本文整理汇总了Python中pymatgen.alchemy.materials.TransformedStructure.to_snl方法的典型用法代码示例。如果您正苦于以下问题：Python TransformedStructure.to_snl方法的具体用法？Python TransformedStructure.to_snl怎么用？Python TransformedStructure.to_snl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.alchemy.materials.TransformedStructure的用法示例。
在下文中一共展示了TransformedStructure.to_snl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: TransformedStructureTest
# 需要导入模块: from pymatgen.alchemy.materials import TransformedStructure [as 别名]
# 或者: from pymatgen.alchemy.materials.TransformedStructure import to_snl [as 别名]
#.........这里部分代码省略.........
"label": "Fe",
},
{
"occu": 1,
"abc": [0.5218619395656168, 0.25000080611787734, 0.7814492408373795],
"xyz": [2.48101, 1.52258, 8.17597],
"species": [{"occu": 1, "element": "Fe"}],
"label": "Fe",
},
],
}
structure = Structure.from_dict(structure_dict)
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual("NaMnPO4", self.trans.final_structure.composition.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(SupercellTransformation.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation("Si4+", 0.5, algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE), 5
)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(["O2-"], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
SETTINGS["VASP_PSP_DIR"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
)
potcar = self.trans.get_vasp_input(MPRelaxSet)["POTCAR"]
self.assertEqual("Na_pv\nFe_pv\nP\nO", "\n".join([p.symbol for p in potcar]))
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual("NaFePO4", self.trans.final_structure.composition.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(test_dir, "transformations.json"), "r"))
d["other_parameters"] = {"tags": ["test"]}
ts = TransformedStructure.from_dict(d)
ts.other_parameters["author"] = "Will"
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4", ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {"author": "Will", "tags": ["test"]})
def test_undo_and_redo_last_change(self):
trans = [SubstitutionTransformation({"Li": "Na"}), SubstitutionTransformation({"Fe": "Mn"})]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4", ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4", ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
# Make sure that this works with filters.
f3 = ContainsSpecieFilter(["O2-"], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter("author", "will")
d = self.trans.as_dict()
self.assertIn("last_modified", d)
self.assertIn("history", d)
self.assertIn("version", d)
self.assertIn("author", d["other_parameters"])
self.assertEqual(Structure.from_dict(d).formula, "Na4 Fe4 P4 O16")
def test_snl(self):
self.trans.set_parameter("author", "will")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([("will", "[email protected]")])
self.assertEqual(len(w), 1, "Warning not raised on type conversion " "with other_parameters")
ts = TransformedStructure.from_snl(snl)
self.assertEqual(ts.history[-1]["@class"], "SubstitutionTransformation")
h = ("testname", "testURL", {"test": "testing"})
snl = StructureNL(ts.final_structure, [("will", "[email protected]")], history=[h])
snl = TransformedStructure.from_snl(snl).to_snl([("notwill", "[email protected]")])
self.assertEqual(snl.history, [h])
self.assertEqual(snl.authors, [("notwill", "[email protected]")])示例2: TransformedStructureTest
# 需要导入模块: from pymatgen.alchemy.materials import TransformedStructure [as 别名]
# 或者: from pymatgen.alchemy.materials.TransformedStructure import to_snl [as 别名]
class TransformedStructureTest(PymatgenTest):
def setUp(self):
structure = PymatgenTest.get_structure("LiFePO4")
self.structure = structure
trans = [SubstitutionTransformation({"Li": "Na"})]
self.trans = TransformedStructure(structure, trans)
def test_append_transformation(self):
t = SubstitutionTransformation({"Fe": "Mn"})
self.trans.append_transformation(t)
self.assertEqual("NaMnPO4",
self.trans.final_structure.composition
.reduced_formula)
self.assertEqual(len(self.trans.structures), 3)
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = [[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(lattice, ["Si4+", "Si4+"], coords)
ts = TransformedStructure(struct, [])
ts.append_transformation(SupercellTransformation
.from_scaling_factors(2, 1, 1))
alt = ts.append_transformation(
PartialRemoveSpecieTransformation(
'Si4+', 0.5,
algo=PartialRemoveSpecieTransformation.ALGO_COMPLETE), 5)
self.assertEqual(len(alt), 2)
def test_append_filter(self):
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
self.trans.append_filter(f3)
def test_get_vasp_input(self):
SETTINGS["PMG_VASP_PSP_DIR"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..",
"test_files"))
potcar = self.trans.get_vasp_input(MPRelaxSet)['POTCAR']
self.assertEqual("Na_pv\nFe_pv\nP\nO",
"\n".join([p.symbol for p in potcar]))
self.assertEqual(len(self.trans.structures), 2)
def test_final_structure(self):
self.assertEqual("NaFePO4", self.trans.final_structure.composition
.reduced_formula)
def test_from_dict(self):
d = json.load(open(os.path.join(test_dir, 'transformations.json'),
'r'))
d['other_parameters'] = {'tags': ['test']}
ts = TransformedStructure.from_dict(d)
ts.other_parameters['author'] = 'Will'
ts.append_transformation(SubstitutionTransformation({"Fe": "Mn"}))
self.assertEqual("MnPO4",
ts.final_structure.composition.reduced_formula)
self.assertEqual(ts.other_parameters, {'author': 'Will',
'tags': ['test']})
def test_undo_and_redo_last_change(self):
trans = [SubstitutionTransformation({"Li": "Na"}),
SubstitutionTransformation({"Fe": "Mn"})]
ts = TransformedStructure(self.structure, trans)
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.undo_last_change()
self.assertEqual("LiFePO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.undo_last_change)
ts.redo_next_change()
self.assertEqual("NaFePO4",
ts.final_structure.composition.reduced_formula)
ts.redo_next_change()
self.assertEqual("NaMnPO4",
ts.final_structure.composition.reduced_formula)
self.assertRaises(IndexError, ts.redo_next_change)
#Make sure that this works with filters.
f3 = ContainsSpecieFilter(['O2-'], strict_compare=True, AND=False)
ts.append_filter(f3)
ts.undo_last_change()
ts.redo_next_change()
def test_as_dict(self):
self.trans.set_parameter('author', 'will')
d = self.trans.as_dict()
self.assertIn('last_modified', d)
self.assertIn('history', d)
self.assertIn('version', d)
self.assertIn('author', d['other_parameters'])
self.assertEqual(Structure.from_dict(d).formula, 'Na4 Fe4 P4 O16')
def test_snl(self):
self.trans.set_parameter('author', 'will')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
snl = self.trans.to_snl([('will', '[email protected]')])
#.........这里部分代码省略.........