def get_energy(self, n, relax=True):
"""
Formation Energy for nth symmetrically distinct interstitial.
"""
if relax and not self._relax_energies:
self._relax_analysis()
if not relax and not self._norelax_energies:
no_inter = self._inter.defectsite_count()
inter_gulp_kw = ('qok',)
val_dict = self._inter.struct_valences
val_dict[self._el] = self._oxi_state # If element not in structure
scd = self._scd
scale_mat = [[scd, 0, 0], [0, scd, 0], [0, 0, scd]]
sc = self._inter.make_supercells_with_defects(scale_mat, self._el)
blk_energy = get_energy_buckingham(sc[0])
for i in range(1, no_inter + 1):
inter_energy = get_energy_buckingham(
sc[i], keywords=inter_gulp_kw, valence_dict=val_dict
)
form_energy = inter_energy - blk_energy
self._norelax_energies.append(form_energy)
if relax:
return self._relax_energies[n]
else:
return self._norelax_energies[n]
def get_energy(self, n, tol=0.5):
"""
Formation Energy for nth symmetrically distinct vacancy.
"""
# generate defect free structure energy
if not self._energies:
no_vac = self._vacancy.defectsite_count()
prev_energies = [0.0] * no_vac
tol_flg = [False] * no_vac
vac_gulp_kw = ("optimise", "conp", "qok")
val_dict = self._vacancy.struct_valences
for sp in range(2, 6):
if not (False in tol_flg):
# print sp
break
scale_mat = [[sp, 0, 0], [0, sp, 0], [0, 0, sp]]
sc = self._vacancy.make_supercells_with_defects(scale_mat)
blk_energy = get_energy_buckingham(sc[0])
no = len(sc[0].sites)
# print no
for i in range(1, no_vac + 1):
if not tol_flg[i - 1]:
vac_energy = get_energy_buckingham(sc[i], keywords=vac_gulp_kw, valence_dict=val_dict)
form_energy = vac_energy - (no - 1) / no * blk_energy
if abs(form_energy - prev_energies[i - 1]) < tol:
tol_flg[i - 1] = True
prev_energies[i - 1] = form_energy
self._energies = prev_energies
self._tol_flg = tol_flg
if not self._tol_flg[n]:
print "Caution: tolerance not reached for {0} vacancy".format(n)
return self._energies[n]
def get_energy(self, n, tol=0.5):
"""
Formation Energy for nth symmetrically distinct vacancy.
"""
#generate defect free structure energy
if not self._energies:
no_vac = self._vacancy.defectsite_count()
prev_energies = [0.0] * no_vac
tol_flg = [False] * no_vac
vac_gulp_kw = ('optimise', 'conp', 'qok')
val_dict = self._vacancy.struct_valences
for sp in range(2, 6):
if not (False in tol_flg):
#print sp
break
scale_mat = [[sp, 0, 0], [0, sp, 0], [0, 0, sp]]
sc = self._vacancy.make_supercells_with_defects(scale_mat)
blk_energy = get_energy_buckingham(sc[0])
no = len(sc[0].sites)
#print no
for i in range(1, no_vac + 1):
if not tol_flg[i - 1]:
vac_energy = get_energy_buckingham(
sc[i], keywords=vac_gulp_kw, valence_dict=val_dict)
form_energy = vac_energy - (no - 1) / no * blk_energy
if abs(form_energy - prev_energies[i - 1]) < tol:
tol_flg[i - 1] = True
prev_energies[i - 1] = form_energy
self._energies = prev_energies
self._tol_flg = tol_flg
if not self._tol_flg[n]:
print "Caution: tolerance not reached for {0} vacancy".format(n)
return self._energies[n]
def get_energy(self, n, relax=True):
"""
Formation Energy for nth symmetrically distinct interstitial.
"""
if relax and not self._relax_energies:
self._relax_analysis()
if not relax and not self._norelax_energies:
no_inter = self._inter.defectsite_count()
inter_gulp_kw = ('qok', )
val_dict = self._inter.struct_valences
val_dict[self._el] = self._oxi_state # If element not in structure
scd = self._scd
scale_mat = [[scd, 0, 0], [0, scd, 0], [0, 0, scd]]
sc = self._inter.make_supercells_with_defects(scale_mat, self._el)
blk_energy = get_energy_buckingham(sc[0])
for i in range(1, no_inter + 1):
inter_energy = get_energy_buckingham(sc[i],
keywords=inter_gulp_kw,
valence_dict=val_dict)
form_energy = inter_energy - blk_energy
self._norelax_energies.append(form_energy)
if relax:
return self._relax_energies[n]
else:
return self._norelax_energies[n]
def test_get_energy_buckingham(self):
enrgy = get_energy_buckingham(self.mgo_uc)
self.assertIsInstance(enrgy, float)
# test with vacancy structure
del self.mgo_uc[0]
energy = get_energy_buckingham(self.mgo_uc,
keywords=('qok', 'optimise', 'conp'),
valence_dict=self.val_dict)
self.assertIsInstance(energy, float)