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Corrected a typo in obs_sen_w4dpsas.h and obs_sen_w4dvar.h when writing the observation impact into output 4D-Var NetCDF file.

Many thanks to Andy Moore for bringing this to my attention.

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.

The observation impact for 4D-Var drivers was updated:

• Added the observation impact operator for IS4DVAR in driver obs_sen_ocean.h. It includes capability to compute the contributions due to initial conditions, surface forcing, and boundary conditions using the OBS_IMPACT_SPLIT option.

• Added missing code for the balance operator in obs_sen_ocean.h.

• Corrected the IO logic in obs_sen_w4dpsas.h and obs_sen_w4dvar.h to distinguish between observation sensitivity and observation impact. The ouput when OBS_IMPACT_SPLIT was not activated was missing for the obsevation sensitivity option.

Many thanks to Andy Moore his help in coding and testing this algorithms.