Questions Regarding Atmospheric Dust and Nitrogen Deposition Forcing in PISCES


I am currently working on preparing the atmospheric forcing for the PISCES module (CROCO V1.3.1), which includes dust, NO3, and NH4. Initially, I tested an extreme case by setting the NO3 and NH4 values in the forcing to exceptionally high levels and shut down all the biological processes that could alter the NO3 and NH4 concentrations. I expected that after a few time steps, the model’s first layer would be filled with extremely high NO3 and NH4 concentrations. However, the results are quite unusual. The attached figure is the first output from the model, which I ran for one hour. It shows only several extremely high rectangular areas instead of the entire field being filled with high concentrations. The model was run with 256 CPUs. Based on what the figure shows, my guess is that there might be some issues with the data exchange in atmospheric forcing reading via MPI.

I have also attached my atmospheric forcing NC file information here. Any assistance would be greatly appreciated.

The atmospheric forcing NC file:netcdf croco_frcbio {
xi_u = 457 ;
xi_v = 458 ;
xi_rho = 458 ;
eta_u = 222 ;
eta_v = 221 ;
eta_rho = 222 ;
time = 1249 ;
double dust_time(time) ;
dust_time:long_name = “time for dust” ;
dust_time:units = “day” ;
double ndepo_time(time) ;
ndepo_time:long_name = “time for nitrate deposition” ;
ndepo_time:units = “day” ;
double nhxdepo_time(time) ;
nhxdepo_time:long_name = “time for ammonium deposition” ;
nhxdepo_time:units = “day” ;
double dust(time, eta_rho, xi_rho) ;
dust:long_name = “Dust Deposition” ;
dust:units = “kg/m2/s” ;
dust:fields = “dust, scalar, series” ;
double ndepo(time, eta_rho, xi_rho) ;
ndepo:long_name = “Nitrate Deposition” ;
ndepo:units = “kgN/m2/s” ;
ndepo:fields = “ndepo, scalar, series” ;
double nhxdepo(time, eta_rho, xi_rho) ;
nhxdepo:long_name = “Ammonium Deposition” ;
nhxdepo:units = “kgN/m2/s” ;
nhxdepo:fields = “nhxdepo, scalar, series” ;

// global attributes:
:title = “GOM3P5km” ;
:date = “2023-12-15 11:28:39.414873” ;
:grd_file = “” ;
:type = “CROCO biology forcing file” ;


@xzhou473 First check that your forcing file is in the CROCO_FILES directory of your run directory and that it is correctly set up in the file. You can also explore the original file to check that there are no problems or outliers in data in your region.