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 O

_{2}
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