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

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Merged
EBB2675 merged 2 commits into from
Feb 26, 2026
Merged

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

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a770bd1
add AtomsState.partial_charge
EBB2675 Feb 26, 2026
01475bd
add test docstring
EBB2675 Feb 26, 2026
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10 changes: 10 additions & 0 deletions src/nomad_simulations/schema_packages/atoms_state.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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`.
""",
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@Bernadette-Mohr Bernadette-Mohr Feb 26, 2026

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I like your definition better than mine, great!

)

spin = Quantity(
type=np.int32,
default=0,
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15 changes: 15 additions & 0 deletions tests/test_atoms_state.py
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@ndaelman-hu ndaelman-hu Feb 26, 2026

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Thank you for the dedication to testing. Since we do not have any automated systems to populate one charge from the other, this test could also be safely removed. This marginally reduces the test stack. Conversely, if you want to safeguard against future normalization improperly deriving one from the other, you can leave it in.

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@EBB2675 EBB2675 Feb 26, 2026

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Conversely, if you want to safeguard against future normalization improperly deriving one from the other, you can leave it in.

Thanks alot, that makes sense. I think i will indeed keep this one test as a lightweight regression guard for the future 👍

Original file line number Diff line number Diff line change
Expand Up @@ -487,6 +487,21 @@ 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):
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:
"""
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