Merge pull request #284 from pyiron/fix_traj_ind

Hotfix: Handle empty indices

pyiron_atomistics/atomistics/job/atomistic.py

@@ -751,17 +751,20 @@ def __init__(self):
 class Trajectory(HasStructure):
     """
     A trajectory instance compatible with the ase.io class
-
-    Args:
-        positions (numpy.ndarray): The array of the trajectory in cartesian coordinates
-        structure (pyiron.atomistics.structure.atoms.Atoms): The initial structure instance from which the species info
-                                                             is derived
-        center_of_mass (bool): False (default) if the specified positions are w.r.t. the origin
-        cells (numpy.ndarray): Optional argument of the cell shape at every time step (Nx3x3 array) when the volume
-                                varies
     """
 
-    def __init__(self, positions, structure, center_of_mass=False, cells=None, indices=None, table_name="trajectory"):
+    def __init__(self, positions, structure, center_of_mass=False, cells=None, indices=None):
+        """
+
+        Args:
+            positions (ndarray): The array of the trajectory in cartesian coordinates
+            structure (pyiron.atomistics.structure.atoms.Atoms): The initial structure instance from which the species
+                                                                 info is derived
+            center_of_mass (bool): False (default) if the specified positions are w.r.t. the origin
+            cells (None/ndarray): Optional argument of the cell shape at every time step (Nx3x3 array) when the volume
+                                  varies
+            indices (None/ndarray): Indices for the species in the structure
+        """
 
         if center_of_mass:
             pos = np.copy(positions)
@@ -789,8 +792,12 @@ def __getitem__(self, item):
             return new_structure
         elif isinstance(item, (list, np.ndarray, slice)):
             snapshots = np.arange(len(self), dtype=int)[item]
-            return Trajectory(positions=self._positions[snapshots], cells=self._cells[snapshots],
-                              structure=self[snapshots[0]], indices=self._indices[snapshots])
+            if self._cells is not None:
+                return Trajectory(positions=self._positions[snapshots], cells=self._cells[snapshots],
+                                  structure=self[snapshots[0]], indices=self._indices[snapshots])
+            else:
+                return Trajectory(positions=self._positions[snapshots], cells=self._cells,
+                                  structure=self[snapshots[0]], indices=self._indices[snapshots])
 
     def _get_structure(self, frame=-1, wrap_atoms=True):
         return self[frame]