adding processes to fasham

[nganju]

Hello-
I am boldly straying into new territory with a very crude sense of biology, so any help is appreciated. We plan to simulate nutrient dynamics in a shallow estuary, where the following processes are most important:

1. nitrification/denitrification in the sediments;
2. uptake of nitrate and ammonium by phytoplankton;
3. uptake of nitrate and ammonium by macro-algae;
4. uptake of nitrate and ammonium by epiphytic primary producers and benthic micro-algae/cyanobacteria;
5. remineralization of ammonium

From looking over fasham.h and Fennel et al (2006), it looks to me like the structure for 1,2, and 5 is present. I have found other modeling papers on 3 and 4, and think that adding modules in fasham.h for these processes is the easiest way to proceed.

Am I thinking about this in the right way? Thanks in advance...

[nganju]

I am adding macroalgae dynamics to fennel.h. I plan on treating it not as a tracer but as a variable whose density changes as a function of nutrients, light, etc. If I add it as 2D (r2dvar) biological tracer will it automatically be advected around by step3d_t or is there an easy hack? Is there a better way to add in a variable of this type?

[kate]

If you add it as a 3D bio tracer it will automatically be advected around. Why wouldn't it be 3D since the nutrients and light are both 3D?

[nganju]

I am still debating how to deal with it...I suppose macroalgae should have a vertical component, as it will grow vertically in response to light and nutrients. But I am not sure I want it advecting around, as in the areas I am working in, it is usually attached to the bottom substrate. Is there a simple way to shut advection off for a tracer (e.g. ifdef MACROALGAE & NBT = 13 then advection = 0)? Thanks for the reply...

[kate]

Oh, it's on the bottom? You can make a 2D array then and it won't advect around. We've done a benthic component. You can search here for the PONsed and OPALsed parts for an example. The patch file also applies 3D iron fields.

[Lei_Shi]

Does ROMS already have existing module (like Fasham/Funnel's biology model) to simulate the bio-geo-chemical processes in the sedement and water-sediment interface? I am very interested to know.

If you want to simulate the bio-geo-chemical processes in the sediment and water-sediement interface you need to couple/include bio-geo-chemical state veriables (2D, even 3D) into the ROMS code. It very much like ocean-atmospheric coupling. Hope there is existing module that you can follow.