Hi Cerda,
Historically, the attraction between atoms is measured as a negative value in energy units and repulsion/destabilization as a positive value (remember Lennard-Jones potential form). Therefore, any stable system of interacting atoms will have negative potential energy due to the net attraction/bonding. The freeEnergy() function from PhononDOS gives U - TS (without the potential energy) and this can be positive or negative depending on the temperature. At 0 K, there is no entropy and U=zero point energy, so pdos.freeEnergy(0*Kelvin) will be positive because ZPE is positive. As T increases, the entropic contribution to free energy increases, and free energy becomes negative when -TS overcomes U. I hope the above answers your question.
With regards,
Suresh
