Fix absorbing_atom index misuse in feff inputs.py (#3256)

Signed-off-by: KaifengZheng <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>

Author: kaifengZheng

pymatgen/io/feff/inputs.py

@@ -407,8 +407,7 @@ def __init__(self, struct, absorbing_atom, radius):
         self.absorbing_atom, self.center_index = get_absorbing_atom_symbol_index(absorbing_atom, struct)
         self.radius = radius
         self._cluster = self._set_cluster()
-        atom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]
-        self.pot_dict = get_atom_map(self._cluster, atom_sym)
+        self.pot_dict = get_atom_map(self._cluster, self.absorbing_atom)
 
     def _set_cluster(self):
         """

tests/files/.pytest-split-durations

@@ -1608,8 +1608,8 @@
     "tests/io/feff/test_sets.py::TestFeffInputSet::test_get_feff_tags": 0.0002768750418908894,
     "tests/io/feff/test_sets.py::TestFeffInputSet::test_large_systems": 0.0024949999642558396,
     "tests/io/feff/test_sets.py::TestFeffInputSet::test_number_of_kpoints": 0.0026772500132210553,
-    "tests/io/feff/test_sets.py::TestFeffInputSet::test_post_distdiff": 0.08853158302372321,
-    "tests/io/feff/test_sets.py::TestFeffInputSet::test_postfeffset": 0.09011012403061613,
+    "tests/io/feff/test_sets.py::TestFeffInputSet::test_post_dist_diff": 0.08853158302372321,
+    "tests/io/feff/test_sets.py::TestFeffInputSet::test_post_feffset": 0.09011012403061613,
     "tests/io/feff/test_sets.py::TestFeffInputSet::test_reciprocal_tags_and_input": 0.02034700004151091,
     "tests/io/feff/test_sets.py::TestFeffInputSet::test_small_system_EXAFS": 0.0005435419734567404,
     "tests/io/feff/test_sets.py::TestFeffInputSet::test_to_and_from_dict": 0.0007752509554848075,

tests/io/feff/test_sets.py

@@ -184,7 +184,7 @@ def test_large_systems(self):
         assert "CIF" not in elnes.tags
         assert "TARGET" not in elnes.tags
 
-    def test_postfeffset(self):
+    def test_post_feffset(self):
         self.mp_xanes.write_input(f"{self.tmp_path}/xanes_3")
         feff_dict_input = FEFFDictSet.from_directory(f"{self.tmp_path}/xanes_3")
         assert feff_dict_input.tags == Tags.from_file(f"{self.tmp_path}/xanes_3/feff.inp")
@@ -223,7 +223,7 @@ def test_postfeffset(self):
         struct_reci = Structure.from_file(f"{self.tmp_path}/Dup_reci/Co2O2.cif")
         assert struct_orig == struct_reci
 
-    def test_post_distdiff(self):
+    def test_post_dist_diff(self):
         feff_dict_input = FEFFDictSet.from_directory(f"{TEST_FILES_DIR}/feff_dist_test")
         assert feff_dict_input.tags == Tags.from_file(f"{TEST_FILES_DIR}/feff_dist_test/feff.inp")
         assert str(feff_dict_input.header()) == str(Header.from_file(f"{TEST_FILES_DIR}/feff_dist_test/HEADER"))
@@ -259,3 +259,10 @@ def test_big_radius(self):
             },
         )
         assert str(dict_set) is not None
+
+    def test_cluster_index(self):
+        # https://github.com/materialsproject/pymatgen/pull/3256
+        cif_file = f"{TEST_FILES_DIR}/Fe3O4.cif"
+        structure = CifParser(cif_file).get_structures()[0]
+        for idx in range(len(structure.species)):
+            assert Atoms(structure, idx, 3).cluster