本文整理汇总了Python中pymatgen.core.structure.IStructure.get_distance方法的典型用法代码示例。如果您正苦于以下问题：Python IStructure.get_distance方法的具体用法？Python IStructure.get_distance怎么用？Python IStructure.get_distance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.core.structure.IStructure的用法示例。
在下文中一共展示了IStructure.get_distance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: IStructureTest
# 需要导入模块: from pymatgen.core.structure import IStructure [as 别名]
# 或者: from pymatgen.core.structure.IStructure import get_distance [as 别名]
class IStructureTest(PymatgenTest):
def setUp(self):
coords = [[0, 0, 0], [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, 0.0000001])
self.assertRaises(StructureError, IStructure, self.lattice,
["Si"] * 2, coords, True)
self.propertied_structure = IStructure(
self.lattice, ["Si"] * 2, coords,
site_properties={'magmom': [5, -5]})
def test_matches(self):
ss = self.struct * 2
self.assertTrue(ss.matches(self.struct))
def test_bad_structure(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
coords.append([0.75, 0.5, 0.75])
self.assertRaises(StructureError, IStructure, self.lattice,
["Si"] * 3, coords, validate_proximity=True)
#these shouldn't raise an error
IStructure(self.lattice, ["Si"] * 2, coords[:2], True)
IStructure(self.lattice, ["Si"], coords[:1], True)
def test_volume_and_density(self):
self.assertAlmostEqual(self.struct.volume, 40.04, 2, "Volume wrong!")
self.assertAlmostEqual(self.struct.density, 2.33, 2,
"Incorrect density")
def test_specie_init(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{Specie('O', -2): 1.0},
{Specie('Mg', 2): 0.8}], coords)
self.assertEqual(s.composition.formula, 'Mg0.8 O1')
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"])
def test_get_spacegroup_data(self):
self.assertEqual(self.struct.get_spacegroup_info(), ('Fd-3m', 227))
def test_fractional_occupations(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{'O': 1.0}, {'Mg': 0.8}],
coords)
self.assertEqual(s.composition.formula, 'Mg0.8 O1')
self.assertFalse(s.is_ordered)
def test_get_distance(self):
self.assertAlmostEqual(self.struct.get_distance(0, 1), 2.35, 2,
"Distance calculated wrongly!")
pt = [0.9, 0.9, 0.8]
self.assertAlmostEqual(self.struct[0].distance_from_point(pt),
1.50332963784, 2,
"Distance calculated wrongly!")
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()
#.........这里部分代码省略.........
示例2: IStructureTest
# 需要导入模块: from pymatgen.core.structure import IStructure [as 别名]
# 或者: from pymatgen.core.structure.IStructure import get_distance [as 别名]
class IStructureTest(PymatgenTest):
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, 0.0000001])
self.assertRaises(StructureError, IStructure, self.lattice,
["Si"] * 2, coords, True)
self.propertied_structure = IStructure(
self.lattice, ["Si"] * 2, coords,
site_properties={'magmom': [5, -5]})
def test_bad_structure(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
coords.append([0.75, 0.5, 0.75])
self.assertRaises(StructureError, IStructure, self.lattice,
["Si"] * 3, coords, validate_proximity=True)
def test_volume_and_density(self):
self.assertAlmostEqual(self.struct.volume, 40.04, 2, "Volume wrong!")
self.assertAlmostEqual(self.struct.density, 2.33, 2,
"Incorrect density")
def test_specie_init(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{Specie('O', -2): 1.0},
{Specie('Mg', 2): 0.8}], coords)
self.assertEqual(str(s.composition), 'Mg2+0.8 O2-1')
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"])
def test_fractional_occupations(self):
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
s = IStructure(self.lattice, [{'O': 1.0}, {'Mg': 0.8}],
coords)
self.assertEqual(str(s.composition), 'Mg0.8 O1')
self.assertFalse(s.is_ordered)
def test_get_distance(self):
self.assertAlmostEqual(self.struct.get_distance(0, 1), 2.35, 2,
"Distance calculated wrongly!")
pt = [0.9, 0.9, 0.8]
self.assertAlmostEqual(self.struct[0].distance_from_point(pt),
1.50332963784, 2,
"Distance calculated wrongly!")
def test_to_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.to_dict)
self.assertIn("sites", struct.to_dict)
d = self.propertied_structure.to_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.to_dict
#.........这里部分代码省略.........