Fix bug for writing to .xyz file after delete

src/elements.f90

@@ -533,6 +533,7 @@ module elements
         !accidentally overwrite values which need to be deleted
         do i = num, 1, -1
             node_num = node_num - ng_node(lat_ele(sorted_index(i)))
+            node_atoms = node_atoms - ng_node(lat_ele(sorted_index(i)))*basisnum(lat_ele(sorted_index(i)))
             if(sorted_index(i) == ele_num) then 
                 r_node(:,:,:,sorted_index(i)) = 0.0_dp
                 type_ele(sorted_index(i)) =''