Made normal modes work with shells and vsites

Made normal modes work with shells and vsites

Implement shells and vsites in normal mode analysis (do_nm routine)
and analysis of eigenvalues and frequencies. The normal mode analysis
is done on real atoms only and the shells are minimized at each step
of the analysis.

Fixes #879

Change-Id: Iac127f51ef4ebd246c9d2417e039778b5952122f