def test_smactStruc_comp_key(self):
"""Test generation of a composition key for `SmactStructure`s."""
s1 = SmactStructure(*self._gen_empty_structure([('Ba', 2,
2), ('O', -2,
1), ('F', -1,
2)]))
s2 = SmactStructure(*self._gen_empty_structure([('Fe', 2,
1), ('Fe', 3,
2), ('O', -2,
4)]))
Ba = Species('Ba', 2)
O = Species('O', -2)
F = Species('F', -1)
Fe2 = Species('Fe', 2)
Fe3 = Species('Fe', 3)
s3 = SmactStructure(*self._gen_empty_structure([(Ba, 2), (O, 1), (F,
2)]))
s4 = SmactStructure(*self._gen_empty_structure([(Fe2, 1), (Fe3,
2), (O,
4)]))
Ba_2OF_2 = "Ba_2_2+F_2_1-O_1_2-"
Fe_3O_4 = "Fe_2_3+Fe_1_2+O_4_2-"
self.assertEqual(s1.composition(), Ba_2OF_2)
self.assertEqual(s2.composition(), Fe_3O_4)
self.assertEqual(s3.composition(), Ba_2OF_2)
self.assertEqual(s4.composition(), Fe_3O_4)
def test_oxidation_states(self):
ox = smact.oxidation_states.Oxidation_state_probability_finder()
self.assertAlmostEqual(
ox.compound_probability([Specie('Fe', +3),
Specie('O', -2)]), 0.74280230326)
self.assertAlmostEqual(
ox.pair_probability(Species('Fe', +3), Species('O', -2)),
0.74280230326)
self.assertEqual(len(ox.get_included_species()), 173)
def compound_probability(self, structure, ignore_stoichiometry=True):
'''
calculate overall probability for structure or composition.
Args:
structure (pymatgen.Structure): Compound for which the probability score will be generated.
Can also be a list of pymatgen or SMACT Species.
ignore_stoichiometry (bool): Whether to weight probabilities by stoichiometry.
Defaults to false as decribed in the original paper.
Returns:
compound_prob (float): Compound probability
'''
# Convert input to list of SMACT Species
if type(structure) == list:
if all(isinstance(i, Species) for i in structure):
pass
elif all(isinstance(i, pmgSpecies) for i in structure):
structure = [Species(i.symbol, i.oxi_state) for i in structure]
else:
raise TypeError(
"Input requires a list of SMACT or Pymatgen species.")
elif type(structure) == Structure:
species = structure.species
if not all(isinstance(i, pmgSpecies) for i in species):
raise TypeError("Structure must have oxidation states.")
else:
structure = [Species(i.symbol, i.oxi_state) for i in structure]
else:
raise TypeError(
"Input requires a list of SMACT or Pymatgen Species or a Structure."
)
# Put most electonegative element last in list by sorting by electroneg
structure.sort(key=lambda x: x.pauling_eneg)
# Define necessary species pairs
anion = structure[-1]
cations = [i for i in structure if i.oxidation > 0]
species_pairs = [(anion, cation) for cation in cations]
# Reduce down to unique pairs if ignoring stoichiometry
if ignore_stoichiometry:
species_pairs = list(set(species_pairs))
# Do the maths
pair_probs = [
self.pair_probability(pair[0], pair[1]) for pair in species_pairs
]
compound_prob = mean(pair_probs)
return compound_prob