Compute the distance (sqrt of two-norm) between <tt>SR1</tt> and <tt>SR2</tt>.
If <tt>constrainedatoms[0] = 0</tt>, then all atoms are included in computing this
distance.  
If <tt>constrainedatoms[0] &gt; 0</tt>, then only constrained atoms are included in 
computing this distance.  

<p>
Also see <tt>setconfig1</tt>, <tt>setconfig2</tt>.
