Fast spinup of ocean biogeochemical models using  Matrix-Free Newton-Krylov (MFNK)

These are some instructions for applying the MFNK method to the spinup of seasonally-forced global
ocean biogeochemical models. For details on this approach see:

S. Khatiwala. Fast spin up of ocean biogeochemical models using matrix-free Newton-Krylov. Ocean Modell., 23:121–129, 2008. (PDF)

I exploit the transport matrix method to apply MFNK. Thus, as a first step, follow the instructions given here
for downloading the TMM code. Once you've downloaded and unarchived  MIT_Matrix_Global_2.8deg.tar.gz, follow the instructions in MIT_Matrix_Global_2.8deg/KielBiogeochem_NDOP_Matrix5_4/Readme. This is an example of a simple biogeochemical model with two coupled tracers, inorganic phosphate (PO4) and dissolved organic phosphate (DOP). The model was devised and implemented by Iris Kriest at IfM GEOMAR/University of Kiel, who has very generously allowed me to share it. Also, some code fragments (notably the insolation routine and the O2 saturation calculation) are taken from the MITgcm biogeochemical model written by Stephanie Dutkiewicz and Mick Follows at MIT. My thanks to them for allowing me to include it in this distribution.

Running this example requires several steps, some not so trivial. So if something doesn't work, or if you find mistakes in the documentation, or have suggestions for improving it, please let me know. You may also find
it useful to first run the 'coarse grained' (CG) version of this model. This exploits the fact that we can readily obtain coarse grained transport matrices. The CG version is much smaller and consequently runs very fast. You can run the example on your desktop/laptop (unlike the full version which requires more resources). See the file MIT_Matrix_Global_2.8deg/KielBiogeochem_NDOP_Matrix5_4/Readme_cg.

Samar Khatiwala

Last updated: 6/4/09