Merge pull request #86 from amepproject/issue-85_cluster_single

adds single particles to cluster list

amep/cluster.py

@@ -940,7 +940,8 @@ def identify(
     sorted_clusters : list
         List of lists, where each list contains the indices of the particles
         that belong to the same cluster. The list is sorted by the number of
-        particles in each cluster.
+        particles in each cluster. Single particles are also included as
+        clusters in this list.
     idx : numpy.ndarray
         Array of shape (N,) containing the cluster ID for each particle. N is 
         the total number of particles.
@@ -1036,18 +1037,18 @@ def identify(
     particle_idx  = set(np.arange(len(coords)))
     clustered_idx = set()
 
-    n = 0
+    cluster_id = 0
     for cl in sorted_clusters:
-
         for i in cl:
-            idx[i] = n
+            idx[i] = cluster_id
             clustered_idx.add(i)
-
-        n += 1
+        cluster_id += 1
 
     # add leftover single particles
     for k in particle_idx - clustered_idx:
-        idx[k] = n
-        n += 1
+        idx[k] = cluster_id
+        sorted_clusters.append([k])
+        cluster_id += 1
+    idx=np.array(idx, dtype=int)
 
     return sorted_clusters, idx