The first experience concerns the ubiquitous presence of resolved gravity-wave activity in MAGCMs. Although one's first impression is that it is noise, comparison between MAGCMs shows it to be a generic feature: the transition between a steep, balanced kinetic energy spectrum and a shallow, unbalanced spectrum, which occurs on the mesoscale in the troposphere and lower stratosphere, migrates up to the synoptic scales by the time one reaches the mesosphere. This means that the nature of large-scale mixing is completely different in the mesosphere as compared with the stratosphere. In particular, the kind of off-line transport calculations that are now routine in the stratosphere, and which rely on the spatio-temporal smoothness of the flow, are not possible in the mesosphere.
The second experience concerns the implementation of gravity-wave drag parameterizations. Although the focus of such parameterizations is usually on drag (momentum transfer), gravity waves generally also transfer energy. If the implementation of a gravity-wave drag parameterization does not respect this fact, it can lead to a violation of the second law of thermodynamics. Recognizing the constraint leads to a rigorous bound on the horizontal phase speed -- and, therefore, to a low-wavenumber cut-off to the vertical wavenumber, for hydrostatic gravity waves.
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