simplify

Author: EBB2675

src/nomad_simulation_parsers/parsers/gaussian/parser.py

@@ -78,14 +78,12 @@ def _select_orientation(system: dict[str, Any]) -> Any:
             or system.get('z_matrix_orientation')
         )
 
-    def get_systems(self, src: dict[str, Any]) -> list[dict[str, Any]]:
+    def get_atoms(self, src):
         runs = src.get('run') or []
         runs = runs if isinstance(runs, list) else [runs]
-        systems: list[dict[str, Any]] = []
+        systems = []
 
         for run in runs:
-            charge = run.get('charge')
-            total_spin = self._get_total_spin(run.get('spin_target'))
             for system in run.get('system', []) or []:
                 orientation = self._select_orientation(system)
                 if orientation is None:
@@ -96,21 +94,9 @@ def get_systems(self, src: dict[str, Any]) -> list[dict[str, Any]]:
 
                 positions = arr[:, -3:]
                 atomic_numbers = arr[:, 1].astype(int) if arr.shape[1] > 1 else []
-                particle_states = []
-                for z in atomic_numbers:
-                    symbol = (
-                        chemical_symbols[z] if 0 <= z < len(chemical_symbols) else None
-                    )
-                    particle_states.append({'chemical_symbol': symbol})
-
-                systems.append(
-                    dict(
-                        positions=positions,
-                        particle_states=particle_states,
-                        total_charge=charge,
-                        total_spin=total_spin,
-                    )
-                )
+                atoms = [{'atomic_number': int(z)} for z in atomic_numbers]
+                systems.append({'positions': positions, 'particle_states': atoms})
+
         return systems
 
     def get_outputs(self, src: dict[str, Any]) -> list[dict[str, Any]]:
@@ -154,7 +140,9 @@ def parse(
 
         meta = MetainfoParser(data_object=Simulation())
         meta.annotation_key = 'out'
-        # meta.max_nested_level = 1
+        # Need to traverse Simulation -> ModelSystem -> particle_states
+        # Depth: Simulation (0) -> model_system (1) -> particle_states (2) -> AtomsState quantities (3)
+        meta.max_nested_level = 3
 
         reader.convert(meta)
         archive.data = meta.data_object

src/nomad_simulation_parsers/schema_packages/gaussian.py

@@ -16,58 +16,40 @@
 
 m_package = SchemaPackage()
 
-add_mapping_annotation(general.Simulation.m_def, OUT_KEY, '@')
-
-
-class Simulation(general.Simulation):
-    add_mapping_annotation(
-        general.Simulation.program, OUT_KEY, ('get_program_data', ['.@'])
-    )
-    add_mapping_annotation(
-        general.Simulation.model_system, OUT_KEY, ('get_systems', ['.@'])
-    )
-    # add_mapping_annotation(
-    #     general.Simulation.outputs, OUT_KEY, ('get_outputs', ['.@'])
-    # )
-
-
-class Program(general.Program):
-    add_mapping_annotation(general.Program.name, OUT_KEY, '.name')
-    add_mapping_annotation(general.Program.version, OUT_KEY, '.version')
-
 
-class ModelSystem(model_system.ModelSystem):
-    add_mapping_annotation(model_system.ModelSystem.positions, OUT_KEY, '.positions')
-    add_mapping_annotation(
-        model_system.ModelSystem.total_charge, OUT_KEY, '.total_charge'
-    )
-    add_mapping_annotation(model_system.ModelSystem.total_spin, OUT_KEY, '.total_spin')
-    add_mapping_annotation(atoms_state.AtomsState.m_def, OUT_KEY, '.particle_states')
+############# Simulation + Program ###################
 
+add_mapping_annotation(general.Simulation.m_def, OUT_KEY, '@')
 
-class AtomsState(atoms_state.AtomsState):
-    add_mapping_annotation(
-        atoms_state.AtomsState.chemical_symbol, OUT_KEY, '.chemical_symbol'
-    )
+add_mapping_annotation(general.Simulation.program, OUT_KEY, '.@')
 
+add_mapping_annotation(general.Program.version, OUT_KEY, '.program_version')
 
-# class Outputs(outputs.Outputs):
-#     add_mapping_annotation(outputs.Outputs.total_energies, OUT_KEY, '.total_energies')
-#     add_mapping_annotation(outputs.Outputs.total_forces, OUT_KEY, '.total_forces')
+############# Atoms / ModelSystem ###################
 
+add_mapping_annotation(
+    general.Simulation.model_system,
+    OUT_KEY,
+    ('get_atoms', ['.@']),
+)
 
-# class TotalEnergy(properties.energies.TotalEnergy):
-#     add_mapping_annotation(
-#         properties.energies.TotalEnergy.value,
-#         OUT_KEY,
-#         '.value || .energy_total || .@',
-#     )
+add_mapping_annotation(
+    model_system.ModelSystem.positions,
+    OUT_KEY,
+    '.positions',
+)
 
+add_mapping_annotation(
+    atoms_state.AtomsState.m_def,
+    OUT_KEY,
+    '.particle_states',
+)
 
-# class TotalForce(properties.forces.TotalForce):
-#     add_mapping_annotation(
-#         properties.forces.TotalForce.value, OUT_KEY, '.value || .forces || .@'
-#     )
+add_mapping_annotation(
+    atoms_state.AtomsState.atomic_number,
+    OUT_KEY,
+    '.atomic_number',
+)
 
 try:
     m_package.__init_metainfo__()