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In a recent forum ​post it was discussed about problem of decoding the KEYWORD in ROMS input parameters scripts processed by inp_par.F. I took a look at this problem and made decode_line more robust to process input lines with all kind of characters after the first comment character [CHAR(33)=!]. Now it is possible to have any kind of characters after the comment. For example:

          DT == 360.0d0  \TAB \TAB ! @ 1 day = 240 timesteps !&*==!!\TAB %%%:

Notice that now:

• Any characters are allowed after the first commnent (!) character including equal sign (=), tabs (\TAB), and additonal comment (!) characters.
• Tabs (\TAB) are allowed after the KEYWORD values. They are not allowed in a location before any of the KEYWORD values (numeric or string) because it may yield an incorrect line decoding.

Many thanks to Simon Spagnol, Mark Hadfield, and John Wilkin for reporting this problem.

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.