Add missing function

simulationworkflowschema/molecular_dynamics.py

@@ -48,6 +48,7 @@
 )
 from nomad.utils import get_logger
 from nomad.units import ureg
+from nomad import atomutils
 from .general import (
     SimulationWorkflowMethod,
     SimulationWorkflowResults,
@@ -1181,6 +1182,46 @@ def get_composition(children_names: List[str]) -> str:
     return formula
 
 
+def mda_universe_from_nomad_atoms(system, logger=None):
+    """Returns an instance of mda.Universe from a NOMAD Atoms-section.
+
+    Args:
+        system: The atoms to transform
+
+    Returns:
+        A new mda.Universe created from the given data.
+    """
+    n_atoms = len(system.positions)
+    n_residues = 1
+    atom_resindex = [0] * n_atoms
+    residue_segindex = [0]
+
+    universe = MDAnalysis.Universe.empty(
+        n_atoms,
+        n_residues=n_residues,
+        atom_resindex=atom_resindex,
+        residue_segindex=residue_segindex,
+        trajectory=True,
+    )
+
+    # Add positions
+    universe.atoms.positions = system.positions.to(ureg.angstrom).magnitude
+
+    # Add atom attributes
+    atom_names = system.labels
+    universe.add_TopologyAttr('name', atom_names)
+    universe.add_TopologyAttr('type', atom_names)
+    universe.add_TopologyAttr('element', atom_names)
+
+    # Add the box dimensions
+    if system.lattice_vectors is not None:
+        universe.atoms.dimensions = atomutils.cell_to_cellpar(
+            system.lattice_vectors.to(ureg.angstrom).magnitude, degrees=True
+        )
+
+    return universe
+
+
 class ThermostatParameters(ArchiveSection):
     """
     Section containing the parameters pertaining to the thermostat for a molecular dynamics run.