本文整理汇总了Python中pymatgen.core.Lattice.cubic方法的典型用法代码示例。如果您正苦于以下问题：Python Lattice.cubic方法的具体用法？Python Lattice.cubic怎么用？Python Lattice.cubic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.Lattice的用法示例。
在下文中一共展示了Lattice.cubic方法的13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_get_supercell_size
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu', 'Ag'], [[0]*3]*5)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0]*3]*3)
sm = StructureMatcher(supercell_size='volume')
self.assertEqual(sm._get_supercell_size(s1, s2),
(1, True))
self.assertEqual(sm._get_supercell_size(s2, s1),
(1, True))
sm = StructureMatcher(supercell_size='num_sites')
self.assertEqual(sm._get_supercell_size(s1, s2),
(2, False))
self.assertEqual(sm._get_supercell_size(s2, s1),
(2, True))
sm = StructureMatcher(supercell_size='Ag')
self.assertEqual(sm._get_supercell_size(s1, s2),
(2, False))
self.assertEqual(sm._get_supercell_size(s2, s1),
(2, True))
sm = StructureMatcher(supercell_size='wfieoh')
self.assertRaises(ValueError, sm._get_supercell_size, s1, s2)示例2: test_fit
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_fit(self):
"""
Take two known matched structures
1) Ensure match
2) Ensure match after translation and rotations
3) Ensure no-match after large site translation
4) Ensure match after site shuffling
"""
sm = StructureMatcher()
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
# Test rotational/translational invariance
op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
np.array([0.4, 0.7, 0.9]))
self.struct_list[1].apply_operation(op)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test failure under large atomic translation
self.struct_list[1].translate_sites([0], [.4, .4, .2],
frac_coords=True)
self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))
self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
frac_coords=True)
# random.shuffle(editor._sites)
self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
#Test FrameworkComporator
sm2 = StructureMatcher(comparator=FrameworkComparator())
lfp = self.get_structure("LiFePO4")
nfp = self.get_structure("NaFePO4")
self.assertTrue(sm2.fit(lfp, nfp))
self.assertFalse(sm.fit(lfp, nfp))
#Test anonymous fit.
self.assertEqual(sm.fit_anonymous(lfp, nfp), True)
self.assertAlmostEqual(sm.get_rms_anonymous(lfp, nfp)[0],
0.060895871160262717)
#Test partial occupancies.
s1 = Structure(Lattice.cubic(3),
[{"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
s2 = Structure(Lattice.cubic(3),
[{"Fe": 0.25}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.75}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
self.assertFalse(sm.fit(s1, s2))
self.assertFalse(sm.fit(s2, s1))
s2 = Structure(Lattice.cubic(3),
[{"Mn": 0.5}, {"Mn": 0.5}, {"Mn": 0.5},
{"Mn": 0.5}],
[[0, 0, 0], [0.25, 0.25, 0.25],
[0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
self.assertEqual(sm.fit_anonymous(s1, s2), True)
self.assertAlmostEqual(sm.get_rms_anonymous(s1, s2)[0], 0)示例3: setUp
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def setUp(self):
c1 = [[0.5] * 3, [0.9] * 3]
c2 = [[0.5] * 3, [0.9, 0.1, 0.1]]
s1 = Structure(Lattice.cubic(5), ['Si', 'Si'], c1)
s2 = Structure(Lattice.cubic(5), ['Si', 'Si'], c2)
structs = []
for s in s1.interpolate(s2, 3, pbc=True):
structs.append(Structure.from_sites(s.sites, to_unit_cell=True))
self.structures = structs
self.vis = MITNEBSet(self.structures)示例4: test_writestring
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_writestring(self):
# Test for the string export of s atructure into the exciting input xml schema
input_string = (
'<input xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
'xsi:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput'
'.xsd">\n <title>Na4 Cl4</title>\n <structure speciespath="./">\n '
'<crystal scale="1.8897543768634038">\n <basevect> 5.62000000'
' 0.00000000 0.00000000</basevect>\n <basevect> '
'0.00000000 5.62000000 0.00000000</basevect>\n '
'<basevect> 0.00000000 0.00000000 5.62000000</basevect>'
'\n </crystal>\n <species speciesfile="Na.xml">\n <atom coord='
'" 0.00000000 0.00000000 0.00000000" />\n <atom coor'
'd=" 0.50000000 0.50000000 0.00000000" />\n <atom co'
'ord=" 0.50000000 0.00000000 0.50000000" />\n <atom '
'coord=" 0.00000000 0.50000000 0.50000000" />\n </spec'
'ies>\n <species speciesfile="Cl.xml">\n <atom coord=" 0.5000'
'0000 0.00000000 0.00000000" />\n <atom coord=" 0.00'
'000000 0.50000000 0.00000000" />\n <atom coord=" 0.'
'00000000 0.00000000 0.50000000" />\n <atom coord=" '
'0.50000000 0.50000000 0.50000000" />\n </species>\n </str'
'ucture>\n</input>\n')
lattice = Lattice.cubic('5.62')
structure = Structure(lattice, ['Na', 'Na', 'Na', 'Na',
'Cl', 'Cl', 'Cl', 'Cl'],
[[0, 0, 0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.0], [0.0, 0.5, 0.0],
[0.0, 0.0, 0.5], [0.5, 0.5, 0.5]])
excin = ExcitingInput(structure)
for l1, l2 in zip(input_string.split("\n"),
excin.write_string('unchanged').split("\n")):
if not l1.strip().startswith("<crystal scale"):
self.assertEqual(l1, l2)示例5: test_out_of_cell_s2_like_s1
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_out_of_cell_s2_like_s1(self):
l = Lattice.cubic(5)
s1 = Structure(l, ["Si", "Ag", "Si"], [[0, 0, -0.02], [0, 0, 0.001], [0.7, 0.4, 0.5]])
s2 = Structure(l, ["Si", "Ag", "Si"], [[0, 0, 0.98], [0, 0, 0.99], [0.7, 0.4, 0.5]])
new_s2 = StructureMatcher(primitive_cell=False).get_s2_like_s1(s1, s2)
dists = np.sum((s1.cart_coords - new_s2.cart_coords) ** 2, axis=-1) ** 0.5
self.assertLess(np.max(dists), 0.1)示例6: test_get_supercells
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_get_supercells(self):
sm = StructureMatcher(comparator=ElementComparator())
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.5)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu'], [[0]*3]*4)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0]*3]*3)
scs = list(sm._get_supercells(s1, s2, 8, False))
for x in scs:
self.assertAlmostEqual(abs(np.linalg.det(x[3])), 8)
self.assertEqual(len(x[0]), 4)
self.assertEqual(len(x[1]), 24)
self.assertEqual(len(scs), 48)
scs = list(sm._get_supercells(s2, s1, 8, True))
for x in scs:
self.assertAlmostEqual(abs(np.linalg.det(x[3])), 8)
self.assertEqual(len(x[0]), 24)
self.assertEqual(len(x[1]), 4)
self.assertEqual(len(scs), 48)示例7: test_get_mask
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_get_mask(self):
sm = StructureMatcher(comparator=ElementComparator())
l = Lattice.cubic(1)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu'], [[0]*3]*4)
s2 = Structure(l, ['Cu', 'Cu', 'Ag'], [[0]*3]*3)
result = [[True, False, True, False],
[True, False, True, False],
[True, True, False, True]]
m, inds, i = sm._get_mask(s1, s2, 1, True)
self.assertTrue(np.all(m == result))
self.assertTrue(i == 2)
self.assertEqual(inds, [2])
#test supercell with match
result = [[1, 1, 0, 0, 1, 1, 0, 0],
[1, 1, 0, 0, 1, 1, 0, 0],
[1, 1, 1, 1, 0, 0, 1, 1]]
m, inds, i = sm._get_mask(s1, s2, 2, True)
self.assertTrue(np.all(m == result))
self.assertTrue(i == 2)
self.assertTrue(np.allclose(inds, np.array([4])))
#test supercell without match
result = [[1, 1, 1, 1, 1, 1],
[0, 0, 0, 0, 1, 1],
[1, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 1, 1]]
m, inds, i = sm._get_mask(s2, s1, 2, True)
self.assertTrue(np.all(m == result))
self.assertTrue(i == 0)
self.assertTrue(np.allclose(inds, np.array([])))
#test s2_supercell
result = [[1, 1, 1], [1, 1, 1],
[0, 0, 1], [0, 0, 1],
[1, 1, 0], [1, 1, 0],
[0, 0, 1], [0, 0, 1]]
m, inds, i = sm._get_mask(s2, s1, 2, False)
self.assertTrue(np.all(m == result))
self.assertTrue(i == 0)
self.assertTrue(np.allclose(inds, np.array([])))
#test for multiple translation indices
s1 = Structure(l, ['Cu', 'Ag', 'Cu', 'Ag', 'Ag'], [[0]*3]*5)
s2 = Structure(l, ['Ag', 'Cu', 'Ag'], [[0]*3]*3)
result = [[1, 0, 1, 0, 0],
[0, 1, 0, 1, 1],
[1, 0, 1, 0, 0]]
m, inds, i = sm._get_mask(s1, s2, 1, True)
self.assertTrue(np.all(m == result))
self.assertTrue(i == 1)
self.assertTrue(np.allclose(inds, [0, 2]))示例8: test_get_supercell_size
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ["Mg", "Cu", "Ag", "Cu", "Ag"], [[0] * 3] * 5)
s2 = Structure(l2, ["Cu", "Cu", "Ag"], [[0] * 3] * 3)
sm = StructureMatcher(supercell_size="volume")
self.assertEqual(sm._get_supercell_size(s1, s2), (1, True))
self.assertEqual(sm._get_supercell_size(s2, s1), (1, True))
sm = StructureMatcher(supercell_size="num_sites")
self.assertEqual(sm._get_supercell_size(s1, s2), (2, False))
self.assertEqual(sm._get_supercell_size(s2, s1), (2, True))
sm = StructureMatcher(supercell_size="Ag")
self.assertEqual(sm._get_supercell_size(s1, s2), (2, False))
self.assertEqual(sm._get_supercell_size(s2, s1), (2, True))
sm = StructureMatcher(supercell_size="wfieoh")
self.assertRaises(ValueError, sm._get_supercell_size, s1, s2)示例9: test_nelect
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_nelect(self):
coords = [[0] * 3, [0.5] * 3, [0.75] * 3]
lattice = Lattice.cubic(4)
s = Structure(lattice, ['Si', 'Si', 'Fe'], coords)
self.assertAlmostEqual(MITRelaxSet(s).nelect, 16)
# Check that it works even when oxidation states are present. Was a bug
# previously.
s = Structure(lattice, ['Si4+', 'Si4+', 'Fe2+'], coords)
self.assertAlmostEqual(MITRelaxSet(s).nelect, 16)
self.assertAlmostEqual(MPRelaxSet(s).nelect, 22)示例10: test_metal_check
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_metal_check(self):
structure = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3),
["Cu"], [[0, 0, 0]])
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
vis = MITRelaxSet(structure)
incar = vis.incar
# Verify some things
self.assertIn("ISMEAR", str(w[-1].message))示例11: test_get_supercell_size
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def test_get_supercell_size(self):
l = Lattice.cubic(1)
l2 = Lattice.cubic(0.9)
s1 = Structure(l, ['Mg', 'Cu', 'Ag', 'Cu', 'Ag'], [[0]*3]*5)
s2 = Structure(l2, ['Cu', 'Cu', 'Ag'], [[0]*3]*3)
sm = StructureMatcher(supercell_size='volume')
result = sm._get_supercell_size(s1, s2)
self.assertEqual(result[0], 1)
self.assertEqual(result[1], True)
result = sm._get_supercell_size(s2, s1)
self.assertEqual(result[0], 1)
self.assertEqual(result[1], True)
sm = StructureMatcher(supercell_size='num_sites')
result = sm._get_supercell_size(s1, s2)
self.assertEqual(result[0], 2)
self.assertEqual(result[1], False)
result = sm._get_supercell_size(s2, s1)
self.assertEqual(result[0], 2)
self.assertEqual(result[1], True)示例12: setUp
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
def setUp(self):
parser = CifParser(os.path.join(test_dir, 'Fe.cif'))
self.Fe = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'LiFePO4.cif'))
self.LiFePO4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.ncl.example.GdB4.mcif'))
self.GdB4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.example.NiO.mcif'))
self.NiO_expt = parser.get_structures()[0]
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, site_properties={'magmom': [-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, site_properties={'magmom': [-5, 5, 0, 0]})示例13: Workflow
# 需要导入模块: from pymatgen.core import Lattice [as 别名]
# 或者: from pymatgen.core.Lattice import cubic [as 别名]
if scan:
wf_name += " - SCAN"
wf = Workflow(fws, name=wf_name)
wf = add_additional_fields_to_taskdocs(wf, {"wf_meta": self.wf_meta})
tag = "magnetic_orderings group: >>{}<<".format(self.uuid)
wf = add_tags(wf, [tag, ordered_structure_origins])
return wf
if __name__ == "__main__":
# for trying workflows
from fireworks import LaunchPad
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0.00000, 0.00000, 0.00000], [0.50000, 0.50000, 0.50000]]
NiO = Structure.from_spacegroup(225, latt, species, coords)
wf_deformation = get_wf_magnetic_deformation(NiO)
wf_orderings = MagneticOrderingsWF(NiO).get_wf()
lpad = LaunchPad.auto_load()
lpad.add_wf(wf_orderings)
lpad.add_wf(wf_deformation)