本文整理汇总了Python中pymatgen.io.cif.CifParser类的典型用法代码示例。如果您正苦于以下问题：Python CifParser类的具体用法？Python CifParser怎么用？Python CifParser使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了CifParser类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_implicit_hydrogen
def test_implicit_hydrogen(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
parser = CifParser(os.path.join(test_dir, 'Senegalite_implicit_hydrogen.cif'))
for s in parser.get_structures():
self.assertEqual(s.formula, "Al8 P4 O32")
self.assertEqual(sum(s.site_properties['implicit_hydrogens']), 20)示例2: test_one_line_symm
def test_one_line_symm(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
f = os.path.join(test_dir, "OneLineSymmP1.cif")
p = CifParser(f)
s = p.get_structures()[0]
self.assertEqual(s.formula, "Ga4 Pb2 O8")示例3: test_bad_cif
def test_bad_cif(self):
f = os.path.join(test_dir, "bad_occu.cif")
p = CifParser(f)
self.assertRaises(ValueError, p.get_structures)
p = CifParser(f, occupancy_tolerance=2)
s = p.get_structures()[0]
self.assertAlmostEqual(s[0].species_and_occu["Al3+"], 0.5)示例4: test_no_symmops
def test_no_symmops(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
f = self.TEST_FILES_DIR / "nosymm.cif"
p = CifParser(f)
s = p.get_structures()[0]
self.assertEqual(s.formula, "H96 C60 O8")示例5: test_one_line_symm
def test_one_line_symm(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
f = self.TEST_FILES_DIR / "OneLineSymmP1.cif"
p = CifParser(f)
s = p.get_structures()[0]
self.assertEqual(s.formula, "Ga4 Pb2 O8")示例6: setUp
def setUp(self):
warnings.filterwarnings("ignore")
self.mcif = CifParser(self.TEST_FILES_DIR / "magnetic.example.NiO.mcif")
self.mcif_ncl = CifParser(self.TEST_FILES_DIR / "magnetic.ncl.example.GdB4.mcif")
self.mcif_incom = CifParser(self.TEST_FILES_DIR / "magnetic.incommensurate.example.Cr.mcif")
self.mcif_disord = CifParser(self.TEST_FILES_DIR / "magnetic.disordered.example.CuMnO2.mcif")
self.mcif_ncl2 = CifParser(self.TEST_FILES_DIR / "Mn3Ge_IR2.mcif")示例7: test_jahn_teller_structure_analysis
def test_jahn_teller_structure_analysis(self):
parser = CifParser(os.path.join(test_dir, 'LiFePO4.cif'))
LiFePO4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
Fe3O4 = parser.get_structures()[0]
self.assertTrue(self.jt.is_jahn_teller_active(LiFePO4))
self.assertTrue(self.jt.is_jahn_teller_active(Fe3O4))
LiFePO4_analysis = {
'active': True,
'strength': 'weak',
'sites': [
{
'ligand': 'O2-',
'ligand_bond_length_spread': 0.2111,
'ligand_bond_lengths': [2.1382,
2.0840,
2.0863,
2.2383,
2.2951,
2.2215],
'strength': 'weak',
'motif': 'oct',
'motif_order_parameter': 0.1441,
'site_indices': [4, 5, 6, 7],
'species': 'Fe2+',
'spin_state': 'unknown'
}
]
}
self.assertDictEqual(LiFePO4_analysis, self.jt.get_analysis(LiFePO4))示例8: test_no_symmops
def test_no_symmops(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
f = os.path.join(test_dir, "nosymm.cif")
p = CifParser(f)
s = p.get_structures()[0]
self.assertEqual(s.formula, "H96 C60 O8")示例9: setUp
def setUp(self):
"""
Setup Fe3O4 structure for testing multiple oxidation states
"""
cif_ob = CifParser(os.path.join(test_dir, "Fe3O4.cif"))
self._struct = cif_ob.get_structures()[0]
self._valrad_evaluator = ValenceIonicRadiusEvaluator(self._struct)
self._length = len(self._struct.sites)示例10: test_missing_atom_site_type_with_oxistates
def test_missing_atom_site_type_with_oxistates(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
parser = CifParser(self.TEST_FILES_DIR / 'P24Ru4H252C296S24N16.cif')
c = Composition({'S0+': 24, 'Ru0+': 4, 'H0+': 252, 'C0+': 296,
'N0+': 16, 'P0+': 24})
for s in parser.get_structures(False):
self.assertEqual(s.composition, c)示例11: test_replacing_finite_precision_frac_coords
def test_replacing_finite_precision_frac_coords(self):
f = self.TEST_FILES_DIR / "cif_finite_precision_frac_coord_error.cif"
with warnings.catch_warnings():
p = CifParser(f)
s = p.get_structures()[0]
self.assertEqual(str(s.composition), "N5+24")
self.assertIn("Some fractional co-ordinates rounded to ideal values to "
"avoid finite precision errors.", p.errors)示例12: test_bad_cif
def test_bad_cif(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
f = self.TEST_FILES_DIR / "bad_occu.cif"
p = CifParser(f)
self.assertRaises(ValueError, p.get_structures)
p = CifParser(f, occupancy_tolerance=2)
s = p.get_structures()[0]
self.assertAlmostEqual(s[0].species["Al3+"], 0.5)示例13: test_bad_cif
def test_bad_cif(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
f = os.path.join(test_dir, "bad_occu.cif")
p = CifParser(f)
self.assertRaises(ValueError, p.get_structures)
p = CifParser(f, occupancy_tolerance=2)
s = p.get_structures()[0]
self.assertAlmostEqual(s[0].species_and_occu["Al3+"], 0.5)示例14: test_cluster_from_file
def test_cluster_from_file(self):
r = CifParser(os.path.join(test_dir, "CoO19128.cif"))
structure = r.get_structures()[0]
atoms = Atoms(structure, "O", 10.0)
atoms.write_file("ATOMS_test")
mol_1 = Atoms.cluster_from_file("ATOMS_test")
mol_2 = Atoms.cluster_from_file(os.path.join(test_dir, "ATOMS"))
self.assertEqual(mol_1.formula, mol_2.formula)
self.assertEqual(len(mol_1), len(mol_2))
os.remove("ATOMS_test")示例15: setUp
def setUp(self):
self.mcif = CifParser(os.path.join(test_dir,
"magnetic.example.NiO.mcif"))
self.mcif_ncl = CifParser(os.path.join(test_dir,
"magnetic.ncl.example.GdB4.mcif"))
self.mcif_incom = CifParser(os.path.join(test_dir,
"magnetic.incommensurate.example.Cr.mcif"))
self.mcif_disord = CifParser(os.path.join(test_dir,
"magnetic.disordered.example.CuMnO2.mcif"))
self.mcif_ncl2 = CifParser(os.path.join(test_dir,
"Mn3Ge_IR2.mcif"))