Kumagai Correction (#196)

* plot fed

* plot fef

* plot fed

* plot fed

* plot fed

* plot fed

* remove uid

* remove uid

* add pydefect back

* test lint

pymatgen/analysis/defects/corrections/kumagai.py

@@ -40,7 +40,7 @@
 
 def _check_import_pydefect() -> None:
     """Import pydefect if it is installed."""
-    if __has_pydefect__:
+    if not __has_pydefect__:
         msg = "vise/pydefect is not installed. Please install it first."
         raise ModuleNotFoundError(
             msg,

pyproject.toml

@@ -35,12 +35,13 @@ dev = ["pre-commit>=2.12.1"]
 docs = [
   "jupyter-book>=0.13.1",
 ]
-optional = ["pydefect>=0.6.2", "dscribe>=2.0.0", "numba"]
+optional = ["pydefect", "dscribe>=2.0.0", "numba"]
 
 strict = [
   "pymatgen==2024.5.1",
   "dscribe==2.1.0",
   "mp-pyrho==0.4.4",
+  "pydefect==0.9.4",
 ]
 
 tests = ["pytest==8.2.0", "pytest-cov==5.0.0", "nbmake==1.5.3"]

tests/test_corrections.py

@@ -3,6 +3,7 @@
     get_freysoldt_correction,
     plot_plnr_avg,
 )
+from pymatgen.analysis.defects.corrections.kumagai import get_efnv_correction, get_structure_with_pot
 
 
 def test_freysoldt(data_Mg_Ga) -> None:
@@ -71,17 +72,23 @@ def test_freysoldt_sxdefect_compare(v_N_GaN) -> None:
         assert results[q] == pytest.approx(references[q], abs=1e-3)
 
 
-# def test_kumagai(test_dir):
-#     sb = get_structure_with_pot(test_dir / "Mg_Ga" / "bulk_sc")
-#     sd0 = get_structure_with_pot(test_dir / "Mg_Ga" / "q=0")
-#     sd1 = get_structure_with_pot(test_dir / "Mg_Ga" / "q=1")
+def test_kumagai(test_dir):
+    sb = get_structure_with_pot(test_dir / "Mg_Ga" / "bulk_sc")
+    sd0 = get_structure_with_pot(test_dir / "Mg_Ga" / "q=0")
+    sd1 = get_structure_with_pot(test_dir / "Mg_Ga" / "q=1")
 
-#     res0 = get_efnv_correction(
-#         0, sd0, sb, dielectric_tensor=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]
-#     )
-#     assert res0.correction_energy == pytest.approx(0, abs=1e-4)
+    res0 = get_efnv_correction(
+        0, sd0, sb, dielectric_tensor=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+    )
+    assert res0.correction_energy == pytest.approx(0, abs=1e-4)
+
+    res1 = get_efnv_correction(
+        1, sd1, sb, dielectric_tensor=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+    )
+    assert res1.correction_energy > 0
 
-#     res1 = get_efnv_correction(
-#         1, sd1, sb, dielectric_tensor=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]
-#     )
-#     assert res1.correction_energy > 0
+def test_kumagai_missing():
+    from pymatgen.analysis.defects.corrections import kumagai
+    kumagai.__has_pydefect__ = False
+    with pytest.raises(ImportError):
+        kumagai._check_import_pydefect()