Updates to box variables adding new sub_box variables and propagating changes through all of the modes

src/mode_create.f90

@@ -137,8 +137,12 @@ module mode_create
 
         !The last thing we do is setup the sub_box_boundaries
         call alloc_sub_box(1)
+        sub_box_num = 1
         sub_box_ori(:,:,1) = orient
         sub_box_bd(:,1) = box_bd
+        sub_box_array_bd(1,:,1) = 1
+        sub_box_array_bd(2,1,1) = atom_num
+        sub_box_array_bd(2,2,1) = ele_num
     end subroutine create
     !This subroutine parses the command and pulls out information needed for mode_create
     subroutine parse_command()