Fix overlap command

src/opt_delete.f90

@@ -126,13 +126,24 @@ module opt_delete
                                         end if
 
                                         !Now zero out the larger index
-                                        if(i < nei) then 
-                                            which_cell(:,i) = 0
-                                            cycle atom_loop
+                                        if(first) then 
+                                            if(i > nei) then 
+                                                which_cell(:,i) = 0
+                                                cycle atom_loop
+                                            else
+                                                which_cell(:,nei) = 0 
+                                                cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci) = 0
+                                            end if
                                         else
-                                            which_cell(:,nei) = 0 
-                                            cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci) = 0
+                                            if(i < nei) then 
+                                                which_cell(:,i) = 0
+                                                cycle atom_loop
+                                            else
+                                                which_cell(:,nei) = 0 
+                                                cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci) = 0
+                                            end if
                                         end if
+
                                     end if
                                 end if
                             end do