There are two fundamental assumptions in almost all DFT codes.
1) The first is called the
Born-Oppenheimer approximation.
I recommend reading the wiki-link here, but in short the BO-approximation states that the electrons has a adiabatic behavior
in relation to the quantum mechanics of the atoms. Therefore we can solve the electronic Schrödinger equation separate from
nucleus Schrödinger equation.
2) The movement of the nucleus are treaded as a classical particles, and furthermore it is assumed that nucleus are frozen in their
position with out any movement of all. This means that the potential from nucleus does not depend on time, and hence we can solve
the time-independent electronic Schrödinger equation instead of the time-dependent. However if the nucleus is not allowed to move, we know from thermodynamics, that the temperature must be zero. (Phonon is a quantized mode of vibration, but with no movement of the nucleus, there are no
vibration modes, and hence there are no phonons at T=0)
This two assumption is foundation for most DFT calculations, and therefore it is basic assumption that the calculation is performed at zero temperature.
However, if you want perform a very crude approximation how your system depends on the temperature you can adjust the fermi temperature, however
the reason for this being a crude approximation is that the second approximation is still being imposed despite it being wrong.
If your referee ask for a temperature, then your reply should be: "The calculation is performed at T=0, but with a fermi temperature of 300 K. And there is no phonon-electron interaction included in the simulation."