def test_get_energy(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0], [1.0, 3.0, 0.00],
[0.00, -2.0, 3.0]])
s = Structure(lattice, [{
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}, {
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}, {
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}, {
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}], coords)
m = EwaldElectrostaticModel()
# large tolerance because scipy constants changed between 0.16.1 and 0.17
self.assertAlmostEqual(m.get_energy(s), -264.66364858,
2) # Result from GULP
s2 = Structure.from_file(os.path.join(test_dir, "Li2O.cif"))
self.assertAlmostEqual(m.get_energy(s2), -145.39050015844839, 4)
def test_get_energy(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0], [1.0, 3.0, 0.00],
[0.00, -2.0, 3.0]])
s = Structure(lattice, [{
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}, {
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}, {
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}, {
"Si4+": 0.5,
"O2-": 0.25,
"P5+": 0.25
}], coords)
m = EwaldElectrostaticModel()
self.assertAlmostEqual(m.get_energy(s), 44.1070954178)
s2 = Structure.from_file(os.path.join(test_dir, "Li2O.cif"))
self.assertAlmostEqual(m.get_energy(s2), -145.39049924661001)
def Find_Lowest_Energy_Structure_Electrostatics(self):
"""
Find oxidized/reduced combination with lowest electrostatic energy
"""
n_Na = self.structure.composition['Na']
n_S = self.structure.composition['S']
n_O = self.structure.composition['O']
n_N = self.structure.composition['N']
n_Fe = self.structure.composition['Fe']
n_Fe_reduced = self.variable_magnetization_dict['Fe']['n_reduced']
n_Fe_oxidized = n_Fe-n_Fe_reduced
N_charge = ( 2.*n_O-6.*n_S-n_Na-3.*n_Fe_oxidized-2.*n_Fe_reduced )/n_N
oxidation_states = {'Na':+1, 'Fe':+3, 'O':-2,'S':+6,'N':N_charge}
Fe_2plus = pymatgen.Specie('Fe',oxidation_state=+2)
structure_with_charges = self.structure.copy()
structure_with_charges.add_oxidation_state_by_element(oxidation_states)
# identify Fe sites
list_Fe_indices = []
for i,site in enumerate(structure_with_charges):
if site.specie.symbol == 'Fe':
list_Fe_indices.append(i)
# Generate all possible permutation of sites and compute
# Ewald energy
ewald_model = EwaldElectrostaticModel(acc_factor=6)
list_reduced_sets = []
list_ewald_energy = []
for reduced_set in itertools.combinations(list_Fe_indices,n_Fe_reduced):
list_reduced_sets.append(reduced_set)
struct = structure_with_charges.copy()
for i in reduced_set:
struct.replace(i, Fe_2plus)
list_ewald_energy.append(ewald_model.get_energy(struct))
if len(list_ewald_energy) == 0:
# all sites are oxidized. No sorting involved
list_reduced_site_indices = []
list_oxidized_site_indices = list_Fe_indices
else:
# some reduction takes place. Identify best electrostatic choice
imin = np.argmin(list_ewald_energy)
list_reduced_site_indices = list_reduced_sets[imin]
list_oxidized_site_indices = []
for i in list_Fe_indices:
if i not in list_reduced_site_indices:
list_oxidized_site_indices.append(i)
return list_reduced_site_indices, list_oxidized_site_indices
def test_get_energy(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0],
[1.0, 3.0, 0.00],
[0.00, -2.0, 3.0]])
s = Structure(lattice,
[{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25}], coords)
m = EwaldElectrostaticModel()
self.assertAlmostEqual(m.get_energy(s), 44.1070954178)
s2 = read_structure(os.path.join(test_dir, "Li2O.cif"))
self.assertAlmostEqual(m.get_energy(s2), -36.3476248117)
def test_get_energy(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0],
[1.0, 3.0, 0.00],
[0.00, -2.0, 3.0]])
s = Structure(lattice,
[{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25}], coords)
m = EwaldElectrostaticModel()
# large tolerance because scipy constants changed between 0.16.1 and 0.17
self.assertAlmostEqual(m.get_energy(s), -264.66364858, 2) # Result from GULP
s2 = Structure.from_file(os.path.join(test_dir, "Li2O.cif"))
self.assertAlmostEqual(m.get_energy(s2), -145.39050015844839, 4)
def test_get_energy(self):
coords = [[0, 0, 0], [0.75, 0.75, 0.75], [0.5, 0.5, 0.5], [0.25, 0.25, 0.25]]
lattice = Lattice([[3.0, 0.0, 0.0], [1.0, 3.0, 0.00], [0.00, -2.0, 3.0]])
s = Structure(
lattice,
[
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
{"Si4+": 0.5, "O2-": 0.25, "P5+": 0.25},
],
coords,
)
m = EwaldElectrostaticModel()
self.assertAlmostEqual(m.get_energy(s), -40.655658979571228)
s2 = Structure.from_file(os.path.join(test_dir, "Li2O.cif"))
self.assertAlmostEqual(m.get_energy(s2), -145.39050015844839)
def test_to_from_dict(self):
m = EwaldElectrostaticModel()
d = m.as_dict()
self.assertIsInstance(EwaldElectrostaticModel.from_dict(d), EwaldElectrostaticModel)
def test_to_from_dict(self):
m = EwaldElectrostaticModel()
d = m.as_dict()
self.assertIsInstance(
EwaldElectrostaticModel.from_dict(d), EwaldElectrostaticModel
)
structure[2] = {"Fe2+": 1 / 3, "Li+": 2 / 3}
structure[3] = {"S2-": 1}
structure[4] = {"O2-": 1}
structure
structure.make_supercell([2, 2, 2])
structure
enum = EnumerateStructureTransformation()
enumerated = enum.apply_transformation(
structure, return_ranked_list=100) # return no more than 100 structures
structures = [d["structure"] for d in enumerated]
print("%d structures returned." % len(structures))
from pymatgen.analysis.energy_models import EwaldElectrostaticModel
ed = EwaldElectrostaticModel()
#ed.get_energy(structures[1])
structures20 = structures[:20]
batch_write_input(elect_stru, vasp_input_set=MPRelaxSet)
# elect_stru=structures20=structures[::10]
# for st in elect_stru:
# print(ed.get_energy(st))
# from pymatgen.transformations.standard_transformations import PartialRemoveSpecieTransformation
# vac_list=[]
# for ii in range (1,11):
# strut=structures[ii]