Generalized coupled biology and sediment models interface, final phase

[arango]

This is the final phase of the redesign of the coupled biology and sediment models in ROMS which started with ​src:ticket:375. This update removes the dependency of these models on mod_param.F, mod_ncparam.F, and mod_scalars.F. No longer there is a need to modifying these files when customizing or expanding these models.

• The ecosystem and sediment models metadata indices are now assigned in a new file xxx_var.h which is included in module mod_ncparm.F as:

  #ifdef BIOLOGY
  # if defined BIO_FENNEL
  #  include <fennel_var.h>
  # elif defined ECOSIM
  #  include <ecosim_var.h>
  # elif defined NEMURO
  #  include <nemuro_var.h>
  # elif defined NPZD_FRANKS
  #  include <npzd_Franks_var.h>
  # elif defined NPZD_POWELL
  #  include <npzd_Powell_var.h>
  # elif defined NPZD_IRON
  #  include <npzd_iron_var.h>
  # endif
  #endif
  
  #if defined SEDIMENT || defined BBL_MODEL
  #  include <sediment_var.h>
  #endif
  

• The ecosystem model tracer indices (idbio(:) and friends) are now set-up in their respective xxx_mod.h instead of mod_scalars.F. Everything including their declaration is moved to mod_biology.F which includes the file xxx_mod.h.

• As in the ecosystem model, the sediment model tracer indices (idmud(:), isand(:) and friends) are now set-up in new file sediment_mod.h instead of mod_scalars.F. Everything including their declaration is moved to mod_sediment.F which includes the new file sediment_mod.h.

• All the declarations associated with the ecosystem and sediment models was moved from mod_param.F to their respective xxx_mod.h and now they are declared in modules mod_biology.F and mod_sediment.F, respectively.

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

  #ifdef SEDIMENT
  # include <sediment_def.h>
  #endif
  

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

  #ifdef SEDIMENT
  # include <sediment_wrt.h>
  #endif
  

• All the sediment model kernel variables declarations are moved from mod_average.F, mod_grid.F, and mod_ocean.F to a new module mod_sedbed.F. This new module includes the file sedbed_mod.h to facilitate customization.

Several files have minor changes to facilitate this redesign. It will be very easy in the future to add new ecosystem models or expand existing ones.

WARNING: If adding new tracer indices to any of these models, the user need to select a unique and meaningful five character index (like, itemp for temperature) and check for conflicts in mod_ncparam.F or mod_scalars.F. The new metadata in varinfo.dat must be consistent with the new index.