Added a Red Tide Ecosystem Model

[arango]

Added the Red Tide Ecosystem Model for Alexandrium fundyense. It can be activated with CPP option RED_TIDE. This model is primarily designed for the Gulf of Maine.

As code it, the user needs to provide the bottom cyst concentration (cyst_bottom; cell/m2; 2D array) and the observed dissolved inorganic nutrient (DIN; micromoles; 3D array). The cyst_bottom and DIN fields can be provided in a separated forcing NetCDF file. See varinfo.dat for the metadata for these input variables.

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Many thanks to Dennis McGillicudy and Ruoying He for providing us their code. This model was rewritten from scratch.

Also, many thanks to Sasha Shchepetkin for providing us his updated semi-Lagrangian code sinking and ascending used for vertical swimming.

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References:

Stock, C.A., D.J. McGillicudy, A.R. Solow, and D.M. Anderson, 2005: Evaluating hypotheses for the initiation and development of Alexandrium fundyense blooms in the western Gulf of Maine using a couple physical-biological model, Deep-Sea Research II, 52, 2715-2744.

He, R., D.J. McGillicuddy, B.A. Keafer, and D.M. Anderson, 2008: Historic 2005 toxic bloom of Alexandrium fundyence in the western Gulf of Maine: 2, Coupled biophysical modeling, J. Geophys. Res., 113, C07040, doi:10.1029/2007JC004602

[arango]

The file read_biopar.F was not in the updated list. I missed that one.