mostly working implementation of particle cell

src/nomad_simulations/schema_packages/atoms_state.py

@@ -559,7 +559,6 @@ class State(Entity):
 
     def __init__(self, m_def: 'Section' = None, m_context: 'Context' = None, **kwargs):
         super().__init__(m_def, m_context, **kwargs)
-        self.labels = None
 
 
 class AtomsState(State):
@@ -651,7 +650,3 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
             self.chemical_symbol = self.resolve_chemical_symbol(logger=logger)
         if self.atomic_number is None:
             self.atomic_number = self.resolve_atomic_number(logger=logger)
-
-        # Set the labels
-        if self.chemical_symbol is not None:
-            self.labels = self.chemical_symbol

src/nomad_simulations/schema_packages/general.py

@@ -225,7 +225,9 @@ def _set_system_branch_depth(
             )
 
     #! Generalize from checks for atomic systems, error with CG input
-    def resolve_composition_formula(self, system_parent: ModelSystem) -> None:
+    def resolve_composition_formula(
+        self, system_parent: ModelSystem, logger: 'BoundLogger'
+    ) -> None:
         """Determine and set the composition formula for `system_parent` and all of its
         descendants.
 
@@ -246,13 +248,15 @@ def set_composition_formula(
                 to the atom indices stored in system.
             """
             if not subsystems:
-                atom_indices = (
-                    system.atom_indices if system.atom_indices is not None else []
+                particle_indices = (
+                    system.particle_indices
+                    if system.particle_indices is not None
+                    else []
                 )
                 subsystem_labels = (
-                    [np.array(labels)[atom_indices]]
+                    [np.array(labels)[particle_indices]]
                     if labels
-                    else ['Unknown' for atom in range(len(atom_indices))]
+                    else ['Unknown' for atom in range(len(particle_indices))]
                 )
             else:
                 subsystem_labels = [
@@ -284,18 +288,7 @@ def get_composition_recurs(system: ModelSystem, labels: list[str]) -> None:
         # ! CG: system_parent.cell[0].particles_state instead of atoms_state!
         labels = []
         if system_parent.cell is not None:
-            if system_parent.cell[0].name == 'AtomicCell':
-                labels = (
-                    [atom.labels for atom in system_parent.cell[0].atoms_state]
-                    if system_parent.cell[0].atoms_state is not None
-                    else []
-                )
-            elif system_parent.cell[0].name == 'ParticleCell':
-                labels = (
-                    [atom.labels for atom in system_parent.cell[0].particles_state]
-                    if system_parent.cell[0].particles_state is not None
-                    else []
-                )
+            labels = system_parent.cell[0].get('labels', logger=logger)
 
         get_composition_recurs(system=system_parent, labels=labels)
 
@@ -322,7 +315,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
 
             if is_not_representative(model_system=system_parent, logger=logger):
                 continue
-            self.resolve_composition_formula(system_parent=system_parent)
+            self.resolve_composition_formula(system_parent=system_parent, logger=logger)
 
 
 m_package.__init_metainfo__()

src/nomad_simulations/schema_packages/model_method.py

@@ -544,7 +544,7 @@ def resolve_orbital_references(
             # If the child is not an "active_atom", the normalization will not run
             if active_atom.type != 'active_atom':
                 continue
-            indices = active_atom.atom_indices
+            indices = active_atom.particle_indices
             for index in indices:
                 try:
                     active_atoms_state = atoms_state[index]