本文整理汇总了Python中pymatgen.Structure.add_spin_by_site方法的典型用法代码示例。如果您正苦于以下问题：Python Structure.add_spin_by_site方法的具体用法？Python Structure.add_spin_by_site怎么用？Python Structure.add_spin_by_site使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pymatgen.Structure的用法示例。
在下文中一共展示了Structure.add_spin_by_site方法的2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_write
# 需要导入模块: from pymatgen import Structure [as 别名]
# 或者: from pymatgen.Structure import add_spin_by_site [as 别名]
#.........这里部分代码省略.........
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Gd Gd0 1 0.317460 0.817460 0.000000 1.0
Gd Gd1 1 0.182540 0.317460 0.000000 1.0
Gd Gd2 1 0.817460 0.682540 0.000000 1.0
Gd Gd3 1 0.682540 0.182540 0.000000 1.0
B B4 1 0.000000 0.000000 0.202900 1.0
B B5 1 0.500000 0.500000 0.797100 1.0
B B6 1 0.000000 0.000000 0.797100 1.0
B B7 1 0.500000 0.500000 0.202900 1.0
B B8 1 0.175900 0.038000 0.500000 1.0
B B9 1 0.962000 0.175900 0.500000 1.0
B B10 1 0.038000 0.824100 0.500000 1.0
B B11 1 0.675900 0.462000 0.500000 1.0
B B12 1 0.324100 0.538000 0.500000 1.0
B B13 1 0.824100 0.962000 0.500000 1.0
B B14 1 0.538000 0.675900 0.500000 1.0
B B15 1 0.462000 0.324100 0.500000 1.0
B B16 1 0.086700 0.586700 0.500000 1.0
B B17 1 0.413300 0.086700 0.500000 1.0
B B18 1 0.586700 0.913300 0.500000 1.0
B B19 1 0.913300 0.413300 0.500000 1.0
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
Gd0 0.00000 0.00000 7.14178
Gd1 0.00000 0.00000 7.14178
Gd2 0.00000 0.00000 -7.14178
Gd3 0.00000 0.00000 -7.14178
"""
self.assertEqual(cw.__str__(), cw_ref_string_magnitudes)
# test we're getting correct magmoms in ncl case
s_ncl2 = self.mcif_ncl2.get_structures()[0]
list_magmoms = [list(m) for m in s_ncl2.site_properties['magmom']]
self.assertEqual(list_magmoms[0][0], 0.0)
self.assertAlmostEqual(list_magmoms[0][1], 5.9160793408726366)
self.assertAlmostEqual(list_magmoms[1][0], -5.1234749999999991)
self.assertAlmostEqual(list_magmoms[1][1], 2.9580396704363183)
# test creating an structure without oxidation state doesn't raise errors
s_manual = Structure(Lattice.cubic(4.2), ["Cs", "Cl"],[[0, 0, 0], [0.5, 0.5, 0.5]])
s_manual.add_spin_by_site([1, -1])
cw = CifWriter(s_manual, write_magmoms=True)
# check oxidation state
cw_manual_oxi_string = """# generated using pymatgen
data_CsCl
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 4.20000000
_cell_length_b 4.20000000
_cell_length_c 4.20000000
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural CsCl
_chemical_formula_sum 'Cs1 Cl1'
_cell_volume 74.08800000
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Cs+ 1.0
Cl+ 1.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Cs+ Cs0 1 0.000000 0.000000 0.000000 1
Cl+ Cl1 1 0.500000 0.500000 0.500000 1
loop_
_atom_site_moment_label
_atom_site_moment_crystalaxis_x
_atom_site_moment_crystalaxis_y
_atom_site_moment_crystalaxis_z
"""
s_manual.add_oxidation_state_by_site([1,1])
cw = CifWriter(s_manual, write_magmoms=True)
self.assertEqual(cw.__str__(), cw_manual_oxi_string)示例2: MagOrderingTransformationTest
# 需要导入模块: from pymatgen import Structure [as 别名]
# 或者: from pymatgen.Structure import add_spin_by_site [as 别名]
class MagOrderingTransformationTest(PymatgenTest):
def setUp(self):
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0],
[0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5],
[0, 0, 0],
[0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt, species, coords)
self.NiO_AFM_111.add_spin_by_site([-5, 5, 0, 0])
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt, species, coords)
self.NiO_AFM_001.add_spin_by_site([-5, 5, 0, 0])
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
trans = AutoOxiStateDecorationTransformation()
self.Fe3O4_oxi = trans.apply_transformation(self.Fe3O4)
parser = CifParser(os.path.join(test_dir, 'Li8Fe2NiCoO8.cif'))
self.Li8Fe2NiCoO8 = parser.get_structures()[0]
self.Li8Fe2NiCoO8.remove_oxidation_states()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
def test_apply_transformation(self):
trans = MagOrderingTransformation({"Fe": 5})
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
s = p.structure
alls = trans.apply_transformation(s, 10)
self.assertEqual(len(alls), 3)
f = SpacegroupAnalyzer(alls[0]["structure"], 0.1)
self.assertEqual(f.get_space_group_number(), 31)
model = IsingModel(5, 5)
trans = MagOrderingTransformation({"Fe": 5},
energy_model=model)
alls2 = trans.apply_transformation(s, 10)
# Ising model with +J penalizes similar neighbor magmom.
self.assertNotEqual(alls[0]["structure"], alls2[0]["structure"])
self.assertEqual(alls[0]["structure"], alls2[2]["structure"])
s = self.get_structure('Li2O')
# Li2O doesn't have magnetism of course, but this is to test the
# enumeration.
trans = MagOrderingTransformation({"Li+": 1}, max_cell_size=3)
alls = trans.apply_transformation(s, 100)
# TODO: check this is correct, unclear what len(alls) should be
self.assertEqual(len(alls), 12)
trans = MagOrderingTransformation({"Ni": 5})
alls = trans.apply_transformation(self.NiO.get_primitive_structure(),
return_ranked_list=10)
self.assertEqual(self.NiO_AFM_111.lattice, alls[0]["structure"].lattice)
self.assertEqual(self.NiO_AFM_001.lattice, alls[1]["structure"].lattice)
def test_ferrimagnetic(self):
trans = MagOrderingTransformation({"Fe": 5}, order_parameter=0.75,
max_cell_size=1)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
s = p.structure
alls = trans.apply_transformation(s, 10)
self.assertEqual(len(alls), 2)
def test_as_from_dict(self):
trans = MagOrderingTransformation({"Fe": 5}, order_parameter=0.75)
d = trans.as_dict()
# Check json encodability
s = json.dumps(d)
trans = MagOrderingTransformation.from_dict(d)
self.assertEqual(trans.mag_species_spin, {"Fe": 5})
from pymatgen.analysis.energy_models import SymmetryModel
self.assertIsInstance(trans.energy_model, SymmetryModel)
def test_zero_spin_case(self):
# ensure that zero spin case maintains sites and formula
s = self.get_structure('Li2O')
trans = MagOrderingTransformation({"Li+": 0.0}, order_parameter=0.5)
#.........这里部分代码省略.........