The definition of frequency is best described in its unit which is cycles/second or Hertz (Hz). It is a basic property of any oscillatory phenomena whether it be an atom moving with periodic motion, a light wave, or a mass moving back and forth on a spring. 1 Hz = 1 cycle/second = 1 full revolution/second etc.
In the case of periodic motion, frequency is the number of cycles undergone by a body in one unit of time. For example if you consider one year as the unit of time then earth completes one cycle around the sun during a year. Then frequency is just one per year. On the other hand if your unit of time is one day, then it will take 365 days to complete one cycle and hence the frequency is 1/365 per day.
One also uses angular frequency in angular motion of rigid bodies. If for a complete 2π rotation a rigid body takes T seconds, then angular frequency is defined as ω = 2π/T = 2πf.
Periodic systems are seen quite often in physical or biological sciences or even in economics. Examples are your heart beat, your pulse rate, day-night effect, summer-winter effect, phases of the moon, tides of ocean.....
In the case of an atom, it's spacial(spatial) dimensions are of the order of 10-8 cm or less. In this length scale, deterministic classical theories are replaced by quantum theories based on principles of probability. One constructs a wave function which yields a probability density when you calculate it's mod square function. Wave function has a spacial frequency (not temporal) meaning that it has a periodic structure in space and time dependent factor of it is a pure phase.