本文整理汇总了Python中pymatgen.core.structure.IStructure类的典型用法代码示例。如果您正苦于以下问题：Python IStructure类的具体用法？Python IStructure怎么用？Python IStructure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IStructure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_interpolate_lattice
def test_interpolate_lattice(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
l2 = Lattice.from_lengths_and_angles([3,4,4], [100,100,70])
struct2 = IStructure(l2, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 2, interpolate_lattices=True)
self.assertArrayAlmostEqual(struct.lattice.abc,
int_s[0].lattice.abc)
self.assertArrayAlmostEqual(struct.lattice.angles,
int_s[0].lattice.angles)
self.assertArrayAlmostEqual(struct2.lattice.abc,
int_s[2].lattice.abc)
self.assertArrayAlmostEqual(struct2.lattice.angles,
int_s[2].lattice.angles)
int_angles = [110.3976469, 94.5359731, 64.5165856]
self.assertArrayAlmostEqual(int_angles,
int_s[1].lattice.angles)
# Assert that volume is monotonic
self.assertTrue(struct2.lattice.volume >= int_s[1].lattice.volume)
self.assertTrue(int_s[1].lattice.volume >= struct.lattice.volume)示例2: test_from_dict
def test_from_dict(self):
d = self.propertied_structure.as_dict()
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
d = self.propertied_structure.as_dict(0)
s2 = IStructure.from_dict(d)
self.assertEqual(s, s2)
d = {'lattice': {'a': 3.8401979337, 'volume': 40.044794644251596,
'c': 3.8401979337177736, 'b': 3.840198994344244,
'matrix': [[3.8401979337, 0.0, 0.0],
[1.9200989668, 3.3257101909, 0.0],
[0.0, -2.2171384943, 3.1355090603]],
'alpha': 119.9999908639842, 'beta': 90.0,
'gamma': 60.000009137322195},
'sites': [{'properties': {'magmom': 5}, 'abc': [0.0, 0.0, 0.0],
'occu': 1.0, 'species': [{'occu': 1.0,
'oxidation_state': -2,
'properties': {'spin': 3},
'element': 'O'}],
'label': 'O2-', 'xyz': [0.0, 0.0, 0.0]},
{'properties': {'magmom': -5},
'abc': [0.75, 0.5, 0.75],
'occu': 0.8, 'species': [{'occu': 0.8,
'oxidation_state': 2,
'properties': {'spin': 2},
'element': 'Mg'}],
'label': 'Mg2+:0.800',
'xyz': [3.8401979336749994, 1.2247250003039056e-06,
2.351631795225]}]}
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
self.assertEqual(s[0].specie.spin, 3)
self.assertEqual(type(s), IStructure)示例3: test_get_primitive_structure
def test_get_primitive_structure(self):
coords = [[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5], [0.5, 0, 0.5]]
fcc_ag = IStructure(Lattice.cubic(4.09), ["Ag"] * 4, coords)
self.assertEqual(len(fcc_ag.get_primitive_structure()), 1)
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
bcc_li = IStructure(Lattice.cubic(4.09), ["Li"] * 2, coords)
self.assertEqual(len(bcc_li.get_primitive_structure()), 1)示例4: test_primitive_structure_volume_check
def test_primitive_structure_volume_check(self):
l = Lattice.tetragonal(10, 30)
coords = [[0.5, 0.8, 0], [0.5, 0.2, 0],
[0.5, 0.8, 0.333], [0.5, 0.5, 0.333],
[0.5, 0.5, 0.666], [0.5, 0.2, 0.666]]
s = IStructure(l, ["Ag"] * 6, coords)
sprim = s.get_primitive_structure(tolerance=0.1)
self.assertEqual(len(sprim), 6)示例5: test_interpolate_lattice_rotation
def test_interpolate_lattice_rotation(self):
l1 = Lattice([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
l2 = Lattice([[-1.01, 0, 0], [0, -1.01, 0], [0, 0, 1]])
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
struct1 = IStructure(l1, ["Si"] * 2, coords)
struct2 = IStructure(l2, ["Si"] * 2, coords)
int_s = struct1.interpolate(struct2, 2, interpolate_lattices=True)
# Assert that volume is monotonic
self.assertTrue(struct2.lattice.volume >= int_s[1].lattice.volume)
self.assertTrue(int_s[1].lattice.volume >= struct1.lattice.volume)示例6: test_get_sorted_structure
def test_get_sorted_structure(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, ["O", "Li"], coords, site_properties={"charge": [-2, 1]})
sorted_s = s.get_sorted_structure()
self.assertEqual(sorted_s[0].species_and_occu, Composition("Li"))
self.assertEqual(sorted_s[1].species_and_occu, Composition("O"))
self.assertEqual(sorted_s[0].charge, 1)
self.assertEqual(sorted_s[1].charge, -2)
s = IStructure(self.lattice, ["Se", "C", "Se", "C"], [[0] * 3, [0.5] * 3, [0.25] * 3, [0.75] * 3])
self.assertEqual([site.specie.symbol for site in s.get_sorted_structure()], ["C", "C", "Se", "Se"])示例7: test_interpolate
def test_interpolate(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 10)
for s in int_s:
self.assertIsNotNone(s, "Interpolation Failed!")
self.assertEqual(int_s[0].lattice, s.lattice)
self.assertArrayEqual(int_s[1][1].frac_coords, [0.725, 0.5, 0.725])
badlattice = [[1, 0.00, 0.00], [0, 1, 0.00], [0.00, 0, 1]]
struct2 = IStructure(badlattice, ["Si"] * 2, coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si", "Fe"], coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
# Test autosort feature.
s1 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3),
["Fe"], [[0, 0, 0]])
s1.pop(0)
s2 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3),
["Fe"], [[0, 0, 0]])
s2.pop(2)
random.shuffle(s2)
for s in s1.interpolate(s2, autosort_tol=0.5):
self.assertArrayAlmostEqual(s1[0].frac_coords, s[0].frac_coords)
self.assertArrayAlmostEqual(s1[2].frac_coords, s[2].frac_coords)
# Make sure autosort has no effect on simpler interpolations,
# and with shuffled sites.
s1 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3),
["Fe"], [[0, 0, 0]])
s2 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3),
["Fe"], [[0, 0, 0]])
s2[0] = "Fe", [0.01, 0.01, 0.01]
random.shuffle(s2)
for s in s1.interpolate(s2, autosort_tol=0.5):
self.assertArrayAlmostEqual(s1[1].frac_coords, s[1].frac_coords)
self.assertArrayAlmostEqual(s1[2].frac_coords, s[2].frac_coords)
self.assertArrayAlmostEqual(s1[3].frac_coords, s[3].frac_coords)示例8: setUp
def setUp(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
self.lattice = Lattice(
[[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
)
self.struct = IStructure(self.lattice, ["Si"] * 2, coords)
self.assertEqual(len(self.struct), 2, "Wrong number of sites in structure!")
self.assertTrue(self.struct.is_ordered)
self.assertTrue(self.struct.ntypesp == 1)
coords = list()
coords.append([0, 0, 0])
coords.append([0.0, 0, 0.0000001])
self.assertRaises(StructureError, IStructure, self.lattice, ["Si"] * 2, coords, True)
self.propertied_structure = IStructure(self.lattice, ["Si"] * 2, coords, site_properties={"magmom": [5, -5]})示例9: test_to_from_file_string
def test_to_from_file_string(self):
for fmt in ["cif", "json", "poscar", "cssr"]:
s = self.struct.to(fmt=fmt)
self.assertIsNotNone(s)
ss = IStructure.from_str(s, fmt=fmt)
self.assertArrayAlmostEqual(
ss.lattice.lengths_and_angles,
self.struct.lattice.lengths_and_angles, decimal=5)
self.assertArrayAlmostEqual(ss.frac_coords, self.struct.frac_coords)
self.assertIsInstance(ss, IStructure)
self.struct.to(filename="POSCAR.testing")
self.assertTrue(os.path.exists("POSCAR.testing"))
os.remove("POSCAR.testing")
self.struct.to(filename="Si_testing.yaml")
self.assertTrue(os.path.exists("Si_testing.yaml"))
s = Structure.from_file("Si_testing.yaml")
self.assertEqual(s, self.struct)
os.remove("Si_testing.yaml")
self.struct.to(filename="POSCAR.testing.gz")
s = Structure.from_file("POSCAR.testing.gz")
self.assertEqual(s, self.struct)
os.remove("POSCAR.testing.gz")示例10: test_interpolate_lattice
def test_interpolate_lattice(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
l2 = Lattice.from_lengths_and_angles([3, 4, 4], [100, 100, 70])
struct2 = IStructure(l2, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 2, interpolate_lattices=True)
self.assertArrayAlmostEqual(struct.lattice.abc, int_s[0].lattice.abc)
self.assertArrayAlmostEqual(struct.lattice.angles, int_s[0].lattice.angles)
self.assertArrayAlmostEqual(struct2.lattice.abc, int_s[2].lattice.abc)
self.assertArrayAlmostEqual(struct2.lattice.angles, int_s[2].lattice.angles)
int_angles = [(a + struct2.lattice.angles[i]) / 2 for i, a in enumerate(struct.lattice.angles)]
self.assertArrayAlmostEqual(int_angles, int_s[1].lattice.angles)示例11: test_copy
def test_copy(self):
new_struct = self.propertied_structure.copy(site_properties={"charge": [2, 3]})
self.assertEqual(new_struct[0].magmom, 5)
self.assertEqual(new_struct[1].magmom, -5)
self.assertEqual(new_struct[0].charge, 2)
self.assertEqual(new_struct[1].charge, 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.0, 0, 0.0000001])
structure = IStructure(self.lattice, ["O", "Si"], coords, site_properties={"magmom": [5, -5]})
new_struct = structure.copy(site_properties={"charge": [2, 3]}, sanitize=True)
self.assertEqual(new_struct[0].magmom, -5)
self.assertEqual(new_struct[1].magmom, 5)
self.assertEqual(new_struct[0].charge, 3)
self.assertEqual(new_struct[1].charge, 2)
self.assertAlmostEqual(new_struct.volume, structure.volume)示例12: test_from_dict
def test_from_dict(self):
d = self.propertied_structure.to_dict
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
d = {
"lattice": {
"a": 3.8401979337,
"volume": 40.044794644251596,
"c": 3.8401979337177736,
"b": 3.840198994344244,
"matrix": [
[3.8401979337, 0.0, 0.0],
[1.9200989668, 3.3257101909, 0.0],
[0.0, -2.2171384943, 3.1355090603],
],
"alpha": 119.9999908639842,
"beta": 90.0,
"gamma": 60.000009137322195,
},
"sites": [
{
"properties": {"magmom": 5},
"abc": [0.0, 0.0, 0.0],
"occu": 1.0,
"species": [{"occu": 1.0, "oxidation_state": -2, "properties": {"spin": 3}, "element": "O"}],
"label": "O2-",
"xyz": [0.0, 0.0, 0.0],
},
{
"properties": {"magmom": -5},
"abc": [0.75, 0.5, 0.75],
"occu": 0.8,
"species": [{"occu": 0.8, "oxidation_state": 2, "properties": {"spin": 2}, "element": "Mg"}],
"label": "Mg2+:0.800",
"xyz": [3.8401979336749994, 1.2247250003039056e-06, 2.351631795225],
},
],
}
s = IStructure.from_dict(d)
self.assertEqual(s[0].magmom, 5)
self.assertEqual(s[0].specie.spin, 3)
self.assertEqual(type(s), IStructure)示例13: featurize
def featurize(self, structure):
"""Convert a pymatgen Structure to an immutable IStructure,
Args:
structure (`pymatgen.core.structure.Structure`): A structure.
Returns:
(`pymatgen.core.structure.IStructure`): An immutable IStructure
object.
"""
return [IStructure.from_sites(structure)]示例14: test_as_dict
def test_as_dict(self):
si = Specie("Si", 4)
mn = Element("Mn")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, [{si: 0.5, mn: 0.5}, {si: 0.5}],
coords)
self.assertIn("lattice", struct.as_dict())
self.assertIn("sites", struct.as_dict())
d = self.propertied_structure.as_dict()
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{Specie('O', -2,
properties={"spin": 3}): 1.0},
{Specie('Mg', 2,
properties={"spin": 2}): 0.8}],
coords, site_properties={'magmom': [5, -5]})
d = s.as_dict()
self.assertEqual(d['sites'][0]['properties']['magmom'], 5)
self.assertEqual(d['sites'][0]['species'][0]['properties']['spin'], 3)
d = s.as_dict(0)
self.assertNotIn("volume", d['lattice'])
self.assertNotIn("xyz", d['sites'][0])示例15: test_interpolate
def test_interpolate(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
struct = IStructure(self.lattice, ["Si"] * 2, coords)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si"] * 2, coords2)
int_s = struct.interpolate(struct2, 10)
for s in int_s:
self.assertIsNotNone(s, "Interpolation Failed!")
self.assertArrayEqual(int_s[1][1].frac_coords, [0.725, 0.5, 0.725])
badlattice = [[1, 0.00, 0.00], [0, 1, 0.00], [0.00, 0, 1]]
struct2 = IStructure(badlattice, ["Si"] * 2, coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)
coords2 = list()
coords2.append([0, 0, 0])
coords2.append([0.5, 0.5, 0.5])
struct2 = IStructure(self.struct.lattice, ["Si", "Fe"], coords2)
self.assertRaises(ValueError, struct.interpolate, struct2)