Ocean Modeling Discussion

The formulations of nutrient uptake with the implicit scheme are detailed in the attached file below. You can see from the derivation of PO4_uptake that with the formulation Bio(i,k,iPO4_)=Bio(i,k,iPO4_)/(1+cff6), the phosphorus uptake is indeed equal to R_P2N*TNU.

Hi Matheus,

Yes if you want to use climatology data, let say for NO3, you can create a netcdf file with your data. Then in roms.in you add the path for your file:

CLMNAME == /path/to/your/NO3_clm.nc

and in bio_Fennel.in you turn on climatology for NO3 (first variable, phytoplankton would be 4th ...

When you define CARBON you introduce 4 new tracers: TIC, alkalinity, SdetritusC and LdetritusC. However, if you define CARBON+RIVER_DON you introduce an additional tracer: RdetritusC. This is why in fennel_mod.h you add 4 tracers when CARBON is defined and then 1 tracer when RIVER_DON is defined ...

I just noticed the same compiling error due to the following combination of CPP options:
WET_DRY
BIO_FENNEL
DIAGNOSTICS_BIO

The error is due to an extra space line 158 of fennel.h ( if def should be ifdef )


#ifdef MASKING
& rmask, &
# if defined WET_DRY
& rmask_wet, &
# if def DIAGNOSTICS_BIO ...

Ah true, sorry I forgot that OpenMP and MPDATA are not compatible anymore. I used it several years ago with an older version of ROMS.

I did use MPDATA with OpenMP a few years back and it worked well. Give it a try to see if it solves your problem with negative values.

Hi Drivas,

Have you tried the MPDATA advection scheme? It helps to prevent negative data in the biological variables, see this post

Cheers,

Arnaud

I used to run ROMS with TS_MPDATA and OpenMP several years ago but it seems that this combination doesn't work anymore (not sure why). I just hit the same wall...