fix_modify energy concept

Dear LAMMPS users,

I have a question about the fix_modify energy command. I know that it is necessary to set this command to yes in the case of energy minimization with some fixes, e.g., addforce. Also, I know this command does not affect the dynamics of the problem and only affects the output potential energy. But, I think it may matter whether we include or exclude this command when deriving some quantities directly from the potential energy of the system. One example is in the case of computing elastic constants based on the second derivative of the strain energy (a measure of potential energy) with respect to the strain.

As I know the potential energy is solely defined based on the relative distances of particles in the framework of a specific potential function. The manual states that some fixes calculate a contribution to the potential energy of the system. I want to know if this contribution affects the “physics” of the problem. In other words, what is the actual potential energy of the system, pe or pe+contribution?

Any comments are appreciated.