re-initialize neighbor lists at end to clear out the occasional list entry

src/create_bonds.cpp

@@ -298,6 +298,7 @@ void CreateBonds::many()
       }
     }
   }
+  neighbor->init();
 
   // recount bonds
 

src/delete_atoms.cpp

@@ -416,6 +416,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
       break;
     }
   }
+  neighbor->init();
 }
 
 /* ----------------------------------------------------------------------