def relax(self):
"""
Optimize interstitial structures
"""
no_inter = self._inter.defectsite_count()
inter_gulp_kw = ('optimise', 'conp', 'qok')
val_dict = self._inter.struct_valences
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, rlx_struct = get_energy_relax_structure_buckingham(sc[0])
self._relax_structs.append(rlx_struct)
self._relax_energies.append(blk_energy)
val_dict[self._el] = self._oxi_state # If element not in structure
for i in range(1, no_inter + 1):
try:
energy, rlx_struct = get_energy_relax_structure_buckingham(
sc[i], keywords=inter_gulp_kw, valence_dict=val_dict)
self._relax_energies.append(energy)
self._relax_structs.append(rlx_struct)
except:
self._relax_energies.append(None)
self._relax_structs.append(None)
def is_empty(lst):
for value in lst:
if value:
return False
return True
if is_empty(self._relax_energies):
raise IOError('Relaxation failed')
def relax(self):
"""
Optimize interstitial structures
"""
no_inter = self._inter.defectsite_count()
inter_gulp_kw = ('optimise', 'conp', 'qok')
val_dict = self._inter.struct_valences
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, rlx_struct = get_energy_relax_structure_buckingham(sc[0])
self._relax_structs.append(rlx_struct)
self._relax_energies.append(blk_energy)
val_dict[self._el] = self._oxi_state # If element not in structure
for i in range(1, no_inter + 1):
try:
energy, rlx_struct = get_energy_relax_structure_buckingham(
sc[i], keywords=inter_gulp_kw, valence_dict=val_dict
)
self._relax_energies.append(energy)
self._relax_structs.append(rlx_struct)
except:
self._relax_energies.append(None)
self._relax_structs.append(None)
def is_empty(lst):
for value in lst:
if value:
return False
return True
if is_empty(self._relax_energies):
raise IOError('Relaxation failed')
def _relax_analysis(self):
"""
Optimize interstitial structures
"""
no_inter = self._inter.defectsite_count()
inter_gulp_kw = ('optimise', 'conp', 'qok')
val_dict = self._inter.struct_valences
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, rlx_struct = get_energy_relax_structure_buckingham(sc[0])
self._relax_struct.append(rlx_struct)
val_dict[self._el] = self._oxi_state # If element not in structure
for i in range(1, no_inter + 1):
energy, rlx_struct = get_energy_relax_structure_buckingham(
sc[i], keywords=inter_gulp_kw, valence_dict=val_dict)
form_energy = energy - blk_energy
self._relax_energies.append(form_energy)
self._relax_struct.append(rlx_struct)
def _relax_analysis(self):
"""
Optimize interstitial structures
"""
no_inter = self._inter.defectsite_count()
inter_gulp_kw = ('optimise', 'conp', 'qok')
val_dict = self._inter.struct_valences
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, rlx_struct = get_energy_relax_structure_buckingham(sc[0])
self._relax_struct.append(rlx_struct)
val_dict[self._el] = self._oxi_state # If element not in structure
for i in range(1, no_inter + 1):
energy, rlx_struct = get_energy_relax_structure_buckingham(
sc[i], keywords=inter_gulp_kw, valence_dict=val_dict
)
form_energy = energy - blk_energy
self._relax_energies.append(form_energy)
self._relax_struct.append(rlx_struct)
def relax(self):
energy, rlx_struct = get_energy_relax_structure_buckingham(
self._unrelax_struct)
self._relax_struct = rlx_struct
def test_get_energy_relax_structure_buckingham(self):
enrgy, struct = get_energy_relax_structure_buckingham(self.mgo_uc)
self.assertIsInstance(enrgy, float)
self.assertIsInstance(struct, Structure)
site_len = len(struct.sites)
self.assertEqual(site_len, len(self.mgo_uc.sites))
def relax(self):
energy, rlx_struct = get_energy_relax_structure_buckingham(
self._unrelax_struct)
self._relax_struct = rlx_struct
