Generalized coupled biology and sediment models interface

[arango]

I updated the interface for the various ecosystem model in ROMS. This allows a lot of flexibility and customization:

• The ecosystem model input parameters are declared in an new file xxx_mod.h which is included in module mod_biology.F as:

  #ifdef BIOLOGY
  # if defined BIO_FENNEL
  #  include <fennel_mod.h>
  # elif defined ECOSIM
  #  include <ecosim_mod.h>
  # elif defined NEMURO
  #  include <nemuro_mod.h>
  # elif defined NPZD_FRANKS
  #  include <npzd_Franks_mod.h>
  # elif defined NPZD_IRON
  #  include <npzd_iron_mod.h>
  # elif defined NPZD_POWELL
  #  include <npzd_Powell_mod.h>
  # endif
  #endif
  

• The input parameters are now read from a new file xxx_inp.h which is included in inp_par.F as

  #ifdef BIOLOGY
  # if defined BIO_FENNEL
  #  include <fennel_inp.h>
  # elif defined NEMURO
  #  include <nemuro_inp.h>
  # elif defined NPZD_FRANKS
  #  include <npzd_Franks_inp.h>
  # elif defined NPZD_POWELL
  #  include <npzd_Powell_inp.h>
  # elif defined NPZD_IRON
  #  include <npzd_iron_inp.h>
  # elif defined ECOSIM
  #  include <ecosim_inp.h>
  # endif
  #endif
  
  #ifdef SEDIMENT
  # include <sediment_inp.h>
  #endif
  

• The ecosystem model input parameters are defined (all output NetCDF files) in a new file xxx_def.h which is included in def_info.F as:

  #if defined BIOLOGY && defined SOLVE3D
  # if defined BIO_FENNEL
  #  include <fennel_def.h>
  # elif defined ECOSIM
  #  include <ecosim_def.h>
  # elif defined NEMURO
  #  include <nemuro_def.h>
  # elif defined NPZD_FRANKS
  #  include <npzd_Franks_def.h>
  # elif defined NPZD_IRON
  #  include <npzd_iron_def.h>
  # elif defined NPZD_POWELL
  #  include <npzd_Powell_def.h>
  # endif
  #endif
  

• The ecosystem model input parameters are written (all output NetCDF files) in a new file xxx_wrt.h which is included in wrt_info.F as:

  #if defined BIOLOGY && defined SOLVE3D
  # if defined BIO_FENNEL
  #  include <fennel_wrt.h>
  # elif defined ECOSIM
  #  include <ecosim_wrt.h>
  # elif defined NEMURO
  #  include <nemuro_wrt.h>
  # elif defined NPZD_FRANKS
  #  include <npzd_Franks_wrt.h>
  # elif defined NPZD_IRON
  #  include <npzd_iron_wrt.h>
  # elif defined NPZD_POWELL
  #  include <npzd_Powell_wrt.h>
  # endif
  #endif
  

Check any of these files if you are adding a new ecosystem model into ROMS for guidance. Note that all the new ecosystem *.h files are located in ROMS/Nonlinear/Biology and included within <...> to allow the user to customize any of them in the project directory while keeping the distributed code intact (check the build script for details).

The input parameters for the NEMURO model were not written in the output NetCDF file before. I missed this one.

Also, notice that currently only sediment_inp.h is available for the sediment model. This will change in the future as this model evolves and more input parameters are required.

I also fixed couple unbounded local arrays bugs in ecosim.h and the sink tracer indices for the silica group.