def test_mini_lambda_table(self):
sp = SubstitutionProbability(lambda_table=get_table(), alpha=-5.0)
o2 = Species("O", -2)
s2 = Species("S", -2)
li1 = Species("Li", 1)
na1 = Species("Na", 1)
self.assertAlmostEqual(sp.prob(s2, o2), 0.124342317272, 5, "probability isn't correct")
self.assertAlmostEqual(sp.pair_corr(li1, na1), 1.65425296864, 5, "correlation isn't correct")
prob = sp.cond_prob_list([o2, li1], [na1, li1])
self.assertAlmostEqual(prob, 0.00102673915742, 5, "probability isn't correct")
class ProbabilityBenchmarker:
"""Benchmarking tests for pymatgen SubstitutionProbability."""
@timeit
def run_tests(self):
"""Run all tests."""
self.__sp_setup()
self.__pair_corr()
@timeit
def __sp_setup(self):
"""Set up SubstitutionProbability."""
self.sp = SubstitutionProbability()
@timeit
def __pair_corr(self):
"""Get pair correlation."""
pairs = cwr(self.sp.species, 2)
for s1, s2 in pairs:
self.sp.pair_corr(s1, s2)
def test_mini_lambda_table(self):
sp = SubstitutionProbability(lambda_table=get_table(), alpha= -5.)
o2 = Specie('O', -2)
s2 = Specie('S', -2)
li1 = Specie('Li', 1)
na1 = Specie('Na', 1)
self.assertAlmostEqual(sp.prob(s2, o2), 0.124342317272, 5
, "probability isn't correct")
self.assertAlmostEqual(sp.pair_corr(li1, na1), 1.65425296864, 5
, "correlation isn't correct")
prob = sp.cond_prob_list([o2, li1], [na1, li1])
self.assertAlmostEqual(prob, 0.00102673915742, 5
, "probability isn't correct")
def test_full_lambda_table(self):
"""
This test tests specific values in the data folder. If the
json is updated, these tests will have to be as well
"""
sp = SubstitutionProbability(alpha=-5.0)
sp1 = Species("Fe", 4)
sp3 = Species("Mn", 3)
prob1 = sp.prob(sp1, sp3)
self.assertAlmostEqual(prob1, 1.69243954552e-05, 5, "probability isn't correct")
sp2 = Species("Pt", 4)
sp4 = Species("Pd", 4)
prob2 = sp.prob(sp2, sp4)
self.assertAlmostEqual(prob2, 4.7174906021e-05, 5, "probability isn't correct")
corr = sp.pair_corr(Species("Cu", 2), Species("Fe", 2))
self.assertAlmostEqual(corr, 6.82496631637, 5, "probability isn't correct")
prob3 = sp.cond_prob_list([sp1, sp2], [sp3, sp4])
self.assertAlmostEqual(prob3, 0.000300298841302, 6, "probability isn't correct")
def test_full_lambda_table(self):
"""
This test tests specific values in the data folder. If the
json is updated, these tests will have to be as well
"""
sp = SubstitutionProbability(alpha= -5.)
sp1 = Specie('Fe', 4)
sp3 = Specie('Mn', 3)
prob1 = sp.prob(sp1, sp3)
self.assertAlmostEqual(prob1, 1.69243954552e-05, 5
, "probability isn't correct")
sp2 = Specie('Pt', 4)
sp4 = Specie('Pd', 4)
prob2 = sp.prob(sp2, sp4)
self.assertAlmostEqual(prob2, 4.7174906021e-05, 5
, "probability isn't correct")
corr = sp.pair_corr(Specie("Cu", 2), Specie("Fe", 2))
self.assertAlmostEqual(corr, 6.82496631637, 5
, "probability isn't correct")
prob3 = sp.cond_prob_list([sp1, sp2], [sp3, sp4])
self.assertAlmostEqual(prob3, 0.000300298841302, 6
, "probability isn't correct")