free energy calculation for large cell

Hi all:
Recently I asked a question about calculating free energy using lammps and I was told there is a USER-Phonon package. I tried the package and that is really nice package. However, I find it is compiled to calculate phonon for regular lattice structure since it requires a map file for supercell calculations. In my case, I want to calculate the free energy of some defects that needs large cell. So there is no way to provide a map file as required in this package because of the presence of defects.
Can you give me some advice in this regards? Does anyone have experience about using finite difference method to calculate the force and then phonon properties? I read some paper using lammps to do so.
Thank you very much!

Estimation of free energy in MD is difficult in general. The most reliable methods are based on constructing a thermodynamically reversible path between a reference state and the state of interest, integrating dG/dlambda as you go, where g is the free energy and lambda is the path parameter. For each particular application, there are specialized methods that have been developed. I am not aware of methods that have been developed for defect free energies. I suggest you do a literature search for vacancy free energy in simple materials (Lennard-Jones, cubic metal crystals using EAM, etc.). However, you should first ask yourself “Do I really need to know the free energy?”

Aidan