The "temperature of an atom" is something very different from the temperature of a material with billions of atoms. For the material, what matters most is usually vibrations of atoms, where the nucleus contributes the most to kinetic energy, because it is heavy, and the electronic configuration contributes to potential energy.

For an atom, you basically have to do quantum physics and talk about von Neuman entropy of it's quantum state. This kind of temperature is very removed from the everyday concepts of "heat" and "heat transfer".