Added parsing of masses and (partial) charges

Author: Bernadette-Mohr

src/nomad_simulation_parsers/parsers/gromacs/parser.py

@@ -531,6 +531,28 @@ def get_atom_labels(self, index: int = 0) -> list[str]:
             labels = ['CGX'] * len(labels)
         return labels
 
+    def get_atom_parameters(self) -> list[dict[str, Any]]:
+        """Return per-atom topology parameters as a list of dicts.
+
+        Each dict contains 'label' (str) plus, when available from MDAnalysis:
+        'mass' (float, amu) and 'charge' (float, elementary charge).
+        """
+        labels = self.get_atom_labels(0)
+        result: list[dict[str, Any]] = [{'label': lbl} for lbl in labels]
+        universe = self.data_object.universe
+        if universe is not None:
+            try:
+                for i, mass in enumerate(universe.atoms.masses):
+                    result[i]['mass'] = float(mass)
+            except Exception:
+                pass
+            try:
+                for i, charge in enumerate(universe.atoms.charges):
+                    result[i]['charge'] = float(charge)
+            except Exception:
+                pass
+        return result
+
     def get_outputs(self) -> list[dict[str, Any]]:
         outputs = []
         for step in self._thermodynamic_steps:
@@ -566,10 +588,15 @@ def get_bond_list(self) -> np.ndarray | None:
         return result
 
     def get_configurations(self) -> list[dict[str, Any]]:
+        # Topology is frame-independent; compute once at index 0.
+        atom_parameters = self.get_atom_parameters()
+        n_atoms = self.data_object.get_n_atoms(0)
+
         configurations = []
         for n, _ in enumerate(self._trajectory_steps_sampled):
             config = dict(
-                labels=self.get_atom_labels(n),
+                n_atoms=n_atoms,
+                labels=atom_parameters,
                 positions=self.data_object.get_positions(n),
                 velocities=self.data_object.get_velocities(n),
                 lattice_vectors=self.data_object.get_lattice_vectors(n),

src/nomad_simulation_parsers/schema_packages/gromacs.py

@@ -97,7 +97,14 @@ class Program(general.Program):
 
 
 class AtomsState(model_system.AtomsState):
-    add_mapping_annotation(model_system.AtomsState.label, TPR_KEY, '.@')
+    add_mapping_annotation(model_system.AtomsState.label, TPR_KEY, '.label')
+    add_mapping_annotation(model_system.AtomsState.mass, TPR_KEY, '.mass', unit='amu')
+    add_mapping_annotation(
+        model_system.AtomsState.partial_charge,
+        TPR_KEY,
+        '.charge',
+        unit='elementary_charge',
+    )
 
 
 class AtomicCell(model_system.Representation):