Fixed 2 Bugs in the setupCalculation function

1.  ensure_adsorbate_after_substrate now also works with configuration SETS.

2. For a single Configuration object the hash is now provided via configuration.getHash(). This ensures that the folder of the calculation matches the hash name

sample/helpers/setup.py

@@ -565,7 +565,9 @@ def setupCalculation(config,
         substrate_control_file = ControlFile(substrate_control_file)
 
     if type(config).__name__ == 'Configuration':
-        h = config.getUntransformedHash()
+        #h = config.getUntransformedHash()
+        #R.B. bugfix -> the above seems to be unreasonable and gives the wrong hash for the calculation folder name
+        h = config.getHash()
     elif type(config).__name__ == 'tuple':
         h = config
         config = proj.getConfiguration(h)
@@ -594,7 +596,8 @@ def setupCalculation(config,
                                                   add_area_prefix=add_area_prefix,
                                                   substrate_displacements=substrate_displacements,
                                                   only_substrates=only_substrates,
-                                                  remove_atoms_below_threshold=remove_atoms_below_threshold)
+                                                  remove_atoms_below_threshold=remove_atoms_below_threshold,
+                                                  ensure_adsorbate_after_substrate=ensure_adsorbate_after_substrate)
             if verbose: print("list_of_calc_dirs: ", list_of_calc_dirs)
         return list_of_calc_dirs
     else: