Merge remote-tracking branch 'origin/develop' into nonlocal-correlation

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,

src/nomad_simulations/schema_packages/force_field.py

@@ -353,7 +353,7 @@ def normalize(self, archive, logger) -> None:
                 except ValueError as e:
                     logger.warning(
                         f'Unable to derive tabulated forces from energies in {self.name},'
-                        f'Unkown error occurred in derivation: {e}'
+                        f'Unknown error occurred in derivation: {e}'
                     )
 
             if self.forces is not None and self.energies is None:
@@ -399,7 +399,7 @@ def normalize(self, archive, logger) -> None:
                 except ValueError as e:
                     logger.warning(
                         f'Unable to derive tabulated energies from forces in {self.name},'
-                        f'Unkown error occurred in derivation: {e}'
+                        f'Unknown error occurred in derivation: {e}'
                     )
 
 

src/nomad_simulations/schema_packages/model_method.py

@@ -223,11 +223,13 @@ def normalize(self, archive, logger):
             )
 
 
-class ExplicitDispersionModel(BaseModelMethod):
-    """Explicit dispersion / vdW treatment used together with an ab-initio method.
+class EmpiricalDispersionModel(BaseModelMethod):
+    """Empirical dispersion correction used together with an ab-initio method.
 
     Covers pairwise-additive (D2/D3/D3(BJ)/D4), density-dependent (TS/TS-SCS),
-    many-body dispersion (MBD, e.g. MBD@rsSCS), and exchange-hole based (XDM) models.
+    many-body dispersion (MBD, e.g. MBD@rsSCS), and exchange-hole based XDM.
+    In literature, `DFT-D` is often used as an umbrella label; this schema stores
+    the concrete generation explicitly when available (e.g. D2, D3, D3BJ, D4).
 
     References
     ----------
@@ -241,7 +243,7 @@ class ExplicitDispersionModel(BaseModelMethod):
 
     model = Quantity(
         type=MEnum(
-            # Pairwise / density-dependent
+            # Pairwise / density-dependent empirical models
             'D2',
             'D3',
             'D3BJ',
@@ -257,7 +259,7 @@ class ExplicitDispersionModel(BaseModelMethod):
             'XDM',
         ),
         description="""
-        Identifier of the explicit dispersion / vdW model.
+        Identifier of the empirical dispersion correction model.
         """,
     )
 
@@ -266,11 +268,10 @@ class ExplicitDispersionModel(BaseModelMethod):
         description='Short-range damping: D3{zero,BJ}, TS{fermi}, XDM{rational}.',
     )
 
-    xc_partner_ref = Quantity(
-        type=Reference(SectionProxy('XCFunctional')),
-        description="""
-        Reference to the baseline `XCFunctional` section this model is paired with.
-        """,
+    # TODO later: link to XCComponent(s)
+    xc_partner = Quantity(
+        type=str,
+        description="Base XC functional used/tuned for (e.g. 'PBE', 'SCAN', 'B3LYP').",
     )
 
 

src/nomad_simulations/schema_packages/numerical_settings.py

@@ -1287,9 +1287,9 @@ class SolvationSettings(NumericalSettings):
     )
 
 
-class DispersionKnob(ArchiveSection):
+class EmpiricalDispersionKnob(ArchiveSection):
     """
-    A single typed numerical knob for an explicit dispersion / vdW correction.
+    A single typed numerical knob for an empirical dispersion correction.
 
     This is a "typed physical constraint" record: it stores one scalar value
     together with semantics that disambiguate what the value controls.
@@ -1305,14 +1305,12 @@ class DispersionKnob(ArchiveSection):
             'a1',
             'a2',
             'sR',
-            # Nonlocal kernel parameter
-            'b',
             # Many-body screening / range separation
             'beta',
         ),
         description="""
         Identifies the dispersion parameter using standard notation.
-        (e.g. s6, a1, beta, b).
+        (e.g. s6, a1, beta).
 
         All dispersion knobs are dimensionless.
         """,
@@ -1323,7 +1321,6 @@ class DispersionKnob(ArchiveSection):
             'pairwise',
             'three_body_atm',
             'many_body',
-            'nonlocal_kernel',
             'density_partitioning',
         ),
         description="""
@@ -1339,13 +1336,13 @@ class DispersionKnob(ArchiveSection):
     )
 
 
-class DispersionSettings(NumericalSettings):
+class EmpiricalDispersionSettings(NumericalSettings):
     """
-    Numerical and evaluation settings for an explicit dispersion / vdW correction.
+    Numerical and evaluation settings for an empirical dispersion correction.
 
     This section contains discrete switches and environment choices (e.g. whether
     to include higher-order dispersion terms, which density partitioning is used),
-    as well as typed scalar parameters stored as `DispersionKnob`.
+    as well as typed scalar parameters stored as `EmpiricalDispersionKnob`.
     """
 
     # switches for term inclusion / order
@@ -1405,14 +1402,14 @@ class DispersionSettings(NumericalSettings):
 
     # typed scalar parameters
     knobs = SubSection(
-        sub_section=DispersionKnob.m_def,
+        sub_section=EmpiricalDispersionKnob.m_def,
         repeats=True,
         description="""
         Typed scalar parameters (knobs) for the dispersion correction.
 
         Examples:
           • D3BJ:  s6/s8 (pairwise), a1/a2 (pairwise), optionally s9 (three_body_atm)
-          • rVV10: b (nonlocal_kernel)
+          • MBD@rsSCS: beta (many_body)
         """,
     )
 

src/nomad_simulations/schema_packages/properties/molecular_orbitals.py

@@ -27,7 +27,11 @@ class MolecularOrbitals(ElectronicEigenvalues):
 
     # References
     basis_set_ref = Quantity(
-        type=Reference(SectionProxy('AtomCenteredBasisSet')),
+        type=Reference(
+            SectionProxy(
+                'nomad_simulations.schema_packages.basis_set.AtomCenteredBasisSet'
+            )
+        ),
         description="""
         Reference to the atom-centered basis set in which these molecular
         orbitals are expanded.

src/nomad_simulations/schema_packages/workflow/equation_of_state.py

@@ -215,7 +215,7 @@ def normalize(self, archive: EntryArchive, logger: BoundLogger) -> None:
                     )
                     self.eos_fit.append(eos_fit)
                 except Exception:
-                    logger.warning('EOS fit unsuccesful.')
+                    logger.warning('EOS fit unsuccessful.')
 
 
 class EquationOfState(ParallelWorkflow):

src/nomad_simulations/schema_packages/workflow/geometry_optimization.py

@@ -30,7 +30,7 @@ class GeometryOptimizationMethod(SimulationWorkflowMethod):
 
         | `"atomic"`             | the atomic coordinates alone are updated |
 
-        | `"cell_volume"`         | `"atomic"` + cell lattice paramters are updated isotropically |
+        | `"cell_volume"`         | `"atomic"` + cell lattice parameters are updated isotropically |
 
         | `"cell_shape"`        | `"cell_volume"` but without the isotropic constraint: all cell parameters are updated |
 
@@ -42,7 +42,7 @@ class GeometryOptimizationMethod(SimulationWorkflowMethod):
         shape=[],
         description="""
         The method used for geometry optimization. Some known possible values are:
-        `"steepest_descent"`, `"conjugant_gradient"`, `"low_memory_broyden_fletcher_goldfarb_shanno"`.
+        `"steepest_descent"`, `"conjugate_gradient"`, `"low_memory_broyden_fletcher_goldfarb_shanno"`.
         """,
     )
 
@@ -100,7 +100,7 @@ class GeometryOptimizationMethod(SimulationWorkflowMethod):
 
 
 class GeometryOptimizationResults(SimulationWorkflowResults):
-    _label = 'Geometry optimiztation results'
+    _label = 'Geometry optimization results'
 
     n_steps = Quantity(
         type=int,

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:
     """

tests/test_model_method.py

@@ -10,7 +10,7 @@
     DFT,
     TB,
     ActiveSpace,
-    ExplicitDispersionModel,
+    EmpiricalDispersionModel,
     ImplicitSolvationModel,
     MultireferencePT,
     MultireferenceSCF,
@@ -631,7 +631,7 @@ def test_dft_contributions_solvation_dispersion_relativity_normalize():
         refractive_index=1.33,
     )
 
-    edm = ExplicitDispersionModel(
+    edm = EmpiricalDispersionModel(
         model='D3BJ',
         damping_function='BJ',
     )
@@ -651,7 +651,7 @@ def test_dft_contributions_solvation_dispersion_relativity_normalize():
 
     assert len(dft.contributions) == 3
     assert isinstance(dft.contributions[0], ImplicitSolvationModel)
-    assert isinstance(dft.contributions[1], ExplicitDispersionModel)
+    assert isinstance(dft.contributions[1], EmpiricalDispersionModel)
     assert isinstance(dft.contributions[2], RelativityModel)
 
     # Solvation

tests/test_numerical_settings.py

@@ -4,8 +4,8 @@
 from nomad.units import ureg
 
 from nomad_simulations.schema_packages.numerical_settings import (
-    DispersionKnob,
-    DispersionSettings,
+    EmpiricalDispersionKnob,
+    EmpiricalDispersionSettings,
     KLinePath,
     KMesh,
     KSpaceFunctionalities,
@@ -491,27 +491,27 @@ def test_resolve_points(self, k_line_path: KLinePath):
         assert np.allclose(k_line_path.points, points)
 
 
-class TestDispersionSettings:
+class TestEmpiricalDispersionSettings:
     """
     Tests for dispersion numerical settings schema:
-      - typed physical constraints via DispersionKnob
-      - container section DispersionSettings
+      - typed physical constraints via EmpiricalDispersionKnob
+      - container section EmpiricalDispersionSettings
     """
 
     def test_knobs_roundtrip_and_normalize_noop(self):
         """
         Knobs should be storable and survive normalize() unchanged
         (no special normalization is defined currently).
         """
-        dns = DispersionSettings(
+        dns = EmpiricalDispersionSettings(
             include_c8=True,
             include_three_body_atm=False,
             partition_scheme='Hirshfeld',
             density_source='valence-only',
             knobs=[
-                DispersionKnob(kind='s6', applies_to='pairwise', value=1.0),
-                DispersionKnob(kind='a1', applies_to='pairwise', value=0.40),
-                DispersionKnob(kind='a2', applies_to='pairwise', value=4.00),
+                EmpiricalDispersionKnob(kind='s6', applies_to='pairwise', value=1.0),
+                EmpiricalDispersionKnob(kind='a1', applies_to='pairwise', value=0.40),
+                EmpiricalDispersionKnob(kind='a2', applies_to='pairwise', value=4.00),
             ],
         )
 
@@ -543,7 +543,7 @@ def test_switch_fields(
         """
         Basic storage test for the inclusion switches and max_dispersion_order.
         """
-        dns = DispersionSettings(
+        dns = EmpiricalDispersionSettings(
             include_three_body_atm=include_three_body_atm,
             include_c8=include_c8,
             include_c10=include_c10,
@@ -570,7 +570,7 @@ def test_environment_fields(self, partition_scheme, charge_model, density_source
         """
         Storage test for environment/charge/density-source categorical fields.
         """
-        dns = DispersionSettings(
+        dns = EmpiricalDispersionSettings(
             partition_scheme=partition_scheme,
             charge_model=charge_model,
             density_source=density_source,
@@ -586,10 +586,12 @@ def test_multiple_knobs_same_kind_allowed(self):
         It should be allowed to store multiple knobs of the same kind if they
         apply to different contributions (or even if not, schema-wise).
         """
-        dns = DispersionSettings(
+        dns = EmpiricalDispersionSettings(
             knobs=[
-                DispersionKnob(kind='s9', applies_to='three_body_atm', value=1.0),
-                DispersionKnob(kind='s9', applies_to='pairwise', value=0.0),
+                EmpiricalDispersionKnob(
+                    kind='s9', applies_to='three_body_atm', value=1.0
+                ),
+                EmpiricalDispersionKnob(kind='s9', applies_to='pairwise', value=0.0),
             ]
         )
         dns.normalize(EntryArchive(), logger=logger)