Thermal Conductivity of Diamond at 300 Kelvin

Your system size is entirely too small to support any of the long wave length phononic contributions to the thermal conductivity hence the unreasonably low number. Basically there is nothing in a perfect crystal to scatter those phonons so you need a really big system to get the full phonon mean free path. Try plotting thermal conductivity vs system size and keep increasing size until your reach a steady state value.

See paper by Padget: for an example calculation using CNTs.

setup problem