enhance unit test and add scrambled POTCARs

Author: DanielYang59

dev_scripts/potcar_scrambler.py

@@ -21,7 +21,7 @@
 
 class PotcarScrambler:
     """
-    Takes a POTCAR and replaces its values with completely random values
+    Takes a POTCAR and replaces its values with completely random values.
     Does type matching and attempts precision matching on floats to ensure
     file is read correctly by Potcar and PotcarSingle classes.
 
@@ -40,14 +40,15 @@ class PotcarScrambler:
 
     def __init__(self, potcars: Potcar | PotcarSingle) -> None:
         self.PSP_list = [potcars] if isinstance(potcars, PotcarSingle) else potcars
-        self.scrambled_potcars_str = ""
+        self.scrambled_potcars_str: str = ""
         for psp in self.PSP_list:
             scrambled_potcar_str = self.scramble_single_potcar(psp)
             self.scrambled_potcars_str += scrambled_potcar_str
 
     def _rand_float_from_str_with_prec(self, input_str: str, bloat: float = 1.5) -> float:
-        n_prec = len(input_str.split(".")[1])
-        bd = max(1, bloat * abs(float(input_str)))  # ensure we don't get 0
+        """Generate a random float from str to replace true values."""
+        n_prec: int = len(input_str.split(".")[1])
+        bd: float = max(1.0, bloat * abs(float(input_str)))  # ensure we don't get 0
         return round(bd * np.random.default_rng().random(), n_prec)
 
     def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
@@ -124,14 +125,16 @@ def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         return scrambled_potcar_str
 
     def to_file(self, filename: str) -> None:
+        """Write scrambled POTCAR to file."""
         with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod
     def from_file(cls, input_filename: str, output_filename: str | None = None) -> Self:
+        """Read a POTCAR from file and generate a scrambled version."""
         psp = Potcar.from_file(input_filename)
         psp_scrambled = cls(psp)
-        if output_filename:
+        if output_filename is not None:
             psp_scrambled.to_file(output_filename)
         return psp_scrambled
 

src/pymatgen/io/vasp/inputs.py

@@ -2128,11 +2128,13 @@ def __repr__(self) -> str:
 
     @property
     def electron_configuration(self) -> list[tuple[int, str, int]] | None:
-        """Valence electronic configuration corresponding to the ZVAL.
+        """Valence electronic configuration corresponding to the ZVAL,
+        read from the "Atomic configuration" section of POTCAR.
 
         If the POTCAR defines a non-integer number of electrons,
             the configuration is not well-defined, and None is returned.
         """
+        # TODO: test non integer cases
         if not self.nelectrons.is_integer():
             warnings.warn(
                 "POTCAR has non-integer charge, electron configuration not well-defined.",
@@ -2144,10 +2146,15 @@ def electron_configuration(self) -> list[tuple[int, str, int]] | None:
         full_config: list[tuple[int, str, int]] = el.full_electronic_structure
         nelect: float = self.nelectrons
         config: list[tuple[int, str, int]] = []
+
         while nelect > 0:
-            e_config: tuple[int, str, int] = full_config.pop(-1)
-            config.append(e_config)
-            nelect -= e_config[-1]
+            n, l, num_e = full_config.pop(-1)
+            # Skip fully filled d/f orbitals if there are higher n orbitals
+            if l in {"d", "f"} and num_e in {10, 14} and any(n_ > n for n_, _, _ in full_config):
+                continue
+            config.append((n, l, num_e))
+            nelect -= num_e
+
         return config
 
     @property

tests/files/io/vasp/inputs/fake_potcars/POTCAR.Be.gz

@@ -1377,13 +1377,60 @@ def test_nelectrons(self):
         assert self.psingle_Mn_pv.nelectrons == 13
         assert self.psingle_Fe.nelectrons == 8
 
-    def test_electron_config(self):
+    def test_electron_configuration(self):
+        # TODO: use `approx` to compare floats
+
+        # Test s-block  (Li: 2s1)
+        assert PotcarSingle.from_file(f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Li.gz").electron_configuration == [
+            (2, "s", 1),
+        ]
+
+        # Test p-block  (O: 2s2 sp4)
+        assert PotcarSingle.from_file(f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE_54/POTCAR.O.gz").electron_configuration == [
+            (2, "s", 2),
+            (2, "p", 4),
+        ]
+
+        # Test d-block (Fe: 4s1 3d7)
+        assert self.psingle_Fe.electron_configuration == [(3, "d", 7), (4, "s", 1)]
+
+        # Test f-block (Ce: 5s2 6s2 5p6 5d1 4f1)
+        assert PotcarSingle.from_file(f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Ce.gz").electron_configuration == [
+            (5, "s", 2),
+            (6, "s", 2),
+            (5, "p", 6),
+            (5, "d", 1),
+            (4, "f", 1),
+        ]
+
+        # Test "sv" POTCARs (K_sv: 3s2 4s1 3p6)
+        assert PotcarSingle.from_file(
+            f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE_54/POTCAR.K_sv.gz"
+        ).electron_configuration == [
+            (3, "s", 2),
+            (4, "s", 1),
+            (3, "p", 6),
+        ]
+
+        # Test "pv" POTCARs
         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)]
+
+        # Test non-integer occupancy (Be: 2s1.99 2p0.01)
+        assert PotcarSingle.from_file(f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE_54/POTCAR.Be.gz").electron_configuration == [
+            (2, "s", 1.99),
+            (2, "p", 0.01),
+        ]
+
+        # Test another non-integer occupancy (H.25: 1s0.25)
+        assert PotcarSingle.from_file(
+            f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE_54/POTCAR.H.25.gz"
+        ).electron_configuration == [
+            (1, "s", 0.25),
+        ]
 
     def test_attributes(self):
         for key, val in self.Mn_pv_attrs.items():