Add warning if there are no species in range of site

src/gemdat/transitions.py

@@ -504,17 +504,6 @@ def _calculate_atom_states(
         The value corresponds to the index in the `site_coords`.
         -1 indicates that atom is not at any site.
     """
-
-    def _site_radius_iterator():
-        for label, radius in site_radius.items():
-            if label:
-                grouped = ((k, site) for k, site in enumerate(sites) if site.label == label)
-                key, site_group = zip(*grouped)
-                frac_coords = np.array([site.frac_coords for site in site_group])
-                yield frac_coords, np.array(key), radius
-            else:
-                yield sites.frac_coords, None, radius
-
     lattice = trajectory.get_lattice()
 
     cutoff = max(list(site_radius.values()))
@@ -531,10 +520,23 @@ def _site_radius_iterator():
 
     atom_sites = np.full((traj_cart_coords.shape[0]), NOSITE)
 
-    for coords, key, radius in _site_radius_iterator():
-        cart_coords = lattice.get_cartesian_coords(coords)
+    for label, radius in site_radius.items():
+        if label:
+            grouped = ((k, site) for k, site in enumerate(sites) if site.label == label)
+            key, site_group = zip(*grouped)
+            frac_coords = np.array([site.frac_coords for site in site_group])
+            key = np.array(key)
+        else:
+            frac_coords = sites.frac_coords
+            key = None
+
+        cart_coords = lattice.get_cartesian_coords(frac_coords)
         site_index = periodic_tree.search_tree(cart_coords, radius * site_inner_fraction)
 
+        if site_index.size == 0:
+            warn(f'No floating species in range of {label} ({radius=})', stacklevel=2)
+            continue
+
         siteno, index = site_index.T
 
         if key is not None: