Replace the scaled coordinates of atoms whose <tt>fixed[i] == 0</tt> by those
given in the .cn file <tt>incnfile</tt>.  The scaled coordinates of other atoms
as well as the <tt>H</tt> matrix are not changed.  At the end of <tt>replacefreeatom</tt>
the real coordinates are updated by a call to <tt>SHtoR</tt>.

<p>
Also see <tt>readcn</tt>.
