Python PymatgenTest.get_structure方法代码示例

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_get_kpoint_weights(self):
        for name in ["SrTiO3", "LiFePO4", "Graphite"]:
            s = PymatgenTest.get_structure(name)
            a = SpacegroupAnalyzer(s)
            ir_mesh = a.get_ir_reciprocal_mesh((4, 4, 4))
            weights = [i[1] for i in ir_mesh]
            weights = np.array(weights) / sum(weights)
            for i, w in zip(weights, a.get_kpoint_weights([i[0] for i in
                                                           ir_mesh])):
                self.assertAlmostEqual(i, w)

        for name in ["SrTiO3", "LiFePO4", "Graphite"]:
            s = PymatgenTest.get_structure(name)
            a = SpacegroupAnalyzer(s)
            ir_mesh = a.get_ir_reciprocal_mesh((1, 2, 3))
            weights = [i[1] for i in ir_mesh]
            weights = np.array(weights) / sum(weights)
            for i, w in zip(weights, a.get_kpoint_weights([i[0] for i in
                                                           ir_mesh])):
                self.assertAlmostEqual(i, w)

        v = Vasprun(os.path.join(test_dir, "vasprun.xml"))
        a = SpacegroupAnalyzer(v.final_structure)
        wts = a.get_kpoint_weights(v.actual_kpoints)

        for w1, w2 in zip(v.actual_kpoints_weights, wts):
            self.assertAlmostEqual(w1, w2)

        kpts = [[0, 0, 0], [0.15, 0.15, 0.15], [0.2, 0.2, 0.2]]
        self.assertRaises(ValueError, a.get_kpoint_weights, kpts)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
 def test_batch_write_input(self):
     with ScratchDir("."):
         structures = [PymatgenTest.get_structure("Li2O"),
                       PymatgenTest.get_structure("LiFePO4")]
         batch_write_input(structures)
         for d in ['Li4Fe4P4O16_1', 'Li2O1_0']:
             for f in ["INCAR", "KPOINTS", "POSCAR", "POTCAR"]:
                 self.assertTrue(os.path.exists(os.path.join(d, f)))

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
 def test_modes(self):
     s = PymatgenTest.get_structure("CsCl")
     nacl = PymatgenTest.get_structure("CsCl")
     nacl.replace_species({"Cs": "Na"})
     nacl.scale_lattice(184.384551033)
     p = RLSVolumePredictor(radii_type="ionic", use_bv=False)
     self.assertRaises(ValueError, p.predict, s, nacl)
     p = RLSVolumePredictor(radii_type="ionic-atomic", use_bv=False)
     self.assertAlmostEqual(p.predict(s, nacl), 391.884366481)
     p = RLSVolumePredictor(radii_type="ionic-atomic", use_bv=True)
     self.assertAlmostEqual(p.predict(s, nacl), 342.84905395082535)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_charge_gen(self):
        struc = PymatgenTest.get_structure("VO2")

        #assemble set of defects to get charges for
        vac_gen = VacancyGenerator(struc)
        vacs = list(vac_gen)
        full_subs = []
        for sub_elt in ['V', 'O', 'S']:
            sub_gen = SubstitutionGenerator(struc, sub_elt)
            full_subs.extend( list(sub_gen))
        int_gen = VoronoiInterstitialGenerator(struc, "H")
        inters = list(int_gen)
        defect_list = list(set().union( vacs, full_subs, inters))

        #test simple charges
        true_charges = {'Vac_O_mult4': 2, 'Int_H_Voronoi1_mult8': 0,
                        'Int_H_Voronoi2_mult8': 0, 'Vac_V_mult2': -4,
                        'Sub_S_on_V_mult2': 0, 'Int_H_Voronoi3_mult4': 0,
                        'Int_H_Voronoi4_mult4': 0, 'Sub_O_on_V_mult2': -2,
                        'Sub_S_on_O_mult4': 0, 'Sub_V_on_O_mult4': 1}
        for defect in defect_list:
            scg = SimpleChargeGenerator(defect)
            charged_defects_list = list(scg)
            def_name = charged_defects_list[0].name
            charge = charged_defects_list[0].charge
            self.assertEqual(len(charged_defects_list), 1)
            self.assertEqual( true_charges[def_name], charge)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_wf_functions(self):
        # Test slab trans params generator
        for slab in self.slabs:
            trans_params = get_slab_trans_params(slab)
            trans = SlabTransformation(**trans_params)
            new_slab = trans.apply_transformation(slab.oriented_unit_cell)
            self.assertTrue(np.allclose(new_slab.cart_coords, slab.cart_coords))
            self.assertTrue(np.allclose(new_slab.lattice.matrix,
                                        slab.lattice.matrix))

        # Try something a bit more complicated
        formulas = ['Si', 'Sn', 'SrTiO3', 'Li2O']
        structs = [PymatgenTest.get_structure(s) for s in formulas]
        for struct in structs:
            slabs = generate_all_slabs(struct, max_index=2, min_slab_size=10,
                                       min_vacuum_size=20)
            for slab in slabs:
                trans_params = get_slab_trans_params(slab)
                trans = SlabTransformation(**trans_params)
                new_slab = trans.apply_transformation(slab.oriented_unit_cell)
                old_coords = np.around(slab.frac_coords, 10) % 1
                new_coords = np.around(new_slab.frac_coords, 10) % 1
                self.assertTrue(np.allclose(old_coords, new_coords))
                self.assertTrue(np.allclose(new_slab.lattice.matrix,
                                            slab.lattice.matrix))

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def setUpClass(cls):
        if not os.environ.get("VASP_PSP_DIR"):
            os.environ["VASP_PSP_DIR"] = os.path.join(module_dir,
                                                      "reference_files")
            print(
                'Note: This system is not set up to run VASP jobs. '
                'Please set your VASP_PSP_DIR environment variable.')

        cls.struct_si = PymatgenTest.get_structure("Si")

        cls.ref_incar = Incar.from_file(
            os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
        cls.ref_poscar = Poscar.from_file(
            os.path.join(module_dir, "reference_files", "setup_test",
                         "POSCAR"))
        cls.ref_potcar = Potcar.from_file(
            os.path.join(module_dir, "reference_files", "setup_test",
                         "POTCAR"))
        cls.ref_kpoints = Kpoints.from_file(
            os.path.join(module_dir, "reference_files", "setup_test",
                         "KPOINTS"))
        cls.ref_incar_preserve = Incar.from_file(os.path.join(module_dir,
                                                              "reference_files",
                                                              "preserve_incar",
                                                              "INCAR"))

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
 def test_CsCl_ionic(self):
     s = PymatgenTest.get_structure("CsCl")
     self.assertAlmostEqual(VolumePredictor(ionic_factor=0.20).predict(s),
                            112.36, 1)
     s.replace_species({"Cs": "Li", "Cl": "F"})
     self.assertAlmostEqual(VolumePredictor(ionic_factor=0.20).predict(s),
                            16.974592999999995, 1)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def setUp(self):
        struc = PymatgenTest.get_structure("VO2")
        struc.make_supercell(3)
        struc = struc
        self.vac = Vacancy(struc, struc.sites[0], charge=-3)

        abc = self.vac.bulk_structure.lattice.abc
        axisdata = [np.arange(0., lattval, 0.2) for lattval in abc]
        bldata = [np.array([1. for u in np.arange(0., lattval, 0.2)]) for lattval in abc]
        dldata = [
            np.array([(-1 - np.cos(2 * np.pi * u / lattval)) for u in np.arange(0., lattval, 0.2)]) for lattval in abc
        ]
        self.frey_params = {'axis_grid': axisdata, 'bulk_planar_averages': bldata, 'defect_planar_averages': dldata, 'dielectric': 15}

        v = Vasprun(os.path.join(test_dir, 'vasprun.xml'))
        eigenvalues = v.eigenvalues.copy()
        kptweights = v.actual_kpoints_weights
        potalign = -0.1
        vbm = v.eigenvalue_band_properties[2]
        cbm = v.eigenvalue_band_properties[1]
        self.bandfill_params = { 'eigenvalues': eigenvalues,
                                 'kpoint_weights': kptweights,
                                 'potalign': potalign,
                                 'vbm': vbm, 'cbm': cbm }

        self.band_edge_params = {'hybrid_cbm': 1., 'hybrid_vbm': -1., 'vbm': -0.5,
                                 'cbm': 0.6, 'num_hole_vbm': 1., 'num_elec_cbm': 1.}

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_input_sets(self):
        # Test bulk
        bulk_set = MPSurfaceSet(self.struct_ir, bulk=True)
        self.assertFalse(bulk_set.auto_dipole)
        self.assertIsNone(bulk_set.incar.get('LDIPOL'))
        self.assertIsNone(bulk_set.incar.get('LVTOT'))

        # Test slab
        slab_set = MPSurfaceSet(self.slab_100)
        self.assertTrue(slab_set.auto_dipole)
        self.assertTrue(slab_set.incar.get('LDIPOL'))
        self.assertTrue(slab_set.incar.get('LVTOT'))
        banio3_slab = generate_all_slabs(
            PymatgenTest.get_structure('BaNiO3'), 1, 7.0, 20.0)[0]
        banio3_slab_set = MPSurfaceSet(banio3_slab)
        self.assertTrue(banio3_slab_set.incar['LDAU'], True)

        # Test adsorbates
        fe_ads = self.wf_1.fws[-1].tasks[-1]['additional_fields']['slab'].copy()
        fe_ads.replace_species({'H': 'O', "Ir": "Fe"})
        fe_ads_set = MPSurfaceSet(fe_ads)
        self.assertFalse(fe_ads_set.incar['LDAU'])

        # Test interaction of adsorbates and LDAU
        banio3_ads = banio3_slab.copy()
        banio3_ads.add_adsorbate_atom([-1], 'O', 0.5)
        banio3_ads.add_site_property('surface_properties', ['surface'] * len(
            banio3_slab) + ['adsorbate'])
        banio3_ads_set = MPSurfaceSet(banio3_ads)
        self.assertTrue(banio3_ads_set.incar['LDAU'])
        banio3_ads_set_noldau = MPSurfaceSet(
            banio3_ads, user_incar_settings={'LDAU': False})
        self.assertFalse(banio3_ads_set_noldau.incar['LDAU'])

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_bandedgeshifting(self):
        struc = PymatgenTest.get_structure("VO2")
        struc.make_supercell(3)
        struc = struc
        vac = Vacancy(struc, struc.sites[0], charge=-3)

        besc = BandEdgeShiftingCorrection()
        params = {'hybrid_cbm': 1., 'hybrid_vbm': -1., 'vbm': -0.5, 'cbm': 0.6, 'num_hole_vbm': 0., 'num_elec_cbm': 0.}
        de = DefectEntry(vac, 0., corrections={}, parameters=params, entry_id=None)

        #test with no free carriers
        corr = besc.get_correction(de)
        self.assertEqual(corr['vbm_shift_correction'], 1.5)
        self.assertEqual(corr['elec_cbm_shift_correction'], 0.)
        self.assertEqual(corr['hole_vbm_shift_correction'], 0.)

        #test with free holes
        de.parameters.update({'num_hole_vbm': 1.})
        corr = besc.get_correction(de)
        self.assertEqual(corr['vbm_shift_correction'], 1.5)
        self.assertEqual(corr['elec_cbm_shift_correction'], 0.)
        self.assertEqual(corr['hole_vbm_shift_correction'], 0.5)

        #test with free electrons
        de.parameters.update({'num_hole_vbm': 0., 'num_elec_cbm': 1.})
        corr = besc.get_correction(de)
        self.assertEqual(corr['vbm_shift_correction'], 1.5)
        self.assertEqual(corr['elec_cbm_shift_correction'], 0.4)
        self.assertEqual(corr['hole_vbm_shift_correction'], 0.)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_mutable_sequence_methods(self):
        s = self.structure
        s[0] = "Fe"
        self.assertEqual(s.formula, "Fe1 Si1")
        s[0] = "Fe", [0.5, 0.5, 0.5]
        self.assertEqual(s.formula, "Fe1 Si1")
        self.assertArrayAlmostEqual(s[0].frac_coords, [0.5, 0.5, 0.5])
        s.reverse()
        self.assertEqual(s[0].specie, Element("Si"))
        self.assertArrayAlmostEqual(s[0].frac_coords, [0.75, 0.5, 0.75])
        s[0] = {"Mn": 0.5}
        self.assertEqual(s.formula, "Mn0.5 Fe1")
        del s[1]
        self.assertEqual(s.formula, "Mn0.5")
        s[0] = "Fe", [0.9, 0.9, 0.9], {"magmom": 5}
        self.assertEqual(s.formula, "Fe1")
        self.assertEqual(s[0].magmom, 5)

        # Test atomic replacement.
        s["Fe"] = "Mn"
        self.assertEqual(s.formula, "Mn1")

        # Test slice replacement.
        s = PymatgenTest.get_structure("Li2O")
        s[1:3] = "S"
        self.assertEqual(s.formula, "Li1 S2")

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
 def setUp(self):
     super(TestBulkModulusWorkflow, self).setUp()
     self.struct_si = PymatgenTest.get_structure("Si")
     self.ndeformations = 6
     self.deformations = [(np.identity(3) * (1 + x)).tolist() for x in
                          np.linspace(-0.05, 0.05, self.ndeformations)]
     self.wf_config = {"VASP_CMD": ">>vasp_cmd<<", "DB_FILE": ">>db_file<<"}
     self.wf = wf_bulk_modulus(self.struct_si, self.wf_config)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_dimensionality(self):
        cscl = PymatgenTest.get_structure("CsCl")

        df = Dimensionality(bonds={("Cs", "Cl"): 3.5})
        self.assertEqual(df.featurize(cscl)[0], 1)

        df = Dimensionality(bonds={("Cs", "Cl"): 3.7})
        self.assertEqual(df.featurize(cscl)[0], 3)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def setUp(self):
        """
        1) Basic check for pymatgen configurations.
        2) Setup all test workflow.
        """
        super(TestNudgedElasticBandWorkflow, self).setUp()
        # Structures used for test:
        parent = PymatgenTest.get_structure("Li2O")
        parent.remove_oxidation_states()
        parent.make_supercell(2)
        ep0, ep1 = get_endpoints_from_index(parent, [0, 1])
        neb_dir = [os.path.join(module_dir, "..", "..", "test_files", "neb_wf", "4", "inputs", "{:02}",
                                "POSCAR").format(i) for i in range(5)]
        self.structures = [Structure.from_file(n) for n in neb_dir]

        # Run fake vasp
        test_yaml = os.path.join(module_dir, "../../test_files/neb_wf/config/neb_unittest.yaml")
        with open(test_yaml, 'r') as stream:
            self.config = yaml.safe_load(stream)
            # Use scratch directory as destination directory for testing
            self.config["common_params"]["_fw_env"] = {"run_dest_root": self.scratch_dir}

        # Config 1: The parent structure & two endpoint indexes provided; need relaxation first.
        self.config_1 = copy.deepcopy(self.config)
        self.config_1["common_params"]["is_optimized"] = False
        self.config_1["common_params"]["wf_name"] = "NEB_test_1"

        # Config 2: The parent structure & two endpoint indexes provided; no need to relax.
        self.config_2 = copy.deepcopy(self.config)
        del self.config_2["fireworks"][0]
        self.config_2["common_params"]["is_optimized"] = True
        self.config_2["common_params"]["wf_name"] = "NEB_test_2"

        # Config 3: Two endpoints provided; need to relax two endpoints.
        self.config_3 = copy.deepcopy(self.config)
        del self.config_3["fireworks"][0]
        self.config_3["common_params"]["is_optimized"] = False
        self.config_3["common_params"]["wf_name"] = "NEB_test_3"

        # Config 4: Two relaxed endpoints provided; no need to relax two endpoints.
        self.config_4 = copy.deepcopy(self.config_3)
        del self.config_4["fireworks"][0]
        self.config_4["common_params"]["is_optimized"] = True
        self.config_4["common_params"]["wf_name"] = "NEB_test_4"

        # Config 5: All images including two endpoints are provided.
        self.config_5 = copy.deepcopy(self.config)
        del self.config_5["fireworks"][0: 2]
        self.config_5["common_params"]["wf_name"] = "NEB_test_5"

        self.wf_1 = wf_nudged_elastic_band([parent], parent, self.config_1)
        self.wf_2 = wf_nudged_elastic_band([parent], parent, self.config_2)
        self.wf_3 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_3)
        self.wf_4 = wf_nudged_elastic_band([ep0, ep1], parent, self.config_4)
        self.wf_5 = wf_nudged_elastic_band(self.structures, parent, self.config_5)

        # Workflow without the config file
        self.wf_6 = wf_nudged_elastic_band(self.structures, parent)

# 需要导入模块: from pymatgen.util.testing import PymatgenTest [as 别名]
# 或者: from pymatgen.util.testing.PymatgenTest import get_structure [as 别名]
    def test_substitution(self):
        struc = PymatgenTest.get_structure("VO2")
        V_index = struc.indices_from_symbol("V")[0]

        sub_site = PeriodicSite("Sr", struc[V_index].coords, struc.lattice, coords_are_cartesian=True)
        substitution = Substitution(struc, sub_site)

        # test generation and super cell
        sub_struc = substitution.generate_defect_structure(1)
        self.assertEqual(sub_struc.composition.as_dict(), {"V": 1, "Sr": 1, "O": 4})

        sub_struc = substitution.generate_defect_structure(2)
        self.assertEqual(sub_struc.composition.as_dict(), {"V": 15, "Sr": 1, "O": 32})

        sub_struc = substitution.generate_defect_structure(3)
        self.assertEqual(sub_struc.composition.as_dict(), {"V": 53, "Sr": 1, "O": 108})

        sub_struc = substitution.generate_defect_structure([[2., 0, 0], [0, 0, -3.], [0, 2., 0]])
        self.assertEqual(sub_struc.composition.as_dict(), {"V": 23, "O": 48, "Sr": 1})

        # test charge
        substitution = Substitution(struc, sub_site)
        sub_struc = substitution.generate_defect_structure(1)
        self.assertEqual(sub_struc.charge, 0.0)

        substitution = Substitution(struc, sub_site, charge=1.0)
        sub_struc = substitution.generate_defect_structure(1)
        self.assertEqual(sub_struc.charge, 1.0)

        substitution = Substitution(struc, sub_site, charge=-1.0)
        sub_struc = substitution.generate_defect_structure(1)
        self.assertEqual(sub_struc.charge, -1.0)

        # test multiplicity
        substitution = Substitution(struc, sub_site)
        self.assertEqual(substitution.multiplicity, 2.0)

        O_index = struc.indices_from_symbol("O")[0]
        sub_site = PeriodicSite("Sr", struc[O_index].coords, struc.lattice, coords_are_cartesian=True)
        substitution = Substitution(struc, sub_site)
        self.assertEqual(substitution.multiplicity, 4)

        # Test composition
        self.assertEqual(dict(substitution.defect_composition.as_dict()), {"V": 2, "Sr": 1, "O": 3})

        # test that structure generation doesn't break if velocities existed previously
        # (previously caused failures for structure printing)
        vel_struc = Structure( struc.lattice, struc.species, struc.frac_coords,
                               site_properties= {'velocities': [[0., 0., 0.]]*len(struc) } )
        substitution = Substitution(vel_struc, sub_site)
        sub_struc = substitution.generate_defect_structure(1)

        self.assertTrue( 'velocities' not in sub_struc.site_properties)

        # test value error raised for site not in the structure
        non_site = PeriodicSite( "Sr", struc[V_index].frac_coords - [0., 0., .1], struc.lattice)
        self.assertRaises( ValueError, Substitution, struc, non_site)