From:  Ray Shan <rshan@...1795...> 
Date:  Sat, 21 Oct 2017 10:49:49 +0000 
From the atomic velocities calculate the velocity autocorrelation function, then take the Fourier transform (with Matlab). This will give you the Phonon DOS, provided that your MD trajectories had reached equilibrium.
An alternative to the above is to use the UserPhonon package, which gives you the dynamical matrix directly.
Ray
