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This update contains several changes due to the consolidation with the coupling research svn branch.

• The 2D state variables no longer have three-time levels but four-time ones in the FB AB3-AM4 time-stepping algorithm. For example, their declarations are changed from:

        real(r8), intent(inout) :: ubar(LBi:UBi,LBj:UBj,3)
        real(r8), intent(inout) :: vbar(LBi:UBi,LBj:UBj,3)
        real(r8), intent(inout) :: zeta(LBi:UBi,LBj:UBj,3)
  

  to

        real(r8), intent(inout) :: ubar(LBi:UBi,LBj:UBj,:)
        real(r8), intent(inout) :: vbar(LBi:UBi,LBj:UBj,:)
        real(r8), intent(inout) :: zeta(LBi:UBi,LBj:UBj,:)
  

  When the option ASSUMED_SHAPE is not activated.

• The logic for time-dependent changes in bathymetry due to bed_thick was moved to different routines when SEDIMENT and SED_MORPH are activated.

We are still working on the new GitHub repository for ROMS and hope to make the public announcement soon. So, please be patient with us. We must ensure the entire infrastructure is in place before it becomes public.

The ROMS test repository was updated to include changes to standard input files and Gmake and CMake scripts. The svn test repository will be deprecated after the ROMS GitHub release.

• The GNU and CMake build scripts were updated to add new features:
  
  
  • Introduced environmental variable ROMS_ROOT_DIR to specify the location from where the User cloned/downloaded the ROMS source code. We highly recommend that Users set this environmental variable in their computer logging script.
    
    
  • Introduced the -b option for the build command to compile a specific branch. For example, use:

         build_roms.sh -j 5 -b feature/kernel
    or
         cbuild_roms.sh -j 10 -b feature/wec
    

    to compile the version feature/kernel instead of the default develop branch. The build script will clone the ROMS source code from GitHub into the project sub-directory src. Check out the build scripts for more details. Notice that the feature branches are under development and targeted to advanced users, superusers, and beta testers. Regular and novice users must use the default develop branch.
    
    
  • The build scripts local environmental variable SCRATCH_DIR is renamed to BUILD_DIR, which is a more appropriate name. The ROMS makefile is updated to support both macros for backward compatibility.
    
    
  • The build scripts now report a summary when finished:

    <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
    GNU Build script command:      build_roms.sh -j 10 -b feature/kernel
    ROMS source directory:         /home/arango/ROMS/TestCases/upwelling/Forward/src
    ROMS build  directory:         /home/arango/ROMS/TestCases/upwelling/Forward/Build_romsM
    ROMS downloaded from:          https://github.com/...
    ROMS compiled branch:          feature/kernel
    ROMS Application:              UPWELLING
    Fortran compiler:              ifort
    Fortran flags:                 -fp-model precise -heap-arrays -ip -O3 -traceback -check uninit
    Added CPP Options:             -DAVERAGES -DDIAGNOSTICS_TS -DDIAGNOSTICS_UV -DSTATIONS -DFLOATS -DFLOAT_VWALK -DUV_VIS2 -DMIX_S_UV -DUV_LDRAG -DUV_DRAG_GRID -DANA_DRAG -DBIO_FENNEL
    <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
    

    <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
    CMake Build script command:    cbuild_roms.sh -j 10 -b feature/wec -noclean
    ROMS source directory:         /home/arango/ROMS/TestCases/upwelling/Forward/src
    ROMS build  directory:         /home/arango/ROMS/TestCases/upwelling/Forward/CBuild_romsM
    ROMS downloaded from:          https://github.com/...
    ROMS compiled branch:          feature/wec
    ROMS Application:              UPWELLING
    Fortran compiler:              ifort
    Fortran flags:                 -fp-model precise -heap-arrays -ip -O3 -traceback -check uninit
    Added CPP Options:             -DAVERAGES -DDIAGNOSTICS_TS -DDIAGNOSTICS_UV -DSTATIONS -DFLOATS -DFLOAT_VWALK -DUV_VIS2 -DMIX_S_UV -DUV_LDRAG -DUV_DRAG_GRID -DANA_DRAG -DBIO_FENNEL
    <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
    

• All the ROMS standard input files (roms_*.in) were updated to include the options for Waves Effect on Currents (WEC).

• The metadata YAML dictionary varinfo.yaml was changed to include the Waves Effect on Currents (WEC) fields and the native sea-ice mode (ICE_MODEL).

• This update includes the changes discussed in ​src:ticket:945 to ROMS input scripts (roms_*.in), build scripts (build_roms.* and cbuild_roms.*), and metadata file varinfo.yaml.

• The makefile was updated to rename of macro SCRATCH_DIR to BUILD_DIR. Code was added for backward compatibility with old make configuration files (Compilers/*.mk):

  BUILD_DIR ?= Build_roms
  
  #  Backward compatability with old build scripts and make configuration
  #  files (*.mk). The BUILD_DIR macro is preferred.
  
  ifdef SCRATCH_DIR
    BUILD_DIR := $(SCRATCH_DIR)
  else
    SCRATCH_DIR := $(BUILD_DIR)
  endif
  

• Similarly, the make configuration in Compilers/*.mk were updated to rename macro SCRATCH_DIR to BUILD_DIR.

• Corrected spelling in the source code documentation. We need to use Charnock instead. However, the roughness variable is still charnok_alpha, and the CPP option is still CHARNOK.

• Added the logical switch for implicit omega in read_phypar.F:

  # ifdef OMEGA_IMPLICIT
              IF (Hout(idOvil,ng)) WRITE (out,170) Hout(idOvil,ng),       &
       &         'Hout(idOvil)',                                          &
       &         'Write out omega implicit vertical velocity.'
  # endif