Update Defect initialisation code to match pymatgen update

doped/analysis.py

@@ -318,6 +318,10 @@ def defect_from_structures(
  } # note that we now define the Defect in the bulk supercell, rather than the primitive structure
  # as done during generation. Future work could try mapping the relaxed defect site back to the
  # primitive cell, however interstitials will be very tricky for this...
+ if def_type == "interstitial":
+ for_monty_defect["multiplicity"] = 1 # multiplicity needed for interstitial initialisation with
+ # pymatgen-analysis-defects, so set to 1 here. Set later for interstitials during parsing anyway
+ # (see below)
  defect = MontyDecoder().process_decoded(for_monty_defect)
 
  if not return_all_info:

doped/core.py

@@ -48,7 +48,7 @@
 class DefectEntry(thermo.DefectEntry):
  """
  Subclass of ``pymatgen.analysis.defects.thermo.DefectEntry`` with
- additional attributes used by doped.
+ additional attributes used by ``doped``.
 
  Core Attributes:
  defect:
@@ -1415,7 +1415,7 @@ def __init__(
  ):
  """
  Subclass of ``pymatgen.analysis.defects.core.Defect`` with additional
- attributes and methods used by doped.
+ attributes and methods used by ``doped``.
 
  Args:
  structure (Structure):
@@ -1675,7 +1675,10 @@ def get_supercell_structure(
  )[0]
 
  sc_defect = self.__class__(
- structure=self.structure * sc_mat, site=sc_site, oxi_state=self.oxi_state
+ structure=self.structure * sc_mat,
+ site=sc_site,
+ oxi_state=self.oxi_state,
+ multiplicity=1, # so doesn't break for interstitials
  )
  sc_defect_struct = sc_defect.defect_structure
  sc_defect_struct.remove_oxidation_states()
@@ -1822,11 +1825,11 @@ def doped_defect_from_pmg_defect(defect: core.Defect, bulk_oxi_states=False, **d
  return defect_type._from_pmg_defect(defect, bulk_oxi_states=bulk_oxi_states, **doped_kwargs)
 
 
-class Vacancy(core.Vacancy, Defect):
+class Vacancy(Defect, core.Vacancy):
  def __init__(self, *args, **kwargs):
  """
  Subclass of ``pymatgen.analysis.defects.core.Vacancy`` with additional
- attributes and methods used by doped.
+ attributes and methods used by ``doped``.
  """
  super().__init__(*args, **kwargs)
 
@@ -1838,11 +1841,11 @@ def __repr__(self) -> str:
  return f"{self.name} vacancy defect at site [{frac_coords_string}] in structure"
 
 
-class Substitution(core.Substitution, Defect):
+class Substitution(Defect, core.Substitution):
  def __init__(self, *args, **kwargs):
  """
  Subclass of ``pymatgen.analysis.defects.core.Substitution`` with
- additional attributes and methods used by doped.
+ additional attributes and methods used by ``doped``.
  """
  super().__init__(*args, **kwargs)
 
@@ -1854,12 +1857,14 @@ def __repr__(self) -> str:
  return f"{self.name} substitution defect at site [{frac_coords_string}] in structure"
 
 
-class Interstitial(core.Interstitial, Defect):
+class Interstitial(Defect, core.Interstitial):
  def __init__(self, *args, **kwargs):
  """
  Subclass of ``pymatgen.analysis.defects.core.Interstitial`` with
- additional attributes and methods used by doped.
+ additional attributes and methods used by ``doped``.
  """
+ if "multiplicity" not in kwargs: # will break for Interstitials if not set
+ kwargs["multiplicity"] = 1
  super().__init__(*args, **kwargs)
 
  def __repr__(self) -> str: