update ARCHIVE, DIFFUSE and RADIAL for variable box size; add nitrogen test case

git-svn-id: svn://dasher.wustl.edu/tinker@4 9dbd3ec4-0870-4ad8-bd6a-181c4f7deb04
update ARCHIVE, DIFFUSE and RADIAL, part 2

git-svn-id: svn://dasher.wustl.edu/tinker@5 9dbd3ec4-0870-4ad8-bd6a-181c4f7deb04