An atomic clock is fundamentally an oscillator whose frequency \omega is matched to that of an atomic transition of a two-level atom, \omega_0.
If one atom is sent into the setup in its ground state \left|\downarrow\right\rangle and passed through the first interaction zone, the state would become a superposition of ground and excited states \frac{\left|\downarrow\right\rangle+\left|\uparrow\right\rangle}{\sqrt{2}}, just as it would with a regular Ramsey interferometer.