Fix overlap command

src/opt_delete.f90

@@ -126,6 +126,15 @@ module opt_delete
                                         end if
 
                                         !Now zero out the larger index
+                                        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
                                             if(i < nei) then 
                                                 which_cell(:,i) = 0
                                                 cycle atom_loop
@@ -134,6 +143,8 @@ module opt_delete
                                                 cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci) = 0
                                             end if
                                         end if
+
+                                    end if
                                 end if
                             end do 
                         end do