The value of KMAXX should be the same in bio_2D_x3pV5.F and in numerics_sub.f, change value to 300 in numerics_sub.f.
The f-ratio computation for sp and diatoms frat_sp and frat_lp
leads to divide by zero errors when nitrogen uptake goes to 0.0.
In the file: bio_subs_x3pV5.f
Add " + eps" to the denominator of both equations.
i.e.
should be
do same for frat_lp.
Also, saving community f-ratio as a flux (currently flux 4) is a bad idea because it adds in an f-ratio of 0.0 when uptake is 0.0. It would be better to have to fluxes saved for community nitrate uptake and community ammonimum uptake. The correct f-ratio could then be computed from the output files averaging over the time and space scales of interest.
I have moved, my new contact information is:
Dr. J. Keith Moore
Assistant Professor
Earth System Science
University of California, Irvine
220 Rowland Hall
Irvine, CA 92697-3100
Phone: (949) 824-5391
Email: jkmoore@uci.edu
I would greatly appreciate hearing about any potential problems you might find in the code, suggested improvements for the code, and receiving reprints of papers which use this model or code.
Best Regards,
Keith
Code Files
The file numerics_sub.f was updated to KMAXX=300
The file bio_subs_x3pV5.f was updated to reflect changes
in the frat_sp and frat_lp equations
The tar file jkmoore_code.tar
was updated to reflect above changes
IDL Files
The file jkmoore_idl.tar was missing the file: oceanarea_x3p.dat
The file x3p_routines.pro was updated to include the "get_x3p_coords" routine.
The tar file jkmoore_idl.tar has been updated to reflect the above changes.
Input Files
The file jkmoore_inputs.tar was missing the input file: woa98_sst_surf_m_x3p.dat
There were three NaN values in the two files: bio_slope_x3p_globalV5.dat and hmix_levpd_min25_x3p.dat. Both of these files were corrected and replaced in the tar file: jkmoore_inputs.tar
The tar file jkmoore_inputs.tar has been updated to reflect the above changes.
Final References
DSR pubs are now out, please cite these papers if you use this code:
2002. Moore, J.K., Doney, S.C.,Kleypas, J.A., Glover,D.M., Fung, I.Y., An intermediate complexity marine ecosystem model for the global domain, Deep-Sea Res. II, 49: 403-462.
2002. Moore, J.K., Doney, S.C., Glover, D.M., Fung, I.Y., Iron cycling
and nutrient limitation patterns in surface waters of the world ocean,
Deep-Sea Res. II, 49: 463-508.
Updates to Mixed Layer Model Since Publication
Variable thetaNmax
There is evidence that the maximum chl/C (chl/N) ratio can be higher
in diatoms than other phytoplankton groups (Geider et al., 1997). I suggest
using a thetaNmax of 4.0 for the diatoms and 3.0 for the other phytoplankton
groups. This improves global chlorophyll fields in terms of winter season
gyre values (too high around borders of the gyres in Moore et al. 2002).
In depth-resolved applications this also improves the behavior of diatom
biomass at the deep chlorophyll max.
New lambda function - for all phytoplankton groups
replace: lambda = lambda_no3 * max(frat_sp, 0.5) ! used
in DSR papers
with: lambda = lambda_no3
* (frat_sp * 0.5 + 0.5)
This is a smoother function more true to the data presented by Geider (1992).