add AtomsState.partial_charge for atom-centered fractional charges (#335)

* add AtomsState.partial_charge

* add test docstring

Author: EBB2675

src/nomad_simulations/schema_packages/atoms_state.py

@@ -1114,6 +1114,16 @@ class AtomsState(ParticleState):
         """,
     )
 
+    partial_charge = Quantity(
+        type=np.float64,
+        unit='elementary_charge',
+        description="""
+        Atom-centered partial charge used in force fields or population analyses
+        (e.g., Mulliken, Hirshfeld, CM5, NPA, RESP). This quantity is distinct from
+        the formal integer oxidation-like `charge`.
+        """,
+    )
+
     spin = Quantity(
         type=np.int32,
         default=0,

tests/test_atoms_state.py

@@ -487,6 +487,25 @@ def test_atomic_number_to_symbol(self, atomic_number: int, chemical_symbol: str)
         atom_state.normalize(EntryArchive(), logger)
         assert atom_state.chemical_symbol == chemical_symbol
 
+    def test_partial_charge_is_independent_of_formal_charge(self):
+        """
+        Test that `partial_charge` is preserved independently from the formal
+        integer `charge` after normalization.
+        """
+        atom_state = AtomsState(
+            chemical_symbol='O',
+            charge=-1,
+            partial_charge=-0.42 * ureg.elementary_charge,
+        )
+        atom_state.normalize(EntryArchive(), logger)
+
+        assert atom_state.charge == -1
+        assert atom_state.partial_charge is not None
+        assert (
+            pytest.approx(atom_state.partial_charge.to('elementary_charge').magnitude)
+            == -0.42
+        )
+
 
 class TestCGBeadState:
     """