diff --git a/pycdt/core/defectsmaker.py b/pycdt/core/defectsmaker.py index 820911a..5492203 100644 --- a/pycdt/core/defectsmaker.py +++ b/pycdt/core/defectsmaker.py @@ -18,7 +18,6 @@ import abc -#from monty.string import str2unicode from monty.serialization import dumpfn from pymatgen.core.structure import PeriodicSite, Structure from pymatgen.core.periodic_table import Element, Specie, get_el_sp @@ -246,7 +245,7 @@ def __init__(self, structure): self.oxi_states = {} for key,val in oxi_states.items(): strip_key = ''.join([s for s in key if s.isalpha()]) - self.oxi_states[str2unicode(strip_key)] = val + self.oxi_states[strip_key] = val self.min_max_oxi = {} for s in struct_species: @@ -258,7 +257,7 @@ def __init__(self, structure): continue max_oxi = max(el.common_oxidation_states) min_oxi = min(el.common_oxidation_states) - self.min_max_oxi[str2unicode(el.symbol)] = (min_oxi,max_oxi) + self.min_max_oxi[el.symbol] = (min_oxi,max_oxi) def get_charges(self, defect_type, site_specie=None, sub_specie=None): """ @@ -274,7 +273,7 @@ def get_charges(self, defect_type, site_specie=None, sub_specie=None): """ if defect_type == 'vacancy': vac_symbol = get_el_sp(site_specie).symbol - vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] + vac_oxi_state = self.oxi_states[vac_symbol] if vac_oxi_state < 0: min_oxi = max(vac_oxi_state, self.min_max_oxi[vac_symbol][0]) max_oxi = 0 @@ -289,7 +288,7 @@ def get_charges(self, defect_type, site_specie=None, sub_specie=None): elif defect_type == 'antisite': vac_symbol = get_el_sp(site_specie).symbol - vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] + vac_oxi_state = self.oxi_states[vac_symbol] as_symbol = get_el_sp(sub_specie).symbol if vac_oxi_state > 0: oxi_max = max(self.min_max_oxi[as_symbol][1],0) @@ -304,7 +303,7 @@ def get_charges(self, defect_type, site_specie=None, sub_specie=None): site_specie = get_el_sp(site_specie) sub_specie = get_el_sp(sub_specie) vac_symbol = site_specie.symbol - vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] + vac_oxi_state = self.oxi_states[vac_symbol] max_oxi_sub = max(sub_specie.common_oxidation_states) min_oxi_sub = min(sub_specie.common_oxidation_states) @@ -352,7 +351,7 @@ def __init__(self, structure): self.oxi_states = {} for key,val in oxi_states.items(): strip_key = ''.join([s for s in key if s.isalpha()]) - self.oxi_states[str2unicode(strip_key)] = val + self.oxi_states[strip_key] = val def get_charges(self, defect_type, site_specie=None, sub_specie=None): """ @@ -368,7 +367,7 @@ def get_charges(self, defect_type, site_specie=None, sub_specie=None): """ if defect_type == 'vacancy': vac_symbol = get_el_sp(site_specie).symbol - vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] + vac_oxi_state = self.oxi_states[vac_symbol] if vac_oxi_state == 0: return [-1,0,1] else: @@ -379,9 +378,9 @@ def get_charges(self, defect_type, site_specie=None, sub_specie=None): elif defect_type in ['antisite', 'substitution']: #TODO: may cause some weird states for substitutions. Worth updating in future. vac_symbol = get_el_sp(site_specie).symbol - vac_oxi_state = self.oxi_states[str2unicode(vac_symbol)] + vac_oxi_state = self.oxi_states[vac_symbol] as_symbol = get_el_sp(sub_specie).symbol - as_oxi_state = self.oxi_states[str2unicode(as_symbol)] + as_oxi_state = self.oxi_states[as_symbol] expected_oxi = as_oxi_state - vac_oxi_state if expected_oxi == 0: return [-1,0,1] @@ -565,7 +564,7 @@ def __init__(self, structure, max_min_oxi=None, substitutions=None, self.substitutions = {} self.struct_type = struct_type for key, val in substitutions.items(): - self.substitutions[str2unicode(key)] = val + self.substitutions[key] = val spa = SpacegroupAnalyzer(structure, symprec=1e-2) prim_struct = spa.get_primitive_standard_structure()