IMPORTANT: EcoSim Bio-Optical Diagnostic Terms

[arango]

Updated the EcoSim model to include diagnostics of the optical terms when DIAGNOSTICS_BIO and BIO_OPTIC to write out into output NetCDF file DIANAME various underwater light spectral properties.

• The standard input script ecosim.in now has several logical switches to process:

  ! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
  ! underwater optical diagnostics terms into DIAGNOSTIC output file [Ngrids].
  
    Dout(idSpIr) == T      ! surface_irradiance      surface spectral irradiance
    Dout(iddIrr) == T      ! downward_irradiance     downward spectral irradiance
    Dout(idsIrr) == T      ! scalar_irradiance       scalar spectral irradiance
    Dout(idAcos) == T      ! light_cosine            light spectral average cosine
    Dout(idLatt) == T      ! light_attenuation       diffuse light attenuation
    Dout(idaPHY) == T      ! Phy_absorption          phytoplankton absorption
    Dout(idaDET) == T      ! detrital_absorption     detrital absorption
    Dout(idaCDC) == T      ! CDC_absorption          CDC absorption
    Dout(idsPHY) == T      ! Phy_scattering          phytoplankton scattering
    Dout(idbPHY) == T      ! Phy_backscattering      phytoplankton backscattering
    Dout(idsTOT) == T      ! total_scattering        total scattering
    Dout(idbTOT) == T      ! total_backscattering    total backscattering
  

• The varinfo.dat was updated to include the metadata for the new light spectral properties.

• Added new routines bc_4d.F and exchange_4d.F to process the open boundary conditions for 4D spectral optical fields.

• If ECOSIM is activated, all output NetCDF files contain the light coordinate for all optical spectral variables:

         double light(Nbands) ;
                 light:long_name = "center wavelength of spectral irradiance bands" ;
                 light:units = "nanometer" ;
  

  Currently, ECOSIM is configured with 60 wavelenghts of light spectral bands ranging from 402:5:697 nanometers. Notice that all the def_*.F routines that creates ROMS output NetCDF files were updated to include this light coordinate.

• A new C-preprocessing option BIO_OPTIC is introduced to compute the underwater light spectral properties that are essential for any biogeochemical model. All the EcoSim model routines (ecosim.h, ecosim_def.h, ecosim_inp.h, ecosim_mod.h, ecosim_var.h, and ecosim_wrt.h) were updated.

• All the changes to the ROMS code were tested with the BIO_TOY test case:

• The BIO_TOY application was also updated in the test repository. It now includes Matlab script ecosim_optics.m used to generate the above plots.

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Many thanks to Bronwyn Cahill for her help coding and testing this update to the EcoSim model.