One of the most pernicious problems with models that use realistically small mixing in the ocean interior is that this mixing is not sufficient to eliminate problems with numerical ``digging'' next to realistic bottom topography. Digging is the accumulation of unphysical tracer extrema which are localized near topography. Partial cells (Chapter 26), unfortunately, have not eliminated digging. Smoothing the bottom topography does reduce digging, and smoothing is a method of choice for many modelers.
Another approach to reducing digging is to allow the amount of mixing next to the bottom to be enhanced. Such is perhaps occurring in the real ocean, and so might be a step towards a more realistic simulation. Indeed, in the bottom boundary layer (Chapter 36), an enhanced amount of mixing is enabled through the use of upwind tracer advection. As shown in Section 31.1.3, the mixing from upwind is larger when the currents are stronger, which is arguably a realistic feature. Use of the bottom boundary layer has resulted in a reduced amount of digging as a result of such mixing from the upwind scheme. Additionally, the FCT scheme (Section 31.6) is useful for reducing digging since it effectively reduces to the positive definite upwind scheme near the bottom in order to eliminate the dispersion errors from centered advection. Unfortunately, FCT is quite expensive.
In light of these ideas, it might be sensible to employ upwind tracer advection over the level just above the bottom topography. This approach can be used in combination with another advection scheme in the interior rather than the expensive FCT scheme. Option bottom_upwind enables this scheme. The implementation of option bottom_upwind is quite simple. All that is done is to over-write the advective flux predicted from any of the other advection schemes with the flux computed from upwind. The default implementation is to employ upwind to the lowest level next to the bottom topography. Each of the three advective fluxes entering this box are computed via upwind. Modifications to this approach are straightforward.