Element/Species: order full_electron_structure by energy (#3944)

Author: rkingsbury

src/pymatgen/analysis/magnetism/jahnteller.py

@@ -345,7 +345,7 @@ def _get_number_of_d_electrons(species: Species) -> float:
 
         # taken from get_crystal_field_spin
         elec = species.element.full_electronic_structure
-        if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d":
+        if len(elec) < 4 or elec[-2][1] != "s" or elec[-1][1] != "d":
             raise AttributeError(f"Invalid element {species.symbol} for crystal field calculation.")
         n_electrons = int(elec[-1][2] + elec[-2][2] - species.oxi_state)  # type: ignore[operator]
         if n_electrons < 0 or n_electrons > 10:

src/pymatgen/core/periodic_table.py

@@ -33,6 +33,28 @@
 
 _pt_row_sizes = (2, 8, 8, 18, 18, 32, 32)
 
+_madelung = [
+    (1, "s"),
+    (2, "s"),
+    (2, "p"),
+    (3, "s"),
+    (3, "p"),
+    (4, "s"),
+    (3, "d"),
+    (4, "p"),
+    (5, "s"),
+    (4, "d"),
+    (5, "p"),
+    (6, "s"),
+    (4, "f"),
+    (5, "d"),
+    (6, "p"),
+    (7, "s"),
+    (5, "f"),
+    (6, "d"),
+    (7, "p"),
+]
+
 
 @functools.total_ordering
 @unique
@@ -422,11 +444,12 @@ def icsd_oxidation_states(self) -> tuple[int, ...]:
     @property
     def full_electronic_structure(self) -> list[tuple[int, str, int]]:
         """Full electronic structure as list of tuples, in order of increasing
-        principal (n) and angular momentum (l)  quantum numbers.
+        energy level (according to the Madelung rule). Therefore, the final
+        element in the list gives the electronic structure of the valence shell.
 
         For example, the electronic structure for Fe is represented as:
         [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
-        (3, "d", 6), (4, "s", 2)].
+        (4, "s", 2), (3, "d", 6)].
 
         References:
             Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST
@@ -445,7 +468,13 @@ def parse_orbital(orb_str):
         if data[0][0] == "[":
             sym = data[0].replace("[", "").replace("]", "")
             data = list(Element(sym).full_electronic_structure) + data[1:]
-        return data
+        # sort the final electronic structure by increasing energy level
+        return sorted(data, key=lambda x: _madelung.index((x[0], x[1])))
+
+    @property
+    def n_electrons(self) -> int:
+        """Total number of electrons in the Element."""
+        return sum([t[-1] for t in self.full_electronic_structure])
 
     @property
     def valence(self) -> tuple[int | np.nan, int]:
@@ -1117,7 +1146,8 @@ def electronic_structure(self) -> str:
     @property
     def full_electronic_structure(self) -> list[tuple[int, str, int]]:
         """Full electronic structure as list of tuples, in order of increasing
-        principal (n) and angular momentum (l)  quantum numbers.
+        energy level (according to the Madelung rule). Therefore, the final
+        element in the list gives the electronic structure of the valence shell.
 
         For example, the electronic structure for Fe+2 is represented as:
         [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
@@ -1140,7 +1170,15 @@ def parse_orbital(orb_str):
         if data[0][0] == "[":
             sym = data[0].replace("[", "").replace("]", "")
             data = list(Element(sym).full_electronic_structure) + data[1:]
-        return data
+        # sort the final electronic structure by increasing energy level
+        return sorted(data, key=lambda x: _madelung.index((x[0], x[1])))
+
+    # NOTE - copied exactly from Element. Refactoring / inheritance may improve
+    # robustness
+    @property
+    def n_electrons(self) -> int:
+        """Total number of electrons in the Species."""
+        return sum([t[-1] for t in self.full_electronic_structure])
 
     # NOTE - copied exactly from Element. Refactoring / inheritance may improve
     # robustness
@@ -1319,7 +1357,7 @@ def get_crystal_field_spin(
             raise ValueError("Invalid coordination or spin config")
 
         elec = self.element.full_electronic_structure
-        if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d":
+        if len(elec) < 4 or elec[-2][1] != "s" or elec[-1][1] != "d":
             raise AttributeError(f"Invalid element {self.symbol} for crystal field calculation")
 
         assert self.oxi_state is not None

tests/core/test_periodic_table.py

@@ -74,8 +74,8 @@ def test_full_electronic_structure(self):
                 (2, "p", 6),
                 (3, "s", 2),
                 (3, "p", 6),
-                (3, "d", 6),
                 (4, "s", 2),
+                (3, "d", 6),
             ],
             "Li": [(1, "s", 2), (2, "s", 1)],
             "U": [
@@ -84,19 +84,19 @@ def test_full_electronic_structure(self):
                 (2, "p", 6),
                 (3, "s", 2),
                 (3, "p", 6),
-                (3, "d", 10),
                 (4, "s", 2),
+                (3, "d", 10),
                 (4, "p", 6),
-                (4, "d", 10),
                 (5, "s", 2),
+                (4, "d", 10),
                 (5, "p", 6),
+                (6, "s", 2),
                 (4, "f", 14),
                 (5, "d", 10),
-                (6, "s", 2),
                 (6, "p", 6),
+                (7, "s", 2),
                 (5, "f", 3),
                 (6, "d", 1),
-                (7, "s", 2),
             ],
         }
         for k, v in cases.items():
@@ -169,6 +169,11 @@ def test_from_row_and_group(self):
         for k, v in cases.items():
             assert ElementBase.from_row_and_group(v[0], v[1]) == Element(k)
 
+    def test_n_electrons(self):
+        cases = {"O": 8, "Fe": 26, "Li": 3, "Be": 4}
+        for k, v in cases.items():
+            assert Element(k).n_electrons == v
+
     def test_valence(self):
         cases = {"O": (1, 4), "Fe": (2, 6), "Li": (0, 1), "Be": (0, 2)}
         for k, v in cases.items():
@@ -602,18 +607,20 @@ def test_sort(self):
 
     def test_species_electronic_structure(self):
         assert Species("Fe", 0).electronic_structure == "[Ar].3d6.4s2"
+        assert Species("Fe", 0).n_electrons == 26
         assert Species("Fe", 0).full_electronic_structure == [
             (1, "s", 2),
             (2, "s", 2),
             (2, "p", 6),
             (3, "s", 2),
             (3, "p", 6),
-            (3, "d", 6),
             (4, "s", 2),
+            (3, "d", 6),
         ]
         assert Species("Fe", 0).valence == (2, 6)
 
         assert Species("Fe", 2).electronic_structure == "[Ar].3d6"
+        assert Species("Fe", 2).n_electrons == 24
         assert Species("Fe", 2).full_electronic_structure == [
             (1, "s", 2),
             (2, "s", 2),
@@ -625,6 +632,7 @@ def test_species_electronic_structure(self):
         assert Species("Fe", 2).valence == (2, 6)
 
         assert Species("Fe", 3).electronic_structure == "[Ar].3d5"
+        assert Species("Fe", 3).n_electrons == 23
         assert Species("Fe", 3).full_electronic_structure == [
             (1, "s", 2),
             (2, "s", 2),
@@ -635,12 +643,36 @@ def test_species_electronic_structure(self):
         ]
         assert Species("Fe", 3).valence == (2, 5)
 
+        assert Species("Th", 4).electronic_structure == "[Hg].6p6"
+        assert Species("Th", 4).full_electronic_structure == [
+            (1, "s", 2),
+            (2, "s", 2),
+            (2, "p", 6),
+            (3, "s", 2),
+            (3, "p", 6),
+            (4, "s", 2),
+            (3, "d", 10),
+            (4, "p", 6),
+            (5, "s", 2),
+            (4, "d", 10),
+            (5, "p", 6),
+            (6, "s", 2),
+            (4, "f", 14),
+            (5, "d", 10),
+            (6, "p", 6),
+        ]
+        assert Species("Th", 4).valence == (1, 6)
+
         assert Species("Li", 1).electronic_structure == "1s2"
+        assert Species("Li", 1).n_electrons == 2
         # alkali metals, all p
         for el in ["Na", "K", "Rb", "Cs"]:
             assert Species(el, 1).electronic_structure.split(".")[-1][1::] == "p6", f"Failure for {el} +1"
         for el in ["Ca", "Mg", "Ba", "Sr"]:
             assert Species(el, 2).electronic_structure.split(".")[-1][1::] == "p6", f"Failure for {el} +2"
+        # valence shell should be f (l=3) for all lanthanide ions except La+3 and Lu+3
+        for el in ["Ce", "Nd", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu"]:
+            assert Species(el, 3).valence[0] == 3, f"Failure for {el} +3"
 
         for el in Element:
             for ox in el.common_oxidation_states:

tests/io/vasp/test_inputs.py

@@ -1099,8 +1099,8 @@ def test_nelectrons(self):
         assert self.psingle_Fe.nelectrons == 8
 
     def test_electron_config(self):
-        assert self.psingle_Mn_pv.electron_configuration == [(4, "s", 2), (3, "d", 5), (3, "p", 6)]
-        assert self.psingle_Fe.electron_configuration == [(4, "s", 2), (3, "d", 6)]
+        assert self.psingle_Mn_pv.electron_configuration == [(3, "d", 5), (4, "s", 2), (3, "p", 6)]
+        assert self.psingle_Fe.electron_configuration == [(3, "d", 6), (4, "s", 2)]
 
     def test_attributes(self):
         for key, val in self.Mn_pv_attrs.items():