def test_substitution(self):
struc = PymatgenTest.get_structure("VO2")
V_index = struc.indices_from_symbol("V")[0]
sub_site = PeriodicSite("Sr", struc[V_index].coords, struc.lattice, coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
# test generation and super cell
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 1, "Sr": 1, "O": 4})
sub_struc = substitution.generate_defect_structure(2)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 15, "Sr": 1, "O": 32})
sub_struc = substitution.generate_defect_structure(3)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 53, "Sr": 1, "O": 108})
sub_struc = substitution.generate_defect_structure([[2., 0, 0], [0, 0, -3.], [0, 2., 0]])
self.assertEqual(sub_struc.composition.as_dict(), {"V": 23, "O": 48, "Sr": 1})
# test charge
substitution = Substitution(struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 0.0)
substitution = Substitution(struc, sub_site, charge=1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 1.0)
substitution = Substitution(struc, sub_site, charge=-1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, -1.0)
# test multiplicity
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 2.0)
O_index = struc.indices_from_symbol("O")[0]
sub_site = PeriodicSite("Sr", struc[O_index].coords, struc.lattice, coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 4)
# Test composition
self.assertEqual(dict(substitution.defect_composition.as_dict()), {"V": 2, "Sr": 1, "O": 3})
# test that structure generation doesn't break if velocities existed previously
# (previously caused failures for structure printing)
vel_struc = Structure( struc.lattice, struc.species, struc.frac_coords,
site_properties= {'velocities': [[0., 0., 0.]]*len(struc) } )
substitution = Substitution(vel_struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertTrue( 'velocities' not in sub_struc.site_properties)
# test value error raised for site not in the structure
non_site = PeriodicSite( "Sr", struc[V_index].frac_coords - [0., 0., .1], struc.lattice)
self.assertRaises( ValueError, Substitution, struc, non_site)
def test_substitution(self):
struc = PymatgenTest.get_structure("VO2")
V_index = struc.indices_from_symbol("V")[0]
sub_site = PeriodicSite("Sr", struc[V_index].coords, struc.lattice, coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
# test generation and super cell
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 1, "Sr": 1, "O": 4})
sub_struc = substitution.generate_defect_structure(2)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 15, "Sr": 1, "O": 32})
sub_struc = substitution.generate_defect_structure(3)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 53, "Sr": 1, "O": 108})
sub_struc = substitution.generate_defect_structure([[2., 0, 0], [0, 0, -3.], [0, 2., 0]])
self.assertEqual(sub_struc.composition.as_dict(), {"V": 23, "O": 48, "Sr": 1})
# test charge
substitution = Substitution(struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 0.0)
substitution = Substitution(struc, sub_site, charge=1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 1.0)
substitution = Substitution(struc, sub_site, charge=-1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, -1.0)
# test multiplicity
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 2.0)
O_index = struc.indices_from_symbol("O")[0]
sub_site = PeriodicSite("Sr", struc[O_index].coords, struc.lattice, coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 4)
# Test composition
self.assertEqual(dict(substitution.defect_composition.as_dict()), {"V": 2, "Sr": 1, "O": 3})
# test that structure has all velocities equal if velocities previously existed
# (previously caused failures for structure printing)
vel_struc = Structure( struc.lattice, struc.species, struc.frac_coords,
site_properties= {'velocities': [[0., 0., 0.]]*len(struc) } )
substitution = Substitution(vel_struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertTrue( (np.array(sub_struc.site_properties['velocities']) == 0.).all())
self.assertEqual( len(sub_struc.site_properties['velocities']), len(sub_struc))
def test_convert_cd_to_de(self):
#create a ComputedDefect object similar to legacy format
# Vacancy type first
struc = PymatgenTest.get_structure("VO2")
struc.make_supercell(3)
vac = Vacancy(struc, struc.sites[0], charge=-3)
ids = vac.generate_defect_structure(1)
defect_data = {
"locpot_path": "defect/path/to/files/LOCPOT",
"encut": 520
}
bulk_data = {"locpot_path": "bulk/path/to/files/LOCPOT"}
cse_defect = ComputedStructureEntry(ids, 100., data=defect_data)
cd = ComputedDefect(cse_defect,
struc.sites[0],
charge=-3,
name="Vac_1_O")
b_cse = ComputedStructureEntry(struc, 10., data=bulk_data)
de = convert_cd_to_de(cd, b_cse)
self.assertIsInstance(de.defect, Vacancy)
self.assertIsInstance(de, DefectEntry)
self.assertEqual(de.parameters["defect_path"], "defect/path/to/files")
self.assertEqual(de.parameters["bulk_path"], "bulk/path/to/files")
self.assertEqual(de.parameters["encut"], 520)
self.assertEqual(de.site.specie.symbol, "O")
# try again for substitution type
# (site object had bulk specie for ComputedDefects,
# while it should have substituional site specie for DefectEntrys...)
de_site_type = PeriodicSite("Sb", vac.site.frac_coords, struc.lattice)
sub = Substitution(struc, de_site_type, charge=1)
ids = sub.generate_defect_structure(1)
cse_defect = ComputedStructureEntry(ids, 100., data=defect_data)
cd = ComputedDefect(cse_defect,
struc.sites[0],
charge=1,
name="Sub_1_Sb_on_O")
de = convert_cd_to_de(cd, b_cse)
self.assertIsInstance(de.defect, Substitution)
self.assertIsInstance(de, DefectEntry)
self.assertEqual(de.site.specie.symbol, "Sb")
def test_substitution(self):
struc = PymatgenTest.get_structure("VO2")
V_index = struc.indices_from_symbol("V")[0]
sub_site = PeriodicSite("Sr", struc[V_index].coords, struc.lattice, coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
# test generation and super cell
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 1, "Sr": 1, "O": 4})
sub_struc = substitution.generate_defect_structure(2)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 15, "Sr": 1, "O": 32})
sub_struc = substitution.generate_defect_structure(3)
self.assertEqual(sub_struc.composition.as_dict(), {"V": 53, "Sr": 1, "O": 108})
sub_struc = substitution.generate_defect_structure([[2., 0, 0], [0, 0, -3.], [0, 2., 0]])
self.assertEqual(sub_struc.composition.as_dict(), {"V": 23, "O": 48, "Sr": 1})
# test charge
substitution = Substitution(struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 0.0)
substitution = Substitution(struc, sub_site, charge=1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 1.0)
substitution = Substitution(struc, sub_site, charge=-1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, -1.0)
# test multiplicity
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 2.0)
O_index = struc.indices_from_symbol("O")[0]
sub_site = PeriodicSite("Sr", struc[O_index].coords, struc.lattice, coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 4)
# Test composoition
self.assertEqual(dict(substitution.defect_composition.as_dict()), {"V": 2, "Sr": 1, "O": 3})
supercell_size = 3
structure.make_supercell(supercell_size)
structure_pure = structure.copy()
for el in charge_states_dict:
structure = structure_pure.copy()
for s in structure.sites:
if s.species_string == 'Na':
defect_site = PeriodicSite(el, s.frac_coords, s.lattice)
break
substitution = Substitution(structure, defect_site)
defect_site_coords = defect_site.frac_coords
structure = substitution.generate_defect_structure()
structure.get_sorted_structure()
for charge in charge_states_dict[el]:
path = os.path.join(os.getcwd(), f'{el}-substitution',
f'Charged{charge}')
default_inputs = DefaultInputs(structure)
potcar_symbols = []
for s in default_inputs.potcar_symbols:
if s != 'Na_pv':
potcar_symbols.append(s)
else:
potcar_symbols.append('Na')
potcar = default_inputs.get_potcar(potcar_symbols=potcar_symbols,
potcar_functional='PBE')
def test_substitution(self):
struc = PymatgenTest.get_structure("VO2")
V_index = struc.indices_from_symbol("V")[0]
sub_site = PeriodicSite("Sr",
struc[V_index].coords,
struc.lattice,
coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
# test generation and super cell
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 1,
"Sr": 1,
"O": 4
})
sub_struc = substitution.generate_defect_structure(2)
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 15,
"Sr": 1,
"O": 32
})
sub_struc = substitution.generate_defect_structure(3)
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 53,
"Sr": 1,
"O": 108
})
sub_struc = substitution.generate_defect_structure([[2., 0, 0],
[0, 0, -3.],
[0, 2., 0]])
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 23,
"O": 48,
"Sr": 1
})
# test charge
substitution = Substitution(struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 0.0)
substitution = Substitution(struc, sub_site, charge=1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 1.0)
substitution = Substitution(struc, sub_site, charge=-1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, -1.0)
# test multiplicity
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 2.0)
O_index = struc.indices_from_symbol("O")[0]
sub_site = PeriodicSite("Sr",
struc[O_index].coords,
struc.lattice,
coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 4)
# Test composition
self.assertEqual(dict(substitution.defect_composition.as_dict()), {
"V": 2,
"Sr": 1,
"O": 3
})
# test that structure has all velocities equal if velocities previously existed
# (previously caused failures for structure printing)
vel_struc = Structure(
struc.lattice,
struc.species,
struc.frac_coords,
site_properties={'velocities': [[0., 0., 0.]] * len(struc)})
substitution = Substitution(vel_struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertTrue(
(np.array(sub_struc.site_properties['velocities']) == 0.).all())
self.assertEqual(len(sub_struc.site_properties['velocities']),
len(sub_struc))
def test_substitution(self):
struc = PymatgenTest.get_structure("VO2")
V_index = struc.indices_from_symbol("V")[0]
sub_site = PeriodicSite("Sr",
struc[V_index].coords,
struc.lattice,
coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
# test generation and super cell
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 1,
"Sr": 1,
"O": 4
})
sub_struc = substitution.generate_defect_structure(2)
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 15,
"Sr": 1,
"O": 32
})
sub_struc = substitution.generate_defect_structure(3)
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 53,
"Sr": 1,
"O": 108
})
sub_struc = substitution.generate_defect_structure([[2., 0, 0],
[0, 0, -3.],
[0, 2., 0]])
self.assertEqual(sub_struc.composition.as_dict(), {
"V": 23,
"O": 48,
"Sr": 1
})
# test charge
substitution = Substitution(struc, sub_site)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 0.0)
substitution = Substitution(struc, sub_site, charge=1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, 1.0)
substitution = Substitution(struc, sub_site, charge=-1.0)
sub_struc = substitution.generate_defect_structure(1)
self.assertEqual(sub_struc.charge, -1.0)
# test multiplicity
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 2.0)
O_index = struc.indices_from_symbol("O")[0]
sub_site = PeriodicSite("Sr",
struc[O_index].coords,
struc.lattice,
coords_are_cartesian=True)
substitution = Substitution(struc, sub_site)
self.assertEqual(substitution.multiplicity, 4)
# Test composoition
self.assertEqual(dict(substitution.defect_composition.as_dict()), {
"V": 2,
"Sr": 1,
"O": 3
})