本文整理汇总了Python中pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation.apply_transformation方法的典型用法代码示例。如果您正苦于以下问题：Python EnumerateStructureTransformation.apply_transformation方法的具体用法？Python EnumerateStructureTransformation.apply_transformation怎么用？Python EnumerateStructureTransformation.apply_transformation使用的例子？那么, 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.transformations.advanced_transformations.EnumerateStructureTransformation的用法示例。
在下文中一共展示了EnumerateStructureTransformation.apply_transformation方法的5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_apply_transformation
# 需要导入模块: from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation [as 别名]
# 或者: from pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation import apply_transformation [as 别名]
def test_apply_transformation(self):
enum_trans = EnumerateStructureTransformation(refine_structure=True)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
struct = p.structure
expected_ans = [1, 3, 1]
for i, frac in enumerate([0.25, 0.5, 0.75]):
trans = SubstitutionTransformation({'Fe': {'Fe': frac}})
s = trans.apply_transformation(struct)
oxitrans = OxidationStateDecorationTransformation({'Li': 1,
'Fe': 2,
'P': 5,
'O': -2})
s = oxitrans.apply_transformation(s)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), expected_ans[i])
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertIn("energy", s)
#make sure it works for non-oxidation state decorated structure
trans = SubstitutionTransformation({'Fe': {'Fe': 0.5}})
s = trans.apply_transformation(struct)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), 3)
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertNotIn("energy", s)示例2: test_max_disordered_sites
# 需要导入模块: from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation [as 别名]
# 或者: from pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation import apply_transformation [as 别名]
def test_max_disordered_sites(self):
l = Lattice.cubic(4)
s_orig = Structure(l, [{"Li": 0.2, "Na": 0.2, "K": 0.6}, {"O": 1}],
[[0, 0, 0], [0.5, 0.5, 0.5]])
est = EnumerateStructureTransformation(max_cell_size=None,
max_disordered_sites=5)
s = est.apply_transformation(s_orig)
self.assertEqual(len(s), 8)示例3: test_max_disordered_sites
# 需要导入模块: from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation [as 别名]
# 或者: from pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation import apply_transformation [as 别名]
def test_max_disordered_sites(self):
l = Lattice.cubic(4)
s_orig = Structure(l, [{"Li": 0.2, "Na": 0.2, "K": 0.6}, {"O": 1}],
[[0, 0, 0], [0.5, 0.5, 0.5]])
est = EnumerateStructureTransformation(max_cell_size=None,
max_disordered_sites=5)
dd = est.apply_transformation(s_orig, return_ranked_list=100)
self.assertEqual(len(dd), 9)
for d in dd:
self.assertEqual(len(d["structure"]), 10)示例4: enumerate_ordering
# 需要导入模块: from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation [as 别名]
# 或者: from pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation import apply_transformation [as 别名]
def enumerate_ordering(self, structure):
# Generate the disordered structure first.
s = Structure.from_sites(structure.sites)
for indices, fraction in zip(self._indices, self._fractions):
for ind in indices:
new_sp = {sp: occu * fraction for sp, occu in structure[ind].species_and_occu.items()}
s[ind] = new_sp
# Perform enumeration
from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation
trans = EnumerateStructureTransformation()
return trans.apply_transformation(s, 10000)示例5: enumerate_ordering
# 需要导入模块: from pymatgen.transformations.advanced_transformations import EnumerateStructureTransformation [as 别名]
# 或者: from pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation import apply_transformation [as 别名]
def enumerate_ordering(self, structure):
# Generate the disordered structure first.
editor = StructureEditor(structure)
for indices, fraction in zip(self._indices, self._fractions):
for ind in indices:
new_sp = {sp: occu * fraction
for sp, occu
in structure[ind].species_and_occu.items()}
editor.replace_site(ind, new_sp)
mod_s = editor.modified_structure
# Perform enumeration
from pymatgen.transformations.advanced_transformations import \
EnumerateStructureTransformation
trans = EnumerateStructureTransformation()
return trans.apply_transformation(mod_s, 10000)