Add flag to set all occupancies to 1

src/gemdat/transitions.py

@@ -49,6 +49,7 @@ def __init__(
         events: pd.DataFrame,
         states: np.ndarray,
         inner_states: np.ndarray,
+        set_partial_occupancies_to_1: bool = False,
     ):
         """Store event data for jumps and transitions between sites.
 
@@ -67,16 +68,25 @@ def __init__(
             Input states
         inner_states : np.ndarray
             Input states for inner sites
+        set_partial_occupancies_to_1 : bool
+            Change partial occupancies in the disordered sites and set them to 1.
         """
         if not (sites.is_ordered):
             warn(
                 'Input `sites` are disordered! '
                 'Although the code may work, it was written under the assumption '
                 'that an ordered structure would be passed. '
+                'Use `set_partial_occupancies_to_1=True` to set all occupancies to 1.'
                 'See https://github.com/GEMDAT-repos/GEMDAT/issues/339 for more information.',
                 stacklevel=2,
             )
 
+        if set_partial_occupancies_to_1:
+            for idx, site in enumerate(sites):
+                if site.is_ordered:
+                    continue
+                sites.replace(idx=idx, species=site.species.elements[0], label=site.label)
+
         self.sites = sites
         self.trajectory = trajectory
         self.diff_trajectory = diff_trajectory