本文整理汇总了Python中pymatgen.entries.computed_entries.ComputedStructureEntry.from_dict方法的典型用法代码示例。如果您正苦于以下问题：Python ComputedStructureEntry.from_dict方法的具体用法？Python ComputedStructureEntry.from_dict怎么用？Python ComputedStructureEntry.from_dict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.entries.computed_entries.ComputedStructureEntry的用法示例。
在下文中一共展示了ComputedStructureEntry.from_dict方法的6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_properties
# 需要导入模块: from pymatgen.entries.computed_entries import ComputedStructureEntry [as 别名]
# 或者: from pymatgen.entries.computed_entries.ComputedStructureEntry import from_dict [as 别名]
def test_properties(self):
# Test cases for getting adsorption related quantities for a 1/4
# monolalyer adsorption of O on the low MMI surfaces of Pt, Ni and Rh
for el in self.metals_O_entry_dict.keys():
el_ucell = ComputedStructureEntry.from_dict(self.ucell_entries[el])
for hkl in self.metals_O_entry_dict[el].keys():
for clean in self.metals_O_entry_dict[el][hkl].keys():
for ads in self.metals_O_entry_dict[el][hkl][clean]:
ml = ads.get_unit_primitive_area
self.assertAlmostEqual(ml, 4, 2)
self.assertAlmostEqual(ads.get_monolayer, 1/4, 2)
Nads = ads.Nads_in_slab
self.assertEqual(Nads, 1)
self.assertEqual(ads.Nsurfs_ads_in_slab, 1)
# Determine the correct binding energy
with open(os.path.join(get_path(""),
'isolated_O_entry.txt')) as isolated_O_entry:
isolated_O_entry = json.loads(isolated_O_entry.read())
O = ComputedStructureEntry.from_dict(isolated_O_entry)
gbind = (ads.energy - ml*clean.energy)/Nads - O.energy_per_atom
self.assertEqual(gbind, ads.gibbs_binding_energy())
# Determine the correction Gibbs adsorption energy
eads = Nads * gbind
self.assertEqual(eads, ads.gibbs_binding_energy(eads=True))
se = ads.surface_energy(el_ucell)
self.assertAlmostEqual(se.as_coefficients_dict()[Symbol("delu_O")],
(-1/2)*ads.surface_area**(-1))示例2: load_O_adsorption
# 需要导入模块: from pymatgen.entries.computed_entries import ComputedStructureEntry [as 别名]
# 或者: from pymatgen.entries.computed_entries.ComputedStructureEntry import from_dict [as 别名]
def load_O_adsorption():
# Loads the dictionary for clean and O adsorbed Rh, Pt, and Ni entries
# Load the adsorbate as an entry
with open(os.path.join(get_path(""),
'isolated_O_entry.txt')) as isolated_O_entry:
isolated_O_entry = json.loads(isolated_O_entry.read())
O = ComputedStructureEntry.from_dict(isolated_O_entry)
# entry_dict for the adsorption case, O adsorption on Ni, Rh and Pt
metals_O_entry_dict = {"Ni": {(1, 1, 1): {}, (1, 0, 0): {}},
"Pt": {(1, 1, 1): {}},
"Rh": {(1, 0, 0): {}}
}
with open(os.path.join(get_path(""), "csentries_slabs.json")) as entries:
entries = json.loads(entries.read())
for k in entries.keys():
entry = ComputedStructureEntry.from_dict(entries[k])
for el in metals_O_entry_dict.keys():
if el in k:
if "111" in k:
clean = SlabEntry(entry.structure, entry.energy,
(1,1,1), label=k+"_clean")
metals_O_entry_dict[el][(1, 1, 1)][clean] = []
if "110" in k:
clean = SlabEntry(entry.structure, entry.energy,
(1, 1, 0), label=k + "_clean")
metals_O_entry_dict[el][(1, 1, 0)][clean] = []
if "100" in k:
clean = SlabEntry(entry.structure, entry.energy,
(1,0,0), label=k+"_clean")
metals_O_entry_dict[el][(1, 0, 0)][clean] = []
with open(os.path.join(get_path(""), "csentries_o_ads.json")) as entries:
entries = json.loads(entries.read())
for k in entries.keys():
entry = ComputedStructureEntry.from_dict(entries[k])
for el in metals_O_entry_dict.keys():
if el in k:
if "111" in k:
clean = list(metals_O_entry_dict[el][(1, 1, 1)].keys())[0]
ads = SlabEntry(entry.structure, entry.energy, (1,1,1),
label=k+"_O", adsorbates=[O], clean_entry=clean)
metals_O_entry_dict[el][(1, 1, 1)][clean] = [ads]
if "110" in k:
clean = list(metals_O_entry_dict[el][(1, 1, 0)].keys())[0]
ads = SlabEntry(entry.structure, entry.energy, (1,1,0),
label=k+"_O", adsorbates=[O], clean_entry=clean)
metals_O_entry_dict[el][(1, 1, 0)][clean] = [ads]
if "100" in k:
clean = list(metals_O_entry_dict[el][(1, 0, 0)].keys())[0]
ads = SlabEntry(entry.structure, entry.energy, (1,0,0),
label=k+"_O", adsorbates=[O], clean_entry=clean)
metals_O_entry_dict[el][(1, 0, 0)][clean] = [ads]
return metals_O_entry_dict示例3: get_entry_dict
# 需要导入模块: from pymatgen.entries.computed_entries import ComputedStructureEntry [as 别名]
# 或者: from pymatgen.entries.computed_entries.ComputedStructureEntry import from_dict [as 别名]
def get_entry_dict(filename):
# helper to generate an entry_dict
entry_dict = {}
with open(filename) as entries:
entries = json.loads(entries.read())
for k in entries.keys():
n = k[25:]
miller_index = []
for i, s in enumerate(n):
if s == "_":
break
if s == "-":
continue
t = int(s)
if n[i - 1] == "-":
t *= -1
miller_index.append(t)
hkl = tuple(miller_index)
if hkl not in entry_dict.keys():
entry_dict[hkl] = {}
entry = ComputedStructureEntry.from_dict(entries[k])
entry_dict[hkl][SlabEntry(entry.structure, entry.energy, hkl, label=k)] = []
return entry_dict示例4: setUp
# 需要导入模块: from pymatgen.entries.computed_entries import ComputedStructureEntry [as 别名]
# 或者: from pymatgen.entries.computed_entries.ComputedStructureEntry import from_dict [as 别名]
def setUp(self):
# Load all entries
La_hcp_entry_dict = get_entry_dict(os.path.join(get_path(""),
"La_hcp_entries.txt"))
La_fcc_entry_dict = get_entry_dict(os.path.join(get_path(""),
"La_fcc_entries.txt"))
with open(os.path.join(get_path(""), 'ucell_entries.txt')) as ucell_entries:
ucell_entries = json.loads(ucell_entries.read())
La_hcp_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["La_hcp"])
La_fcc_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["La_fcc"])
# Set up the NanoscaleStabilityClass
self.La_hcp_analyzer = SurfaceEnergyPlotter(La_hcp_entry_dict,
La_hcp_ucell_entry)
self.La_fcc_analyzer = SurfaceEnergyPlotter(La_fcc_entry_dict,
La_fcc_ucell_entry)
self.nanoscale_stability = NanoscaleStability([self.La_fcc_analyzer,
self.La_hcp_analyzer])示例5: test_to_from_dict
# 需要导入模块: from pymatgen.entries.computed_entries import ComputedStructureEntry [as 别名]
# 或者: from pymatgen.entries.computed_entries.ComputedStructureEntry import from_dict [as 别名]
def test_to_from_dict(self):
d = self.entry.to_dict
e = ComputedStructureEntry.from_dict(d)
self.assertAlmostEqual(e.energy, -269.38319884)示例6: convert
# 需要导入模块: from pymatgen.entries.computed_entries import ComputedStructureEntry [as 别名]
# 或者: from pymatgen.entries.computed_entries.ComputedStructureEntry import from_dict [as 别名]
def convert(self, d):
if 'structure' in d:
return ComputedStructureEntry.from_dict(d)
else:
return ComputedEntry.from_dict(d)