added mmerging of trajectories

aiida_nanotech_empa/workflows/cp2k/reftraj_md_workchain.py

@@ -173,13 +173,26 @@ def merge_batches_output(self):
         # merged_traj = []
         # for i_batch in range(self.ctx.n_batches):
         #    merged_traj.extend(self.ctx[f"reftraj_batch_{i_batch}"].outputs.trajectory)
+        positions=[self.ctx.first_structure.outputs.output_trajectory.get_array('positions')]
+        cells=[self.ctx.first_structure.outputs.output_trajectory.get_array('cells')]
+        forces=[self.ctx.first_structure.outputs.output_trajectory.get_array('forces')]
         for batch in self.ctx.batches:
             key = f"reftraj_batch_{batch[0]}_to_{batch[-1]}"
             if not  getattr(
             self.ctx, key).is_finished_ok:
                 self.report(f"Batch {key} failed")
                 return self.exit_codes.ERROR_TERMINATION
-
+            positions.append(getattr(self.ctx, key).outputs.output_trajectory.get_array('positions'))
+            cells.append(getattr(self.ctx, key).outputs.output_trajectory.get_array('cells'))
+            forces.append(getattr(self.ctx, key).outputs.output_trajectory.get_array('forces'))
+
+        positions=np.concatenate(positions)
+        cells=np.concatenate(cells)
+        forces=np.concatenate(forces)
+        symbols = self.ctx.first_structure.outputs.output_trajectory.symbols
+        output_trajectory = TrajectoryData()   
+        output_trajectory.set_trajectory(symbols, positions, cells=cells) 
+        self.out('output_trajectory', self.inputs.trajectory)
         self.report("done")
         return engine.ExitCode(0)