Fix bug in atom_types.

The atom_types were not correctly set because the Potential
object instanciation was done after the cluster creation!
This is an issue.

tests/sprkkr/copper/Cu.py

@@ -12,6 +12,7 @@ from sprkkr.calculator import SPRKKR
 from ase.build import bulk
 
 
+
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
@@ -57,6 +58,8 @@ if 'sprkkr' in sys.argv:
 
 # ######### MsSpec part
 if 'msspec' in sys.argv:
+    pot = SPRKKRPotential(Cu, "Cu/Cu.pot_new", *glob.glob("Cu/*PHAGEN.pot"))
+
     nplanes = 3
     cluster = hemispherical_cluster(Cu, planes=nplanes,
                                     emitter_plane=nplanes-1)
@@ -64,10 +67,7 @@ if 'msspec' in sys.argv:
 
     calc = MSSPEC(folder="calc")
     calc.set_atoms(cluster)
-
-    pot = SPRKKRPotential(Cu, "Cu/Cu.pot", *glob.glob("Cu/*PHAGEN.pot"))
     calc.tmatrix_parameters.potential = pot
-    calc.phagen_parameters.noproto = '.true.'
 
     data = calc.get_theta_scan(level='2p3/2')
     data.view()