Fix antisite generation in mixed-valence systems (#210)

* Use sets to handle mixed valence species and add test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Typing and formatting

* Fix test_ccd.py

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: kavanase

pymatgen/analysis/defects/generators.py

@@ -90,7 +90,7 @@ def __init__(
     def generate(
         self,
         structure: Structure,
-        rm_species: list[str | Species] | None = None,
+        rm_species: set[str | Species] | list[str | Species] | None = None,
         **kwargs,
     ) -> Generator[Vacancy, None, None]:
         """Generate a vacancy defects.
@@ -103,10 +103,10 @@ def generate(
         Returns:
             Generator[Vacancy, None, None]: Generator that yields a list of ``Vacancy`` objects.
         """
-        all_species = [*map(_element_str, structure.composition.elements)]
-        rm_species = all_species if rm_species is None else [*map(str, rm_species)]
+        all_species = {*map(_element_str, structure.composition.elements)}
+        rm_species = all_species if rm_species is None else {*map(str, rm_species)}
 
-        if not set(rm_species).issubset(all_species):
+        if not rm_species.issubset(all_species):
             msg = f"rm_species({rm_species}) must be a subset of the structure's species ({all_species})."
             raise ValueError(
                 msg,
@@ -235,7 +235,7 @@ def generate(
             structure: The bulk structure the anti-site defects are generated from.
             **kwargs: Additional keyword arguments for the ``Substitution.generate`` function.
         """
-        all_species = [*map(_element_str, structure.composition.elements)]
+        all_species = {*map(_element_str, structure.composition.elements)}
         subs = collections.defaultdict(list)
         for u, v in combinations(all_species, 2):
             subs[u].append(v)

tests/conftest.py

@@ -1,5 +1,6 @@
 from collections import defaultdict
 from pathlib import Path
+import numpy as np
 
 import pytest
 from monty.serialization import loadfn
@@ -23,6 +24,15 @@ def gan_struct(test_dir):
     return Structure.from_file(test_dir / "GaN.vasp")
 
 
+@pytest.fixture(scope="session")
+def mixed_valence_struct(test_dir):
+    return Structure(
+        lattice=np.array([[3.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]),
+        species=["Cu+", "Cu+", "Cu2+", "O2-"],
+        coords=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5]],
+    )
+
+
 @pytest.fixture(scope="session")
 def stable_entries_Mg_Ga_N(test_dir):
     return loadfn(test_dir / "stable_entries_Mg_Ga_N.json")

tests/test_ccd.py

@@ -24,7 +24,7 @@ def hd0(v_ga):
     )
     assert hd0.spin_index == 1
     assert pytest.approx(hd0.distortions[1]) == 0.0
-    assert pytest.approx(hd0.omega_eV) == 0.03268045792725
+    assert pytest.approx(hd0.omega_eV, rel=1e-4) == 0.03268045792725
     assert hd0.defect_band == [(138, 0, 1), (138, 1, 1)]
     assert hd0._get_ediff(output_order="bks").shape == (216, 2, 2)
     assert hd0._get_ediff(output_order="skb").shape == (2, 2, 216)

tests/test_generators.py

@@ -55,6 +55,13 @@ def test_antisite_generator(gan_struct) -> None:
     assert sorted(def_names) == ["Ga_N", "N_Ga"]
 
 
+def test_mixed_valence_antisite_generator(mixed_valence_struct) -> None:
+    anti_gen = AntiSiteGenerator().get_defects(mixed_valence_struct)
+    def_names = [defect.name for defect in anti_gen]
+    assert "Cu_Cu" not in def_names
+    assert set(def_names) == {"Cu_O", "O_Cu"}
+
+
 def test_interstitial_generator(gan_struct) -> None:
     gen = InterstitialGenerator().get_defects(
         gan_struct, insertions={"Mg": [[0, 0, 0]]}