How a cesium fountain atomic clock works, currently the primary time standard for the USA -

NIST-F1 is referred to as a fountain clock because it uses a fountain-like movement of atoms to measure frequency and time interval. First, a gas of cesium atoms is introduced into the clock’s vacuum chamber. Six infrared laser beams then are directed at right angles to each other at the center of the chamber. The lasers gently push the cesium atoms together into a ball. In the process of creating this ball, the lasers slow down the movement of the atoms and cool them to temperatures near absolute zero.

Two vertical lasers are used to gently toss the ball upward (the “fountain” action), and then all of the lasers are turned off. This little push is just enough to loft the ball about a meter high through a microwave-filled cavity. Under the influence of gravity, the ball then falls back down through the microwave cavity.
NIST-F1 Cesium Fountain (Block Diagram)

The round trip up and down through the microwave cavity lasts for about 1 second. During the trip, the atomic states of the atoms might or might not be altered as they interact with the microwave signal. When their trip is finished, another laser is pointed at the atoms. Those atoms whose atomic state were altered by the microwave signal emit light (a state known as fluorescence). The photons, or the tiny packets of light that they emit, are measured by a detector.

NIST-F1 – Cesium Fountain Atomic Clock – Link.