本文整理汇总了Python中pymatgen.entries.compatibility.AqueousCorrection类的典型用法代码示例。如果您正苦于以下问题：Python AqueousCorrection类的具体用法？Python AqueousCorrection怎么用？Python AqueousCorrection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AqueousCorrection类的7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: AqueousCorrectionTest
class AqueousCorrectionTest(unittest.TestCase):
def setUp(self):
self.corr = AqueousCorrection("MIT")
def test_compound_energy(self):
entry = ComputedEntry(Composition("H2O"), -16)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -15.10057, 4)
entry = ComputedEntry(Composition("H2O"), -24)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -15.10057, 4)
entry = ComputedEntry(Composition("Cl"), -24)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -24.344373, 4)示例2: AqueousCorrectionTest
class AqueousCorrectionTest(unittest.TestCase):
def setUp(self):
module_dir = os.path.dirname(os.path.abspath(__file__))
fp = os.path.join(module_dir, os.path.pardir, "MITCompatibility.yaml")
self.corr = AqueousCorrection(fp)
def test_compound_energy(self):
O2_entry = self.corr.correct_entry(ComputedEntry(Composition("O2"),
-4.9355 * 2))
H2_entry = self.corr.correct_entry(ComputedEntry(Composition("H2"), 3))
H2O_entry = self.corr.correct_entry(ComputedEntry(Composition("H2O"), 3))
H2O_formation_energy = H2O_entry.energy - (H2_entry.energy +
O2_entry.energy / 2.0)
self.assertAlmostEqual(H2O_formation_energy, -2.46, 2)
entry = ComputedEntry(Composition("H2O"), -16)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -14.916, 4)
entry = ComputedEntry(Composition("H2O"), -24)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -14.916, 4)
entry = ComputedEntry(Composition("Cl"), -24)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -24.344373, 4)示例3: AqueousCorrectionTest
class AqueousCorrectionTest(unittest.TestCase):
def setUp(self):
self.corr = AqueousCorrection("MIT")
def test_compound_energy(self):
O2_entry = self.corr.correct_entry(ComputedEntry(Composition("O2"),
-4.9355 * 2))
H2_entry = self.corr.correct_entry(ComputedEntry(Composition("H2"), 3))
H2O_entry = self.corr.correct_entry(ComputedEntry(Composition("H2O"), 3))
H2O_formation_energy = H2O_entry.energy - (H2_entry.energy +
O2_entry.energy / 2.0)
self.assertAlmostEqual(H2O_formation_energy, -2.46, 2)
entry = ComputedEntry(Composition("H2O"), -16)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -14.916, 4)
entry = ComputedEntry(Composition("H2O"), -24)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -14.916, 4)
entry = ComputedEntry(Composition("Cl"), -24)
entry = self.corr.correct_entry(entry)
self.assertAlmostEqual(entry.energy, -24.344373, 4)示例4: setUp
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)示例5: 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))示例6: setUp
def setUp(self):
self.corr = AqueousCorrection("MIT")示例7: 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))