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We are getting ready to release ROMS on GitHub soon as we continue to make sure that everything is working correctly.

The current plan is to have the ROMS source, Test Cases, and Matlab scripts in the same root directory base. We highly recommend that Users define the ROMS_ROOT_DIR variable in their computer shell logging environment, specifying where the User cloned/downloaded from GitHub the ROMS source code, Test Cases, and Matlab processing software:

 setenv ROMS_ROOT_DIR  MyDownlodLocationDirectory

The build scripts will use this environmental variable when compiling any of the ROMS Test Cases without the need to customize the location of the ROMS source code. Also, it is used for loading the path of Matlab scripts in the startup.m configuration file.

• Updated and documented startup.m .

• Added plot_diff_dirs.m to plot horizontal or vertical sections of the field difference between two directories having the same NetCDF filename at the specified time records.

• Added plot_diff_files.m to plot horizontal or vertical sections of the field difference between two NetCDF files with different filenames at the specified time record.

The ROMS output fields continue growing, and managing the various NetCDF files is becoming daunting. Therefore, we have separated into specific modules for BBL, SeaIce, Sediment, and WEC models, which are sub-directories of ROMS/Nonlinear:

• ROMS/Nonlinear/BBL/bbl_out.F: It processes the Bottom Boundary Layer and Waves variables into history, quicksave, averages, and stations NetCDF files.

• ROMS/Nonlinear/SeaIce/ice_output.F: It processes sea-ice model variables into history, quicksave, and averages NetCDF files.

• ROMS/Nonlinear/Sediment/sediment_out.F: It processes sediment variables into history, quicksave, averages, and stations NetCDF files.

• ROMS/Nonlinear/WEC/wec_out.F: It processes the Waves Effect on Currents variables into history, quicksave, averages, and stations NetCDF files.

It facilitates further field expansion and modifications for each separated model.

For example, in def_his.F, we call routines from the above modules to define the associated history variables:

#if (defined BBL_MODEL || defined WAVES_OUTPUT) && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Define the bottom boundary layer model or wave variables.
!-----------------------------------------------------------------------
!
        CALL bbl_def_nf90 (ng, model, ldef, Hout, HIS,                  &
     &                     t2dgrd, u2dgrd, v2dgrd)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

#if defined ICE_MODEL && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Define sea-ice model variables.
!-----------------------------------------------------------------------
!
        CALL ice_def_nf90 (ng, model, ldef, Hout, HIS,                  &
     &                     t2dgrd, u2dgrd, v2dgrd)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

#if defined SEDIMENT && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Define sediment model variables.
!-----------------------------------------------------------------------
!
        CALL sediment_def_nf90 (ng, model, ldef, Hout, HIS,             &
     &                          t2dgrd, u2dgrd, v2dgrd,                 &
     &                          b3dgrd)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

#if defined WEC_VF && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Define Waves Effect on Currents variables.
!-----------------------------------------------------------------------
!
        CALL wec_def_nf90 (ng, model, ldef, Hout, HIS,                  &
     &                     t2dgrd, u2dgrd, v2dgrd,                      &
     &                     t3dgrd, u3dgrd, v3dgrd, w3dgrd)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

Similarly, the actual writing of the variables in wrt_his.F can be accomplished by calling the respective routines:

#if (defined BBL_MODEL || defined WAVES_OUTPUT) && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Write out the bottom boundary layer model or wave variables.
!-----------------------------------------------------------------------
!
        CALL bbl_wrt_nf90 (ng, model, tile,                             &
     &                     LBi, UBi, LBj, UBj,                          &
     &                     Hout, HIS)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

#if defined ICE_MODEL && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Write out sea-ice model variables.
!-----------------------------------------------------------------------
!
        CALL ice_wrt_nf90 (ng, model, tile,                             &
     &                     LBi, UBi, LBj, UBj,                          &
     &                     Hout, HIS)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

#if defined SEDIMENT && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Write out sediment model variables.
!-----------------------------------------------------------------------
!
        CALL sediment_wrt_nf90 (ng, model, tile,                        &
     &                          LBi, UBi, LBj, UBj,                     &
     &                          Hout, HIS)
        IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

#if defined WEC_VF && defined SOLVE3D
!
!-----------------------------------------------------------------------
! Write out the Waves Effect on Currents variables.
!-----------------------------------------------------------------------
!
      CALL wec_wrt_nf90 (ng, model, tile,                               &
    &                    LBi, UBi, LBj, UBj,                            &
    &                    Hout, HIS)
      IF (FoundError(exit_flag, NoError, __LINE__, MyFile)) RETURN
#endif

The above subroutines are generic and can be called for the quicksave and averages files by replacing the Hout and HIS arguments. There are also subroutines for processing the stations variables. For example, in module sediment_output_mod, we have the following public routines:

      PUBLIC :: sediment_def_nf90
# if defined PIO_LIB && defined DISTRIBUTE
      PUBLIC :: sediment_def_pio
# endif
# ifdef STATIONS
      PUBLIC :: sediment_def_station_nf90
#  if defined PIO_LIB && defined DISTRIBUTE
      PUBLIC :: sediment_def_station_pio
#  endif
# endif
      PUBLIC :: sediment_wrt_nf90
# if defined PIO_LIB && defined DISTRIBUTE
      PUBLIC :: sediment_wrt_pio
# endif
# ifdef STATIONS
      PUBLIC :: sediment_wrt_station_nf90
#  if defined PIO_LIB && defined DISTRIBUTE
      PUBLIC :: sediment_wrt_station_pio
#  endif
# endif

Thus, the output variables code is more compact and categorized.

The option VAR_RHO_2D activates the baroclinic pressure gradient response to the perturbation of the free surface in the presence of stratification and bathymetry. This option does not pass the sanity check of the tangent linear (TLM) and adjoint (ADM) models. Thus, in globaldefs.h we had the constraint,

#ifdef SOLVE3D
# if !(defined ADJOINT || defined TANGENT)
#   define VAR_RHO_2D
# endif
#endif

which also affects the nonlinear kernel. This constraint is removed, and we use VAR_RHO_2D_NOT_YET in the TLM, RPM, and ADM kernels instead. Removing this term can be considered part of the linearization.