本文整理汇总了Python中pymatgen.core.Structure.copy方法的典型用法代码示例。如果您正苦于以下问题：Python Structure.copy方法的具体用法？Python Structure.copy怎么用？Python Structure.copy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的用法示例。
在下文中一共展示了Structure.copy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_supercell_subsets
# 需要导入模块: from pymatgen.core import Structure [as 别名]
# 或者: from pymatgen.core.Structure import copy [as 别名]
def test_supercell_subsets(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True, allow_subset=True,
supercell_size='volume')
sm_no_s = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True, allow_subset=False,
supercell_size='volume')
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7,.4,.5],[0,0,0.1],[0,0,0.2]])
s1.make_supercell([2,1,1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0.1,-0.95],[0,0.1,0],[-.7,.5,.375]])
shuffle = [0,2,1,3,4,5]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test when s1 is exact supercell of s2
result = sm.get_s2_like_s1(s1, s2)
for a, b in zip(s1, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2))
self.assertTrue(sm.fit(s2, s1))
self.assertTrue(sm_no_s.fit(s1, s2))
self.assertTrue(sm_no_s.fit(s2, s1))
rms = (0.048604032430991401, 0.059527539448807391)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, s1), rms))
#test when the supercell is a subset of s2
subset_supercell = s1.copy()
del subset_supercell[0]
result = sm.get_s2_like_s1(subset_supercell, s2)
self.assertEqual(len(result), 6)
for a, b in zip(subset_supercell, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(subset_supercell, s2))
self.assertTrue(sm.fit(s2, subset_supercell))
self.assertFalse(sm_no_s.fit(subset_supercell, s2))
self.assertFalse(sm_no_s.fit(s2, subset_supercell))
rms = (0.053243049896333279, 0.059527539448807336)
self.assertTrue(np.allclose(sm.get_rms_dist(subset_supercell, s2), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, subset_supercell), rms))
#test when s2 (once made a supercell) is a subset of s1
s2_missing_site = s2.copy()
del s2_missing_site[1]
result = sm.get_s2_like_s1(s1, s2_missing_site)
for a, b in zip((s1[i] for i in (0, 2, 4, 5)), result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2_missing_site))
self.assertTrue(sm.fit(s2_missing_site, s1))
self.assertFalse(sm_no_s.fit(s1, s2_missing_site))
self.assertFalse(sm_no_s.fit(s2_missing_site, s1))
rms = (0.029763769724403633, 0.029763769724403987)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2_missing_site), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2_missing_site, s1), rms))示例2: CollinearMagneticStructureAnalyzerTest
# 需要导入模块: from pymatgen.core import Structure [as 别名]
# 或者: from pymatgen.core.Structure import copy [as 别名]
#.........这里部分代码省略.........
mode = "replace_all"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode,
make_primitive=False)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 5, 0, 0])
mode = "replace_all_if_undefined"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 0])
mode = "normalize"
msa = CollinearMagneticStructureAnalyzer(msa.structure,
overwrite_magmom_mode='normalize')
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [1, 0])
def test_get_ferromagnetic_structure(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode="replace_all_if_undefined")
s1 = msa.get_ferromagnetic_structure()
s1_magmoms = [float(m) for m in s1.site_properties['magmom']]
s1_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s1_magmoms, s1_magmoms_ref)
msa2 = CollinearMagneticStructureAnalyzer(self.NiO_AFM_111,
overwrite_magmom_mode="replace_all_if_undefined")
s2 = msa.get_ferromagnetic_structure(make_primitive=False)
s2_magmoms = [float(m) for m in s2.site_properties['magmom']]
s2_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s2_magmoms, s2_magmoms_ref)
s2_prim = msa.get_ferromagnetic_structure(make_primitive=True)
self.assertTrue(CollinearMagneticStructureAnalyzer(s1).matches_ordering(s2_prim))
def test_magnetic_properties(self):
msa = CollinearMagneticStructureAnalyzer(self.GdB4)
self.assertFalse(msa.is_collinear)
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertFalse(msa.is_magnetic)
self.Fe.add_site_property('magmom', [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertTrue(msa.is_magnetic)
self.assertTrue(msa.is_collinear)
self.assertEqual(msa.ordering, Ordering.FM)
msa = CollinearMagneticStructureAnalyzer(self.NiO, make_primitive=False,
overwrite_magmom_mode="replace_all_if_undefined")
self.assertEqual(msa.number_of_magnetic_sites, 4)
self.assertEqual(msa.number_of_unique_magnetic_sites(), 1)
self.assertEqual(msa.types_of_magnetic_specie, [Element('Ni')])
self.assertEqual(msa.get_exchange_group_info(), ('Fm-3m', 225))
def test_str(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_001)
ref_msa_str = """Structure Summary
Lattice
abc : 2.948635277547903 4.17 2.948635277547903
angles : 90.0 90.0 90.0
volume : 36.2558565
A : 2.085 2.085 0.0
B : 0.0 0.0 -4.17
C : -2.085 2.085 0.0
Magmoms Sites
+5.00 PeriodicSite: Ni (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: O (0.0000, 0.0000, -2.0850) [0.0000, 0.5000, 0.0000]
PeriodicSite: O (0.0000, 2.0850, 0.0000) [0.5000, 0.0000, 0.5000]
-5.00 PeriodicSite: Ni (0.0000, 2.0850, -2.0850) [0.5000, 0.5000, 0.5000]"""
# just compare lines form 'Magmoms Sites',
# since lattice param string can vary based on machine precision
self.assertEqual("\n".join(str(msa).split("\n")[-5:-1]),
"\n".join(ref_msa_str.split("\n")[-5:-1]))
def test_round_magmoms(self):
struct = self.NiO_AFM_001.copy()
struct.add_site_property('magmom', [-5.0143, -5.02, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
self.assertTrue(np.allclose(msa.magmoms, [-5.0171, -5.0171, 0.1465, 0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'], 5.0171)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['O'], 0.1465)
struct.add_site_property('magmom', [-5.0143, 4.5, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
self.assertTrue(np.allclose(msa.magmoms, [-5.0143, 4.5, 0.1465, 0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'][0], 4.5)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'][1], 5.0143)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['O'], 0.1465)