def setUp(self):
blk_entry_file = os.path.join(file_loc, 'Cr2O3_defects.json')
blk_entry = loadfn(blk_entry_file, cls=MontyDecoder)
bulk_struct = blk_entry['bulk']['supercell']['structure']
bulk_energy = -100
bulk_entry = ComputedStructureEntry(bulk_struct, bulk_energy)
e_vbm = 0.5
mu_elts = {Element('Cr'): -10, Element('O'): -5}
bandgap = 3.0
self.da = DefectsAnalyzer(bulk_entry, e_vbm, mu_elts, bandgap)
d1_entry_file = os.path.join(file_loc, 'Cr2O3_defects.json')
d1_entry = loadfn(d1_entry_file, cls=MontyDecoder)
structure = d1_entry['vacancies'][0]['supercell']['structure']
site_in_bulk = d1_entry['vacancies'][0]['bulk_supercell_site']
mult = d1_entry['vacancies'][0]['site_multiplicity']
sc_size = d1_entry['vacancies'][0]['supercell']['size']
entry_defect = ComputedStructureEntry(structure, -99)
self.cd = ComputedDefect(entry_defect,
site_in_bulk,
multiplicity=mult,
supercell_size=sc_size,
charge=2,
name='vac_1_Cr')
entry_defect2 = ComputedStructureEntry(structure, -99)
self.cd2 = ComputedDefect(entry_defect2,
site_in_bulk,
multiplicity=mult,
supercell_size=sc_size,
charge=1,
name='vac_1_Cr')
def setUp(self):
entry_file = os.path.join(file_loc, 'vac_cr2o3_struct_entry.json')
entry = loadfn(entry_file, cls=MontyDecoder)
lattice = Lattice([[9.995004137201189, -2.1469568e-08, 0.0],
[-4.997501105922451, 8.655927903729987, 0.0],
[0.0, 0.0, 13.67956098598296]])
coords = [0.1666665000000016, 0.3333334999999984, 0.014505185117094302]
site_in_bulk = PeriodicSite('Cr', coords, lattice)
multiplicity = 12
supercell_size = [2, 2, 1]
q = -2
q_corr = 0.98716
o_corr = 0.39139821874799996
name = "vac_1_Cr"
self.com_def = ComputedDefect(entry, site_in_bulk, multiplicity,
supercell_size, q, q_corr, o_corr, name)
class ComputedDefectTest(PymatgenTest):
def setUp(self):
entry_file = os.path.join(file_loc, 'vac_cr2o3_struct_entry.json')
entry = loadfn(entry_file, cls=MontyDecoder)
lattice = Lattice([[9.995004137201189, -2.1469568e-08, 0.0],
[-4.997501105922451, 8.655927903729987, 0.0],
[0.0, 0.0, 13.67956098598296]])
coords = [0.1666665000000016, 0.3333334999999984, 0.014505185117094302]
site_in_bulk = PeriodicSite('Cr', coords, lattice)
multiplicity = 12
supercell_size = [2, 2, 1]
q = -2
q_corr = 0.98716
o_corr = 0.39139821874799996
name = "vac_1_Cr"
self.com_def = ComputedDefect(entry, site_in_bulk, multiplicity,
supercell_size, q, q_corr, o_corr, name)
def test_as_from_dict(self):
d = self.com_def.as_dict()
comp_def = ComputedDefect.from_dict(d)
self.assertIsInstance(comp_def, ComputedDefect)
with ScratchDir('.'):
dumpfn(self.com_def, 'tmp.json', cls=MontyEncoder)
comp_def = loadfn('tmp.json', cls=MontyDecoder)
self.assertIsInstance(comp_def, ComputedDefect)
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_as_from_dict(self):
d = self.com_def.as_dict()
comp_def = ComputedDefect.from_dict(d)
self.assertIsInstance(comp_def, ComputedDefect)
with ScratchDir('.'):
dumpfn(self.com_def, 'tmp.json', cls=MontyEncoder)
comp_def = loadfn('tmp.json', cls=MontyDecoder)
self.assertIsInstance(comp_def, ComputedDefect)