本文整理汇总了Python中pymatgen.entries.compatibility.MITCompatibility类的典型用法代码示例。如果您正苦于以下问题：Python MITCompatibility类的具体用法？Python MITCompatibility怎么用？Python MITCompatibility使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了MITCompatibility类的17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，您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: test_requires_hubbard
def test_requires_hubbard(self):
compat = MITCompatibility()
self.assertTrue(compat.requires_hubbard("Fe2O3"))
self.assertTrue(compat.requires_hubbard("FeSO4"))
self.assertTrue(compat.requires_hubbard("FeS2"))
self.assertFalse(compat.requires_hubbard("Li2O"))
self.assertTrue(compat.requires_hubbard("FeOF"))
开发者ID:isayev，项目名称:pymatgen，代码行数:7，代码来源:test_compatibility.py
示例2: test_same_potcar_symbol
def test_same_potcar_symbol(self):
# Same symbol different hash thus a different potcar
#Correct Hash Correct Symbol
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': '9530da8244e4dac17580869b4adab115'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
#Incorrect Hash Correct Symbol
entry2 = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'DifferentHash'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'}]})
compat = MITCompatibility()
self.assertEqual(len(compat.process_entries([entry, entry2])), 2)
self.assertEqual(len(self.compat.process_entries([entry, entry2])), 1)
开发者ID:georgeyumnam，项目名称:pymatgen，代码行数:26，代码来源:test_compatibility.py
示例3: setUp
def setUp(self):
self.compat = MITCompatibility(check_potcar_hash=True)
self.ggacompat = MITCompatibility("GGA", check_potcar_hash=True)
self.entry_O = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7af704ddff29da5354831c4609f1cbc5'}]})
self.entry_F = ComputedEntry(
'FeF3', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'F': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE F 08Apr2002',
'hash': '9b0fd56137ce81cfee1eb63a8901c66c'}]})
self.entry_S = ComputedEntry(
'FeS2', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 1.9, 'S': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE S 08Apr2002',
'hash': 'f7f8e4a74a6cbb8d63e41f4373b54df2'}]})
开发者ID:ATNDiaye，项目名称:pymatgen，代码行数:31，代码来源:test_compatibility.py
示例4: TestMITAqueousCompatibility
class TestMITAqueousCompatibility(unittest.TestCase):
def setUp(self):
self.compat = MITCompatibility()
self.aqcompat = MITAqueousCompatibility()
module_dir = os.path.dirname(os.path.abspath(__file__))
fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
self.aqcorr = AqueousCorrection(fp)
def test_aqueous_compat(self):
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
lioh_entry_compat = self.compat.process_entry(lioh_entry)
lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)
def test_potcar_doenst_match_structure(self):
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
self.assertIsNone(self.compat.process_entry(lioh_entry))
开发者ID:image-tester，项目名称:pymatgen，代码行数:56，代码来源:test_compatibility.py
示例5: test_potcar_spec_is_none
def test_potcar_spec_is_none(self):
compat = MITCompatibility(check_potcar_hash=True)
entry = ComputedEntry(
'Li2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [None, None]})
self.assertIsNone(compat.process_entry(entry))
开发者ID:georgeyumnam，项目名称:pymatgen，代码行数:11，代码来源:test_compatibility.py
示例6: test_potcar_doenst_match_structure
def test_potcar_doenst_match_structure(self):
compat = MITCompatibility()
entry = ComputedEntry(
'Li2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
开发者ID:image-tester，项目名称:pymatgen，代码行数:12，代码来源:test_compatibility.py
示例7: test_revert_to_symbols
def test_revert_to_symbols(self):
#Test that you can revert to potcar_symbols if potcar_spec is not present
compat = MITCompatibility()
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000', 'PAW_PBE O 08Apr2002']})
self.assertIsNotNone(compat.process_entry(entry))
#raise if check_potcar_hash is set
self.assertRaises(ValueError, self.compat.process_entry, entry)
开发者ID:georgeyumnam，项目名称:pymatgen，代码行数:13，代码来源:test_compatibility.py
示例8: test_get_explanation_dict
def test_get_explanation_dict(self):
compat = MITCompatibility(check_potcar_hash=False)
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True, 'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel': 'PAW_PBE Fe 06Sep2000',
'hash': '994537de5c4122b7f1b77fb604476db4'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': "7a25bc5b9a5393f46600a4939d357982"}]})
d = compat.get_explanation_dict(entry)
self.assertEqual('MITRelaxSet Potcar Correction', d["corrections"][0][
"name"])
开发者ID:fraricci，项目名称:pymatgen，代码行数:13，代码来源:test_compatibility.py
示例9: test_assimilate
def test_assimilate(self):
entry = self.drone.assimilate(self.test_dir)
for p in ["hubbards", "is_hubbard", "potcar_symbols", "run_type"]:
self.assertIn(p, entry.parameters)
self.assertAlmostEqual(entry.data["efermi"], 1.8301027)
self.assertEqual(entry.composition.reduced_formula, "LiFe4(PO4)4")
self.assertAlmostEqual(entry.energy, -269.38319884)
entry = self.structure_drone.assimilate(self.test_dir)
self.assertEqual(entry.composition.reduced_formula, "LiFe4(PO4)4")
self.assertAlmostEqual(entry.energy, -269.38319884)
self.assertIsInstance(entry, ComputedStructureEntry)
self.assertIsNotNone(entry.structure)
compat = MITCompatibility()
self.assertIsNone(compat.process_entry(entry))
开发者ID:isayev，项目名称:pymatgen，代码行数:14，代码来源:test_hive.py
示例10: test_potcar_doenst_match_structure
def test_potcar_doenst_match_structure(self):
compat = MITCompatibility()
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
self.assertIsNone(compat.process_entry(lioh_entry))
开发者ID:georgeyumnam，项目名称:pymatgen，代码行数:23，代码来源:test_compatibility.py
示例11: test_process_entry
def test_process_entry(self):
compat = MITCompatibility()
#Correct parameters
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNotNone(compat.process_entry(entry))
self.assertAlmostEqual(compat.process_entry(entry).correction,
- 1.723 * 2 -0.66975*3)
entry = ComputedEntry(
'FeF3', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'F': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
'PAW_PBE F 08Apr2002']})
self.assertIsNotNone(compat.process_entry(entry))
#Check actual correction
self.assertAlmostEqual(compat.process_entry(entry).correction, -1.723)
#MIT should not have a U for sulfides
entry = ComputedEntry(
'FeS2', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 1.9, 'S': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
'PAW_PBE S 08Apr2002']})
self.assertIsNotNone(compat.process_entry(entry))
self.assertAlmostEqual(compat.process_entry(entry).correction, -1.113)
#Wrong U value
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 5.2, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#GGA run
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols': ['PAW_PBE Fe 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#Wrong psp
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_symbols': ['PAW_PBE Fe_pv 06Sep2000',
'PAW_PBE O 08Apr2002']})
self.assertIsNone(compat.process_entry(entry))
#Testing processing of elements.
entry = ComputedEntry(
'O', -1, 0.0,
parameters={'is_hubbard': False, 'hubbards': {},
'potcar_symbols': ['PAW_PBE O 08Apr2002'],
'run_type': 'GGA'})
entry = compat.process_entry(entry)
self.assertAlmostEqual(entry.energy, -1)
开发者ID:image-tester，项目名称:pymatgen，代码行数:77，代码来源:test_compatibility.py
示例12: TestMITAqueousCompatibility
class TestMITAqueousCompatibility(unittest.TestCase):
def setUp(self):
self.compat = MITCompatibility(check_potcar_hash=True)
self.aqcompat = MITAqueousCompatibility(check_potcar_hash=True)
module_dir = os.path.dirname(os.path.abspath(__file__))
fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
self.aqcorr = AqueousCorrection(fp)
def test_aqueous_compat(self):
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Li 17Jan2003',
'hash': '9658a0ffb28da97ee7b36709966a0d1c'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7af704ddff29da5354831c4609f1cbc5'},
{"titel": 'PAW_PBE H 15Jun2001',
'hash': "57732e53d8a424e5b3721d0277f14ef0"}]})
lioh_entry_compat = self.compat.process_entry(lioh_entry)
lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)
def test_potcar_doenst_match_structure(self):
compat = MITCompatibility()
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
self.assertIsNone(compat.process_entry(lioh_entry))
开发者ID:ATNDiaye，项目名称:pymatgen，代码行数:61，代码来源:test_compatibility.py
示例13: MITCompatibilityTest
class MITCompatibilityTest(unittest.TestCase):
def setUp(self):
self.compat = MITCompatibility(check_potcar_hash=True)
self.ggacompat = MITCompatibility("GGA", check_potcar_hash=True)
self.entry_O = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7af704ddff29da5354831c4609f1cbc5'}]})
self.entry_F = ComputedEntry(
'FeF3', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 4.0, 'F': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE F 08Apr2002',
'hash': '9b0fd56137ce81cfee1eb63a8901c66c'}]})
self.entry_S = ComputedEntry(
'FeS2', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 1.9, 'S': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE S 08Apr2002',
'hash': 'f7f8e4a74a6cbb8d63e41f4373b54df2'}]})
def test_process_entry(self):
#Correct parameters
self.assertIsNotNone(self.compat.process_entry(self.entry_O))
self.assertIsNotNone(self.compat.process_entry(self.entry_F))
def test_correction_value(self):
#Check actual correction
self.assertAlmostEqual(self.compat.process_entry(self.entry_O).correction,
- 1.723 * 2 -0.66975*3)
self.assertAlmostEqual(self.compat.process_entry(self.entry_F).correction, -1.723)
self.assertAlmostEqual(self.compat.process_entry(self.entry_S).correction, -1.113)
def test_U_value(self):
# MIT should have a U value for Fe containing sulfides
self.assertIsNotNone(self.compat.process_entry(self.entry_S))
# MIT should not have a U value for Ni containing sulfides
entry = ComputedEntry(
'NiS2', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Ni': 1.9, 'S': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Ni 06Sep2000',
'hash': '6aa314a5314ececec9e6f32bd9a47a67'},
{'titel': 'PAW_PBE S 08Apr2002',
'hash': 'f7f8e4a74a6cbb8d63e41f4373b54df2'}]})
self.assertIsNone(self.compat.process_entry(entry))
entry = ComputedEntry(
'NiS2', -2, 0.0,
parameters={'is_hubbard': True,
'hubbards': None,
'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Ni 06Sep2000',
'hash': '6aa314a5314ececec9e6f32bd9a47a67'},
{'titel': 'PAW_PBE S 08Apr2002',
'hash': 'f7f8e4a74a6cbb8d63e41f4373b54df2'}]})
self.assertIsNotNone(self.ggacompat.process_entry(entry))
def test_wrong_U_value(self):
#Wrong U value
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': True,
'hubbards': {'Fe': 5.2, 'O': 0},
'run_type': 'GGA+U',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7af704ddff29da5354831c4609f1cbc5'}]})
self.assertIsNone(self.compat.process_entry(entry))
#GGA run
entry = ComputedEntry(
'Fe2O3', -1, 0.0,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Fe 06Sep2000',
'hash': 'e0051a21ce51eb34a52e9153c17aa32d'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7af704ddff29da5354831c4609f1cbc5'}]})
self.assertIsNone(self.compat.process_entry(entry))
#.........这里部分代码省略.........
开发者ID:ATNDiaye，项目名称:pymatgen，代码行数:101，代码来源:test_compatibility.py
示例14: OxideTypeCorrectionNoPeroxideCorrTest
class OxideTypeCorrectionNoPeroxideCorrTest(unittest.TestCase):
def setUp(self):
self.compat = MITCompatibility(correct_peroxide=False)
def test_oxide_energy_corr(self):
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_li, el_o]
latt = Lattice.from_parameters(3.278, 3.278, 3.278,
60, 60, 60)
coords = [[0.25, 0.25, 0.25],
[0.75, 0.75, 0.75],
[0.0, 0.0, 0.0]]
struct = Structure(latt, elts, coords)
li2o_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
li2o_entry_corrected = self.compat.process_entry(li2o_entry)
self.assertAlmostEqual(li2o_entry_corrected.energy, -3.0 -0.66975, 4)
def test_peroxide_energy_corr(self):
latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884, 89.999674, 60.000510)
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
coords = [[0.666656, 0.666705, 0.750001],
[0.333342, 0.333378, 0.250001],
[0.000001, 0.000041, 0.500001],
[0.000001, 0.000021, 0.000001],
[0.333347, 0.333332, 0.649191],
[0.333322, 0.333353, 0.850803],
[0.666666, 0.666686, 0.350813],
[0.666665, 0.666684, 0.149189]]
struct = Structure(latt, elts, coords)
li2o2_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
li2o2_entry_corrected = self.compat.process_entry(li2o2_entry)
self.assertRaises(AssertionError, self.assertAlmostEqual,
*(li2o2_entry_corrected.energy, -3 - 0.44317 * 4, 4))
self.assertAlmostEqual(li2o2_entry_corrected.energy, -3 - 0.66975 * 4, 4)
def test_ozonide(self):
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_o, el_o, el_o]
latt = Lattice.from_parameters(3.999911, 3.999911, 3.999911,
133.847504, 102.228244, 95.477342)
coords = [[0.513004, 0.513004, 1.000000],
[0.017616, 0.017616, 0.000000],
[0.649993, 0.874790, 0.775203],
[0.099587, 0.874790, 0.224797]]
struct = Structure(latt, elts, coords)
lio3_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
lio3_entry_corrected = self.compat.process_entry(lio3_entry)
self.assertAlmostEqual(lio3_entry_corrected.energy, -3.0 - 3 * 0.66975)
开发者ID:image-tester，项目名称:pymatgen，代码行数:68，代码来源:test_compatibility.py
示例15: OxideTypeCorrectionTest
class OxideTypeCorrectionTest(unittest.TestCase):
def setUp(self):
self.compat = MITCompatibility()
def test_no_struct_compat(self):
lio2_entry_nostruct = ComputedEntry(Composition("Li2O4"), -3,
data={"oxide_type": "superoxide"},
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
lio2_entry_corrected = self.compat.process_entry(lio2_entry_nostruct)
self.assertAlmostEqual(lio2_entry_corrected.energy, -3 - 0.13893*4, 4)
def test_process_entry_superoxide(self):
el_li = Element("Li")
el_o = Element("O")
latt = Lattice([[3.985034, 0.0, 0.0],
[0.0, 4.881506, 0.0],
[0.0, 0.0, 2.959824]])
elts = [el_li, el_li, el_o, el_o, el_o, el_o]
coords = list()
coords.append([0.500000, 0.500000, 0.500000])
coords.append([0.0, 0.0, 0.0])
coords.append([0.632568, 0.085090, 0.500000])
coords.append([0.367432, 0.914910, 0.500000])
coords.append([0.132568, 0.414910, 0.000000])
coords.append([0.867432, 0.585090, 0.000000])
struct = Structure(latt, elts, coords)
lio2_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
lio2_entry_corrected = self.compat.process_entry(lio2_entry)
self.assertAlmostEqual(lio2_entry_corrected.energy, -3 -0.13893*4, 4)
def test_process_entry_peroxide(self):
latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884, 89.999674, 60.000510)
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
coords = [[0.666656, 0.666705, 0.750001],
[0.333342, 0.333378, 0.250001],
[0.000001, 0.000041, 0.500001],
[0.000001, 0.000021, 0.000001],
[0.333347, 0.333332, 0.649191],
[0.333322, 0.333353, 0.850803],
[0.666666, 0.666686, 0.350813],
[0.666665, 0.666684, 0.149189]]
struct = Structure(latt, elts, coords)
li2o2_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
li2o2_entry_corrected = self.compat.process_entry(li2o2_entry)
self.assertAlmostEqual(li2o2_entry_corrected.energy, -3 - 0.44317 * 4, 4)
def test_process_entry_ozonide(self):
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_o, el_o, el_o]
latt = Lattice.from_parameters(3.999911, 3.999911, 3.999911,
133.847504, 102.228244, 95.477342)
coords = [[0.513004, 0.513004, 1.000000],
[0.017616, 0.017616, 0.000000],
[0.649993, 0.874790, 0.775203],
[0.099587, 0.874790, 0.224797]]
struct = Structure(latt, elts, coords)
lio3_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
lio3_entry_corrected = self.compat.process_entry(lio3_entry)
self.assertAlmostEqual(lio3_entry_corrected.energy, -3.0)
def test_process_entry_oxide(self):
el_li = Element("Li")
el_o = Element("O")
elts = [el_li, el_li, el_o]
latt = Lattice.from_parameters(3.278, 3.278, 3.278,
60, 60, 60)
coords = [[0.25, 0.25, 0.25],
[0.75, 0.75, 0.75],
[0.0, 0.0, 0.0]]
struct = Structure(latt, elts, coords)
li2o_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Li 06Sep2000', 'PAW_PBE O 08Apr2002']})
li2o_entry_corrected = self.compat.process_entry(li2o_entry)
#.........这里部分代码省略.........
开发者ID:image-tester，项目名称:pymatgen，代码行数:101，代码来源:test_compatibility.py
示例16: setUp
def setUp(self):
self.compat = MITCompatibility()
开发者ID:image-tester，项目名称:pymatgen，代码行数:2，代码来源:test_compatibility.py
示例17: TestMITAqueousCompatibility
class TestMITAqueousCompatibility(unittest.TestCase):
def setUp(self):
self.compat = MITCompatibility(check_potcar_hash=True)
self.aqcompat = MITAqueousCompatibility(check_potcar_hash=True)
module_dir = os.path.dirname(os.path.abspath(__file__))
fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
self.aqcorr = AqueousCorrection(fp)
def test_aqueous_compat(self):
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_spec': [{'titel':'PAW_PBE Li 17Jan2003',
'hash': '65e83282d1707ec078c1012afbd05be8'},
{'titel': 'PAW_PBE O 08Apr2002',
'hash': '7a25bc5b9a5393f46600a4939d357982'},
{"titel": 'PAW_PBE H 15Jun2001',
'hash': "bb43c666e3d36577264afe07669e9582"}]})
lioh_entry_compat = self.compat.process_entry(lioh_entry)
lioh_entry_compat_aqcorr = self.aqcorr.correct_entry(lioh_entry_compat)
lioh_entry_aqcompat = self.aqcompat.process_entry(lioh_entry)
self.assertAlmostEqual(lioh_entry_compat_aqcorr.energy, lioh_entry_aqcompat.energy, 4)
def test_potcar_doenst_match_structure(self):
compat = MITCompatibility()
el_li = Element("Li")
el_o = Element("O")
el_h = Element("H")
latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
elts = [el_h, el_h, el_li, el_li, el_o, el_o]
coords = [[0.000000, 0.500000, 0.413969],
[0.500000, 0.000000, 0.586031],
[0.000000, 0.000000, 0.000000],
[0.500000, 0.500000, 0.000000],
[0.000000, 0.500000, 0.192672],
[0.500000, 0.000000, 0.807328]]
struct = Structure(latt, elts, coords)
lioh_entry = ComputedStructureEntry(struct, -3,
parameters={'is_hubbard': False,
'hubbards': None,
'run_type': 'GGA',
'potcar_symbols':
['PAW_PBE Fe 17Jan2003', 'PAW_PBE O 08Apr2002', 'PAW_PBE H 15Jun2001']})
self.assertIsNone(compat.process_entry(lioh_entry))
def test_msonable(self):
compat_dict = self.aqcompat.as_dict()
decoder = MontyDecoder()
temp_compat = decoder.process_decoded(compat_dict)
self.assertIsInstance(temp_compat,MITAqueousCompatibility)
def test_dont_error_on_weird_elements(self):
entry = ComputedEntry('AmSi',-1, 0.0,
parameters={
"potcar_spec": [{
"titel": "PAW_PBE Am 08May2007",
"hash": "ed5eebd8a143e35a0c19e9f8a2c42a93"
}, {
"titel": "PAW_PBE Si 05Jan2001",
"hash": "b2b0ea6feb62e7cde209616683b8f7f5"
}]
})
self.assertIsNone(self.compat.process_entry(entry))
开发者ID:ExpHP，项目名称:pymatgen，代码行数:81，代码来源:test_compatibility.py
注：本文中的pymatgen.entries.compatibility.MITCompatibility类示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
客服电话
APP下载
官方微信
请发表评论