Minor updates

pymatgen/analysis/defects/generators.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import collections
+import itertools
 import logging
 from abc import ABCMeta
 from itertools import combinations
@@ -79,8 +80,7 @@ def generate(
         Returns:
             Generator[Vacancy, None, None]: Generator that yields a list of ``Vacancy`` objects.
         """
-        all_species = [*map(str, structure.composition.elements)]
-
+        all_species = [*map(_element_str, structure.composition.elements)]
         if rm_species is None:
             rm_species = all_species
         else:
@@ -397,6 +397,37 @@ def _get_candidate_sites(self, chgcar: Chgcar):
             yield min(g), len(g)
 
 
+def generate_all_native_defects(
+    host: Structure | Chgcar,
+    sub_generator: SubstitutionGenerator | None = None,
+    vac_generator: VacancyGenerator | None = None,
+    int_generator: ChargeInterstitialGenerator | None = None,
+):
+    """Generate all native defects."""
+    if isinstance(host, Chgcar):
+        struct = host.structure
+        chgcar = host
+    elif isinstance(host, Structure):
+        struct = host
+        chgcar = None
+    else:
+        raise ValueError("Host must be a Structure or Chgcar object.")
+
+    species = set(map(_element_str, struct.species))
+    sub_generator = sub_generator or SubstitutionGenerator()
+    vac_generator = vac_generator or VacancyGenerator()
+    # generate all vacancies
+    yield from vac_generator.generate(struct)
+    # generate substitutions for all pairs of species
+    for sp1, sp2 in itertools.combinations(species, 2):
+        yield from sub_generator.generate(struct, {sp1: sp2})
+        yield from sub_generator.generate(struct, {sp2: sp1})
+    # generate interstitials if a chgcar is provided
+    if chgcar is not None:
+        int_generator = int_generator or ChargeInterstitialGenerator()
+        yield from int_generator.generate(chgcar, insert_species=species)
+
+
 def _element_str(sp_or_el: Species | Element) -> str:
     """Convert a species or element to a string."""
     if isinstance(sp_or_el, Species):

pymatgen/analysis/defects/thermo.py

@@ -72,10 +72,12 @@ class DefectEntry(MSONable):
     corrections_metadata: dict[str, Any] = field(default_factory=dict)
     sc_defect_frac_coords: tuple[float, float, float] | None = None
     bulk_entry: ComputedEntry | None = None
+    entry_id: str | None = None
 
     def __post_init__(self) -> None:
         """Post-initialization."""
         self.charge_state = int(self.charge_state)
+        self.entry_id = self.entry_id or self.sc_entry.entry_id
 
     def get_freysoldt_correction(
         self,
@@ -163,6 +165,18 @@ def get_ediff(self) -> float | None:
         else:
             return None
 
+    def get_summary_dict(self) -> dict:
+        """Get a summary dictionary for the defect entry."""
+        corrections_d = {f"correction_{k}": v for k, v in self.corrections.items()}
+        res = {
+            "name": self.defect.name,
+            "charge_state": self.charge_state,
+            "bulk_total_energy": self.bulk_entry.energy if self.bulk_entry else None,
+            "defect_total_energy": self.sc_entry.energy,
+        }
+        res.update(corrections_d)
+        return res
+
 
 @dataclass
 class FormationEnergyDiagram(MSONable):
@@ -535,6 +549,15 @@ def get_concentration(
             energy=fe, temperature=temperature
         )
 
+    def as_dataframe(self):
+        """Return the formation energy diagram as a pandas dataframe."""
+        from pandas import DataFrame
+
+        defect_entries = self.defect_entries
+        l_ = map(lambda x: x.get_summary_dict(), defect_entries)
+        df = DataFrame(l_)
+        return df
+
 
 @dataclass
 class MultiFormationEnergyDiagram(MSONable):

tests/test_generators.py

@@ -8,6 +8,7 @@
     SubstitutionGenerator,
     VacancyGenerator,
     VoronoiInterstitialGenerator,
+    generate_all_native_defects,
 )
 
 
@@ -89,3 +90,8 @@ def test_voronoi_interstitial_generator(chgcar_fe3o4):
         assert defect.site.specie.symbol == "Li"
         cnt += 1
     assert cnt == 4
+
+
+def test_generate_all_native_defects(chgcar_fe3o4):
+    gen = generate_all_native_defects(chgcar_fe3o4)
+    len(list(gen)) == 14

tests/test_thermo.py

@@ -173,6 +173,9 @@ def test_formation_energy(data_Mg_Ga, defect_entries_Mg_Ga, stable_entries_Mg_Ga
         temperature=300,
     ) == pytest.approx(2 * 1.5875937551666035e-17)
 
+    # dataframe conversion
+    fed.as_dataframe()
+
 
 def test_multi(data_Mg_Ga, defect_entries_Mg_Ga, stable_entries_Mg_Ga_N):
     bulk_vasprun = data_Mg_Ga["bulk_sc"]["vasprun"]