(0) Directory "Code": Source Code (TMM and MOPS/RetroMOPS).

Note: Please refer to the versions in "RecentCodeMOPS" and
"RecentCodeRetroMOPS", as these contain some updates and modifications
with respect to:

(a) assignement of variable filenames for diagnostic output (biogeochemical fluxes).
This affects file external_forcing_mods_biogeochem.c. To use flexible filenames
for diagnostic output, in file "parallel.job" add filenames e.g., as follows:

-diag_files "fbgc1_"$nSession".petsc","fbgc2_"$nSession".petsc","fbgc3_"$nSession".petsc", \
            "fbgc4_"$nSession".petsc","fbgc5_"$nSession".petsc","fbgc6_"$nSession".petsc","fbgc7_"$nSession".petsc" \


(b) a consistent structure for running the code without computation of
misfit. This affects files external_forcing_mods_biogeochem.c,
tmm_misfit.h and mops_biogeochem_misfit_data.h. 


Files MOPSoD.tar, MOPSoDstar.tar, MOPSoS.tar and RetroMOPSo.tar extract
to the corresponding directories MOPSoD/  MOPSoDstar/  MOPSoS/ and
RetroMOPSo/ which contain the original code used for the optimisations. 

Code changes among the different model versions used for optimisation
relate to default parameters, parameters to be optimized, model
structure (MOPS, RetroMOPS), weights applied to optimization (e.g., for
masking out specific regions) and the possibility to have output of
diagnostic information (fluxes) to flexible file names (e.g., for
individuals and generations). Some further changes are related to the
location of boolean operators for computation of misfit.

Iris Kriest, 2017-10-16

Difference between MOPSoS and MOPSoD: 

      BGC_INI.F: 
      set default parameters for phytoplankton and
      zooplankton in MOPSoD to those optimized with MOPSoS.

      mops_biogeochem_set_params.F: 
      change list of parameters to be optimized

Difference between MOPSoD and MOPSoDstar:

      mops_biogeochem_misfit_data.h: 
      add weights to computation of misfit for masking out the eastern
      equatorial Pacific
      
      tmm_main.c:
      move PetscBool doMisfit = PETSC_FALSE to global domain

      tmm_misfit.c
      add weights to computation of misfit for masking out the eastern
      equatorial Pacific

Difference between MOPSoDstar and RetroMOPS:

      BGC_INI.F:
      inserted optimized values of MOPSoD for RetroMOPS
      restructured for RetroMOPS
      
      BGC_MODEL.F:
      restructured for RetroMOPS
      
      BGC_PARAMS.h:
      restructured for RetroMOPS
      
      external_forcing_mops_biogeochem.c:
      restructured for RetroMOPS
      diagnostic filenames (for fluxes) are now read from the command line
      evaluate misfit within conditional if (doMisfit) {}      

      mops_biogeochem_misfit_data.h:
      add extern PetscBool doMisfit

      mops_biogeochem_set_params.F:
      restructured for optimization of RetroMOPS