self.disordered_sg.get_spacegroup_number(), 137) self.assertEqual(self.sg4.get_spacegroup_number(), 166) def test_get_hall(self): self.assertEqual(self.sg.get_hall(), '-P 2ac 2n') self.assertEqual(self.disordered_sg.get_hall(), 'P 4n 2n -1n') def test_get_pointgroup(self): self.assertEqual(self.sg.get_point_group(), 'mmm') self.assertEqual(self.disordered_sg.get_point_group(), '4/mmm') def test_get_symmetry_dataset(self): ds = self.sg.get_symmetry_dataset() self.assertEqual(ds['international'], 'Pnma') def test_get_crystal_system(self): crystal_system = self.sg.get_crystal_system() self.assertEqual('orthorhombic', crystal_system) self.assertEqual('tetragonal', self.disordered_sg.get_crystal_system()) def test_get_symmetry_operations(self): fracsymmops = self.sg.get_symmetry_operations() symmops = self.sg.get_symmetry_operations(True) self.assertEqual(len(symmops), 8) latt = self.structure.lattice for fop, op in zip(fracsymmops, symmops): for site in self.structure: newfrac = fop.operate(site.frac_coords) newcart = op.operate(site.coords) self.assertTrue( np.allclose(latt.get_fractional_coords(newcart), newfrac)) found = False newsite = PeriodicSite(site.species_and_occu, newcart, latt, coords_are_cartesian=True) for testsite in self.structure: if newsite.is_periodic_image(testsite, 1e-3): found = True break self.assertTrue(found) def test_get_refined_structure(self): for a in self.sg.get_refined_structure().lattice.angles: self.assertEqual(a, 90) refined = self.disordered_sg.get_refined_structure() for a in refined.lattice.angles: self.assertEqual(a, 90) self.assertEqual(refined.lattice.a, refined.lattice.b) parser = CifParser(os.path.join(test_dir, 'Li2O.cif')) s = parser.get_structures()[0] sg = SymmetryFinder(s, 0.001) self.assertEqual(sg.get_refined_structure().num_sites, 4 * s.num_sites) def test_get_symmetrized_structure(self): symm_struct = self.sg.get_symmetrized_structure() for a in symm_struct.lattice.angles: self.assertEqual(a, 90) self.assertEqual(len(symm_struct.equivalent_sites), 5) symm_struct = self.disordered_sg.get_symmetrized_structure() self.assertEqual(len(symm_struct.equivalent_sites), 8) self.assertEqual(map(len, symm_struct.equivalent_sites), [16, 4, 8, 4, 2, 8, 8, 8]) s1 = symm_struct.equivalent_sites[1][1] s2 = symm_struct[symm_struct.equivalent_indices[1][1]] self.assertEqual(s1, s2) self.assertEqual(self.sg4.get_symmetrized_structure()[0].magmom, 0.1) def test_find_primitive(self): """ F m -3 m Li2O testing of converting to primitive cell """ parser = CifParser(os.path.join(test_dir, 'Li2O.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure) primitive_structure = s.find_primitive() self.assertEqual(primitive_structure.formula, "Li2 O1") # This isn't what is expected. All the angles should be 60 self.assertAlmostEqual(primitive_structure.lattice.alpha, 60) self.assertAlmostEqual(primitive_structure.lattice.beta, 60) self.assertAlmostEqual(primitive_structure.lattice.gamma, 60) self.assertAlmostEqual(primitive_structure.lattice.volume, structure.lattice.volume / 4.0) def test_get_ir_reciprocal_mesh(self): grid = self.sg.get_ir_reciprocal_mesh() self.assertEquals(len(grid), 216) self.assertAlmostEquals(grid[1][0][0], 0.1) self.assertAlmostEquals(grid[1][0][1], 0.0) self.assertAlmostEquals(grid[1][0][2], 0.0) self.assertEquals(grid[1][1], 2) def test_get_conventional_standard_structure(self): parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 9.1980270633769461) self.assertAlmostEqual(conv.lattice.b, 9.1980270633769461) self.assertAlmostEqual(conv.lattice.c, 9.1980270633769461) parser = CifParser(os.path.join(test_dir, 'btet_1915.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 5.0615106678044235) self.assertAlmostEqual(conv.lattice.b, 5.0615106678044235) self.assertAlmostEqual(conv.lattice.c, 4.2327080177761687) parser = CifParser(os.path.join(test_dir, 'orci_1010.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 2.9542233922299999) self.assertAlmostEqual(conv.lattice.b, 4.6330325651443296) self.assertAlmostEqual(conv.lattice.c, 5.373703587040775) parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 4.1430033493799998) self.assertAlmostEqual(conv.lattice.b, 31.437979757624728) self.assertAlmostEqual(conv.lattice.c, 3.99648651) parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 117.53832420192903) self.assertAlmostEqual(conv.lattice.gamma, 90) self.assertAlmostEqual(conv.lattice.a, 14.033435583000625) self.assertAlmostEqual(conv.lattice.b, 3.96052850731) self.assertAlmostEqual(conv.lattice.c, 6.8743926325200002) parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) conv = s.get_conventional_standard_structure() self.assertAlmostEqual(conv.lattice.alpha, 90) self.assertAlmostEqual(conv.lattice.beta, 90) self.assertAlmostEqual(conv.lattice.gamma, 120) self.assertAlmostEqual(conv.lattice.a, 3.699919902005897) self.assertAlmostEqual(conv.lattice.b, 3.699919902005897) self.assertAlmostEqual(conv.lattice.c, 6.9779585500000003) def test_get_primitive_standard_structure(self): parser = CifParser(os.path.join(test_dir, 'bcc_1927.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 109.47122063400001) self.assertAlmostEqual(prim.lattice.beta, 109.47122063400001) self.assertAlmostEqual(prim.lattice.gamma, 109.47122063400001) self.assertAlmostEqual(prim.lattice.a, 7.9657251015812145) self.assertAlmostEqual(prim.lattice.b, 7.9657251015812145) self.assertAlmostEqual(prim.lattice.c, 7.9657251015812145) parser = CifParser(os.path.join(test_dir, 'btet_1915.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 105.015053349) self.assertAlmostEqual(prim.lattice.beta, 105.015053349) self.assertAlmostEqual(prim.lattice.gamma, 118.80658411899999) self.assertAlmostEqual(prim.lattice.a, 4.1579321075608791) self.assertAlmostEqual(prim.lattice.b, 4.1579321075608791) self.assertAlmostEqual(prim.lattice.c, 4.1579321075608791) parser = CifParser(os.path.join(test_dir, 'orci_1010.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 134.78923546600001) self.assertAlmostEqual(prim.lattice.beta, 105.856239333) self.assertAlmostEqual(prim.lattice.gamma, 91.276341676000001) self.assertAlmostEqual(prim.lattice.a, 3.8428217771014852) self.assertAlmostEqual(prim.lattice.b, 3.8428217771014852) self.assertAlmostEqual(prim.lattice.c, 3.8428217771014852) parser = CifParser(os.path.join(test_dir, 'orcc_1003.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 90) self.assertAlmostEqual(prim.lattice.beta, 90) self.assertAlmostEqual(prim.lattice.gamma, 164.985257335) self.assertAlmostEqual(prim.lattice.a, 15.854897098324196) self.assertAlmostEqual(prim.lattice.b, 15.854897098324196) self.assertAlmostEqual(prim.lattice.c, 3.99648651) parser = CifParser(os.path.join(test_dir, 'monoc_1028.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 63.579155761999999) self.assertAlmostEqual(prim.lattice.beta, 116.42084423747779) self.assertAlmostEqual(prim.lattice.gamma, 148.47965136208569) self.assertAlmostEqual(prim.lattice.a, 7.2908007159612325) self.assertAlmostEqual(prim.lattice.b, 7.2908007159612325) self.assertAlmostEqual(prim.lattice.c, 6.8743926325200002) parser = CifParser(os.path.join(test_dir, 'rhomb_1170.cif')) structure = parser.get_structures(False)[0] s = SymmetryFinder(structure, symprec=1e-2) prim = s.get_primitive_standard_structure() self.assertAlmostEqual(prim.lattice.alpha, 90) self.assertAlmostEqual(prim.lattice.beta, 90) self.assertAlmostEqual(prim.lattice.gamma, 120) self.assertAlmostEqual(prim.lattice.a, 3.699919902005897) self.assertAlmostEqual(prim.lattice.b, 3.699919902005897) self.assertAlmostEqual(prim.lattice.c, 6.9779585500000003)
def inter_descript_gen(cif_file, collection, prune_args): """ Generates the interstitial descriptor values for the structures in input cif directory and store them into the database supplied Args: cif_file: cif File collection: Mongo database collection prune_ars: List of keywords to prune the interstitials a) anion: Only the interstitial sites that can be occupied by the anion are kept a) cation: Only the interstitial sites that can be occupied by the smallest cation are kept c) [El, oxi_state]: Only the interstitial sites that can be occupied by the input ion are kept Ex: ['Li', 1] """ # Use the number as struct identifier # Store the remaining string as formula print cif_file dir, filen = os.path.split(cif_file) print filen name = os.path.splitext(filen)[0] item = name.split('--') key = item[0] inter_descript_dict = {'key': key, 'formula': ''.join(item[1].split())} FAIL = 0 SUCC = 1 #read the file to pymatgen struct try: struct = CifParser(cif_file).get_structures(False)[0] except: print 'reading ', cif_file, ' failed' return FAIL symm_finder = SymmetryFinder(struct) inter_descript_dict['structure'] = struct inter_descript_dict['crystal_system'] = symm_finder.get_crystal_system() inter_descript_dict['spacegroup_no'] = symm_finder.get_spacegroup_number() no_symmops = len(symm_finder.get_symmetry_operations()) inter_descript_dict['no_symmops'] = no_symmops try: struct_val_rad = StructWithValenceIonicRadius(struct) valences = struct_val_rad.valences.values() valences.sort() anion_cation_charge_ratio = abs(valences[-1] / valences[0]) radii = struct_val_rad.radii.values() radii.sort() anion_cation_radii_ratio = radii[-1] / radii[0] except: print inter_descript_dict['formula'] print "Unable to identify radii and valences" return FAIL inter_descript_dict['charge_ratio'] = anion_cation_charge_ratio inter_descript_dict['radius_ratio'] = anion_cation_radii_ratio try: inter = Interstitial(struct_val_rad) except: print inter_descript_dict['formula'] print 'interstitial not generated' return FAIL if prune_args[0] == "cation": inter.radius_prune_defectsites( radii[0]) #smallest element in the structure elif prune_args[0] == "anion": inter.radius_prune_defectsites( radii[-1]) #largest element in the structure else: el = prune_args[0] oxi_state = prune_args[1] inter.prune_defectsites(el, oxi_state) inter.prune_close_defectsites() if inter.defectsite_count() > 10: inter.reduce_defectsites() no_inter = inter.defectsite_count() inter_descript_dict['no_inter'] = no_inter #print >>sys.stderr, inter_descript_dict[key]['formula'], "No. of inter", no_inter #Create a list storing a dictionary of properties for each interstitial inter_list = [] for i in range(no_inter): inter_dict = {} inter_dict['coord_no'] = inter.get_defectsite_coordination_number(i) inter_dict['coord_el'] = list(inter.get_coordinated_elements(i)) inter_dict['radius'] = inter.get_radius(i) inter_dict['coord_chrg_sum'] = inter.get_coordsites_charge_sum(i) inter_list.append(inter_dict) inter_descript_dict['interstitials'] = inter_list descriptor_id = collection.insert(inter_descript_dict) return descriptor_id
def inter_descript_gen(cif_file, prune_args): # Use the number as struct identifier # Store the remaining string as formula print cif_file dir, filen = os.path.split(cif_file) print filen name = os.path.splitext(filen)[0] item = name.split('--') key = item[0] inter_descript_dict = {'formula': ''.join(item[1].split())} #read the file to pymatgen struct try: struct = CifParser(cif_file).get_structures(False)[0] except: print 'reading ', cif_file, ' failed' return None, filen symm_finder = SymmetryFinder(struct, symprec=1e-1) inter_descript_dict['crystal_system'] = symm_finder.get_crystal_system() inter_descript_dict['spacegroup_no'] = symm_finder.get_spacegroup_number() no_symmops = len(symm_finder.get_symmetry_operations()) inter_descript_dict['no_symmops'] = no_symmops try: struct_val_rad = StructWithValenceIonicRadius(struct) except: print inter_descript_dict['formula'] print "Unable to identify radii and valences" return None, filen try: inter = Interstitial(struct_val_rad) except: print inter_descript_dict['formula'] print 'interstitial not generated' return None, filen valences = inter.struct_valences.values() valences.sort() try: anion_cation_charge_ratio = abs(valences[-1] / valences[0]) except: #BVAnalyzer fails sometimes and valences are set to 0 print inter_descript_dict['formula'] print valences anion_cation_charge_ratio = 0 inter_descript_dict['charge_ratio'] = anion_cation_charge_ratio radii = inter.struct_radii.values() radii.sort() try: anion_cation_radii_ratio = radii[-1] / radii[0] except: anion_cation_radii_ratio = 0 inter_descript_dict['radius_ratio'] = anion_cation_radii_ratio if prune_args[0] == "cation": inter.radius_prune_defectsites( radii[0]) #smallest element in the structure elif prune_args[0] == "anion": inter.radius_prune_defectsites( radii[-1]) #largest element in the structure else: el = prune_args[0] oxi_state = prune_args[1] print el, oxi_state inter.prune_defectsites(el, oxi_state) inter.prune_close_defectsites() if inter.defectsite_count() > 10: # Something wrong with the symmetry reduction of defects. # Ignoring the outlier return None, filen inter.reduce_defectsites() no_inter = inter.defectsite_count() if no_inter > 5: print "Tag:", key, inter_descript_dict['formula'], no_inter inter_descript_dict['no_inter'] = no_inter #print >>sys.stderr, inter_descript_dict[key]['formula'], "No. of inter", no_inter #ife = InterstitialFormationEnergy(inter) #Create a list storing a dictionary of properties for each interstitial inter_list = [] for i in range(no_inter): inter_dict = {} inter_dict['coords'] = inter.get_defectsite(i).coords inter_dict['coord_no'] = inter.get_defectsite_coordination_number(i) inter_dict['coord_el'] = list(inter.get_coordinated_elements(i)) inter_dict['radius'] = inter.get_radius(i) inter_dict['coord_chrg_sum'] = inter.get_coordsites_charge_sum(i) inter_list.append(inter_dict) inter_descript_dict['interstitials'] = inter_list return key, inter_descript_dict