def test_get_transition_level_and_energy(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.get_transition_level_and_energy(0, 2) == (1.5, 2)
def test_charge_state_concentrations(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = FrozenDefectChargeState(2, 0.1234)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.charge_state_concentrations(0.2, 300) == {
0: 2.520453931443997e-34,
2: 0.1234
}
def test_update_frozen_chgstates(self):
string = "V_Ga -1 0.19E+19\nGa_i 1 0.5E+20"
string = string.splitlines()
defects = [
DefectSpecies('V_Ga', 1, [DefectChargeState(-1, 1, 1)]),
DefectSpecies('Ga_i', 1, [DefectChargeState(1, 1, 1)])
]
update_frozen_chgstates(string, defects, 1, 2)
assert_almost_equal(defects[0].get_concentration(0.1, 300), 1.9e-06)
assert_almost_equal(defects[1].get_concentration(0.1, 300), 5e-05)
def test_fixed_concentration_charge_states(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.fixed_conc_charge_states() == {}
defect.charge_states[2] = FrozenDefectChargeState(2, 0.1234)
assert defect.fixed_conc_charge_states() == {
2: defect.charge_states[2]
}
def test_min_energy_charge_state(self):
charge_state_1 = DefectChargeState(-1, 0.1, 1)
charge_state_2 = DefectChargeState(-2, 0.2, 1)
defect = DefectSpecies('O_i', 1, [charge_state_1, charge_state_2])
self.assertEqual(defect.min_energy_charge_state(0),
defect.charge_states[-1])
self.assertEqual(defect.min_energy_charge_state(2),
defect.charge_states[-2])
def test_variable_concentration_charge_states(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.variable_conc_charge_states() == {
0: charge_state_1,
2: charge_state_2
}
defect.charge_states[2] = FrozenDefectChargeState(2, 0.1234)
assert defect.variable_conc_charge_states() == {0: charge_state_1}
def setUp(self):
name = "V_O"
nsites = 2
mock_charge_states = [
Mock(spec=DefectChargeState),
Mock(spec=DefectChargeState),
]
mock_charge_states[0].charge = 0
mock_charge_states[1].charge = 1
mock_charge_states[0].concentration_is_fixed = False
mock_charge_states[1].concentration_is_fixed = False
self.defect_species = DefectSpecies(name=name,
nsites=nsites,
charge_states=mock_charge_states)
def test_update_frozen_defect_species(self):
string = "V_Ga 0.3285677364522E+20"
string = string.splitlines()
defects = [DefectSpecies('V_Ga', 1, [])]
update_frozen_defect_species(string, defects, 1, 1)
assert_almost_equal(defects[0].get_concentration(0.1, 298),
3.285677364522e-05)
def test_charge_states_by_formation_energy_with_frozen_charge_state(self):
name = "V_O"
nsites = 2
mock_charge_states = [
Mock(spec=DefectChargeState),
Mock(spec=FrozenDefectChargeState),
]
mock_charge_states[0].charge = 0
mock_charge_states[1].charge = 1
defect_species = DefectSpecies(name=name,
nsites=nsites,
charge_states=mock_charge_states)
defect_species.variable_conc_charge_states = Mock(
return_value={0: defect_species.charge_states[0]})
defect_species.charge_states[0].get_formation_energy = Mock(
return_value=0.3)
sorted_charge_states = defect_species.charge_states_by_formation_energy(
e_fermi=0.0)
self.assertEqual(sorted_charge_states,
[defect_species.charge_states[0]])
def test_get_concentrations(self):
charge_state_1 = DefectChargeState(-1, 1.1, 1)
charge_state_2 = DefectChargeState(-2, 1.2, 1)
defect = DefectSpecies('O_i', 1, [charge_state_1, charge_state_2])
assert_almost_equal(defect.get_concentration(0.2, 300),
3.7117030892903665e-14)
defect.fix_concentration(0.1234)
assert_almost_equal(defect.get_concentration(0.2, 300), 0.1234)
def test_defect_species_is_initialised(self):
name = "foo"
nsites = 2
mock_charge_states = [
Mock(spec=DefectChargeState),
Mock(spec=DefectChargeState),
]
mock_charge_states[0].charge = 0
mock_charge_states[1].charge = 1
defect_species = DefectSpecies(name=name,
nsites=nsites,
charge_states=mock_charge_states)
self.assertEqual(defect_species._name, name)
self.assertEqual(defect_species._nsites, nsites)
self.assertEqual(defect_species._charge_states[0],
mock_charge_states[0])
self.assertEqual(defect_species._charge_states[1],
mock_charge_states[1])
self.assertEqual(defect_species._fixed_concentration, None)
class TestDefectSpecies(unittest.TestCase):
def setUp(self):
name = "V_O"
nsites = 2
mock_charge_states = [
Mock(spec=DefectChargeState),
Mock(spec=DefectChargeState),
]
mock_charge_states[0].charge = 0
mock_charge_states[1].charge = 1
mock_charge_states[0].concentration_is_fixed = False
mock_charge_states[1].concentration_is_fixed = False
self.defect_species = DefectSpecies(name=name,
nsites=nsites,
charge_states=mock_charge_states)
def test_name_property(self):
self.assertEqual(self.defect_species.name, self.defect_species._name)
def test_nsites_property(self):
self.assertEqual(self.defect_species.nsites,
self.defect_species._nsites)
def test_charge_states_property(self):
self.assertEqual(self.defect_species.charge_states,
self.defect_species._charge_states)
def test_fixed_concentration_property(self):
self.defect_species._fixed_concentration = 0.1234
self.assertEqual(
self.defect_species.fixed_concentration,
self.defect_species._fixed_concentration,
)
def test_fix_concentration(self):
assert self.defect_species.fixed_concentration == None
self.defect_species.fix_concentration(0.1234)
self.assertEqual(self.defect_species.fixed_concentration, 0.1234)
def test_charge_states_by_formation_energy(self):
self.defect_species.charge_states[0].get_formation_energy = Mock(
return_value=0.3)
self.defect_species.charge_states[1].get_formation_energy = Mock(
return_value=0.1)
self.defect_species.variable_conc_charge_states = Mock(
return_value={
0: self.defect_species.charge_states[0],
1: self.defect_species.charge_states[1],
})
sorted_charge_states = self.defect_species.charge_states_by_formation_energy(
e_fermi=0.0)
self.assertEqual(sorted_charge_states[0],
self.defect_species.charge_states[1])
self.assertEqual(sorted_charge_states[1],
self.defect_species.charge_states[0])
def test_charge_states_by_formation_energy_with_frozen_charge_state(self):
name = "V_O"
nsites = 2
mock_charge_states = [
Mock(spec=DefectChargeState),
Mock(spec=FrozenDefectChargeState),
]
mock_charge_states[0].charge = 0
mock_charge_states[1].charge = 1
defect_species = DefectSpecies(name=name,
nsites=nsites,
charge_states=mock_charge_states)
defect_species.variable_conc_charge_states = Mock(
return_value={0: defect_species.charge_states[0]})
defect_species.charge_states[0].get_formation_energy = Mock(
return_value=0.3)
sorted_charge_states = defect_species.charge_states_by_formation_energy(
e_fermi=0.0)
self.assertEqual(sorted_charge_states,
[defect_species.charge_states[0]])
def test_get_formation_energies(self):
self.defect_species.charge_states[0].get_formation_energy = Mock(
return_value=0.3)
self.defect_species.charge_states[1].get_formation_energy = Mock(
return_value=0.1)
self.defect_species.variable_conc_charge_states = Mock(
return_value={
0: self.defect_species.charge_states[0],
1: self.defect_species.charge_states[1],
})
formation_energies_dict = self.defect_species.get_formation_energies(
0.0)
self.assertEqual(formation_energies_dict, {0: 0.3, 1: 0.1})
def test_min_energy_charge_state(self):
charge_state_1 = DefectChargeState(-1, 0.1, 1)
charge_state_2 = DefectChargeState(-2, 0.2, 1)
defect = DefectSpecies('O_i', 1, [charge_state_1, charge_state_2])
self.assertEqual(defect.min_energy_charge_state(0),
defect.charge_states[-1])
self.assertEqual(defect.min_energy_charge_state(2),
defect.charge_states[-2])
def test_get_concentrations(self):
charge_state_1 = DefectChargeState(-1, 1.1, 1)
charge_state_2 = DefectChargeState(-2, 1.2, 1)
defect = DefectSpecies('O_i', 1, [charge_state_1, charge_state_2])
assert_almost_equal(defect.get_concentration(0.2, 300),
3.7117030892903665e-14)
defect.fix_concentration(0.1234)
assert_almost_equal(defect.get_concentration(0.2, 300), 0.1234)
def test_get_transition_level_and_energy(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.get_transition_level_and_energy(0, 2) == (1.5, 2)
def test_fixed_concentration_charge_states(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.fixed_conc_charge_states() == {}
defect.charge_states[2] = FrozenDefectChargeState(2, 0.1234)
assert defect.fixed_conc_charge_states() == {
2: defect.charge_states[2]
}
def test_variable_concentration_charge_states(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.variable_conc_charge_states() == {
0: charge_state_1,
2: charge_state_2
}
defect.charge_states[2] = FrozenDefectChargeState(2, 0.1234)
assert defect.variable_conc_charge_states() == {0: charge_state_1}
def test_variable_concentration_charge_states(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.variable_conc_charge_states() == {
0: charge_state_1,
2: charge_state_2
}
defect.charge_states[2] = FrozenDefectChargeState(2, 0.1234)
assert defect.variable_conc_charge_states() == {0: charge_state_1}
def test_charge_state_concentrations(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = FrozenDefectChargeState(2, 0.1234)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.charge_state_concentrations(0.2, 300) == {
0: 2.520453931443997e-34,
2: 0.1234
}
def test_defect_charge_contributions(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = FrozenDefectChargeState(2, 0.1234)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.defect_charge_contributions(0.2, 300) == (0.2468, 0.0)
def test_tl_profile(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert_equal(defect.tl_profile(0, 5), [[0, -1], [1.5, 2], [5, 2]])
def test_tl_profile(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = DefectChargeState(2, -1, 1)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert_equal(defect.tl_profile(0, 5), [[0, -1], [1.5, 2], [5, 2]])
def test_defect_charge_contributions(self):
charge_state_1 = DefectChargeState(0, 2, 1)
charge_state_2 = FrozenDefectChargeState(2, 0.1234)
defect = DefectSpecies('V_O', 1, [charge_state_1, charge_state_2])
assert defect.defect_charge_contributions(0.2, 300) == (0.2468, 0.0)