As always, the first thing you should do to avoid the warning is to read the literature so that you understand the theory of the method you are using.
Having done this, you’ll see that free energy minimisation depends on the phonon contribution to the thermodynamics, and so yes it does relate to phonon calculations.
What it almost certainly means is that you didn’t bother to optimise the structure via energy minimisation before starting the free energy minimisation (which leads to poor behaviour since free energy minimisation is usually a small perturbation of the energy minimum). Otherwise this can happen at high temperatures when the quasiharmonic approximation breaks down (see the theory of the method).
Thanks julian.I do know that free energy have vibrational contribution.And that is the reason why I use free energy minimization.
So generatly I should minimize the strucutre using potential energy only ,and then use the optimized structure to do free energy minimization.
Thank you very much