General Principles
Representation of the air flow in the atmospheric boundary layer
Air flow can be imagined as a horizontal flow of numerous rotating eddies, that is, turbulent vortices of various sizes, with each eddy having horizontal and vertical components. The situation looks chaotic, but vertical movement of the components can be measured from the tower.
Physical meaning of the eddy covariance method
At one physical point on the tower, at Time1, Eddy1 moves parcel of air c1 down at the speed w1. Then, at Time2, Eddy2 moves parcel c2 up at the speed w2. Each parcel has gas concentration, pressure, temperature, and humidity. If these factors, along with the speed are known, we can determine the flux. For example, if one knew how many molecules of water went down with eddies at Time 1, and how many molecules went up with eddies at Time2, at the same point, one could calculate the vertical flux of water at this point over this time. So, vertical flux can be presented as a covariance of the vertical wind velocity and the concentration of the entity of interest.
Read more about this topic: Eddy Covariance
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