Redefine element_changes for Defect for fast formation energy / c…

…oncentration calculations

doped/core.py

@@ -818,7 +818,7 @@ def get_eigenvalue_analysis(
 
  return get_eigenvalue_analysis(self, plot=plot, filename=filename, **kwargs)
 
- def _get_chempot_term(self, chemical_potentials=None):
+ def _get_chempot_term(self, chemical_potentials=None) -> float:
  chemical_potentials = chemical_potentials or {}
  element_changes = {elt.symbol: change for elt, change in self.defect.element_changes.items()}
  missing_elts = [elt for elt in element_changes if elt not in chemical_potentials]
@@ -2044,6 +2044,21 @@ def get_charge_states(self, padding: int = 1) -> list[int]:
 
  return charges
 
+ def __setattr__(self, name, value):
+ """
+ Handle attribute updates.
+
+ Safety function to ensure properties (``defect_site``, ``volume``,
+ ``element_changes``) are recomputed whenever any defect attributes
+ are changed, to ensure consistency and correct predictions.
+ """
+ super().__setattr__(name, value)
+ if name in ["site", "structure"]:
+ # delete internal pre-computed attributes, so they are re-computed when needed:
+ for attr in ["_defect_site", "_volume", "_element_changes"]:
+ if hasattr(self, attr):
+ delattr(self, attr)
+
  @property
  def defect_site(self) -> PeriodicSite:
  """
@@ -2084,6 +2099,25 @@ def volume(self) -> float:
 
  return self._volume
 
+ @property
+ def element_changes(self) -> dict[Element, int]:
+ """
+ The stoichiometry changes of the defect, as a dict.
+
+ e.g. {"Mg": -1, "O": +1} for a O-on-Mg antisite in MgO.
+ Redefined from the ``pymatgen-analysis-defects`` method
+ to be far more efficient when used in loops (e.g. for
+ calculating defect concentrations as functions of chemical
+ potentials, temperature etc.).
+
+ Returns:
+ dict[Element, int]: The species changes of the defect.
+ """
+ if not hasattr(self, "_element_changes"):
+ self._element_changes = super().element_changes
+
+ return self._element_changes
+
  def __hash__(self):
  """
  Hash the ``Defect`` object, based on the defect name and site.

doped/generation.py

@@ -2213,8 +2213,8 @@ def __str__(self):
 
  def __repr__(self):
  """
- Returns a string representation of the DefectsGenerator object, and
- prints the DefectsGenerator info.
+ Returns a string representation of the ``DefectsGenerator`` object, and
+ prints the ``DefectsGenerator`` info.
 
  Note that Wyckoff letters can depend on the ordering of elements in
  the conventional standard structure, for which doped uses the ``spglib``
@@ -2300,7 +2300,10 @@ def _sort_defect_entries(
  for defect_entry in defect_entries_dict.values():
  extrinsic_element_list.extend(
  el.symbol
- for el in defect_entry.defect.defect_structure.composition.elements
+ for el in [
+ *defect_entry.defect.structure.composition.elements,
+ *defect_entry.defect.site.species.elements,
+ ]
  if el.symbol not in host_element_list
  )