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 Post subject: ROMS 3.4 Released
PostPosted: Mon Apr 25, 2011 2:00 am 
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ROMS/TOMS 3.4 Released

The latest version of the :arrow: ROMS/TOMS svn repository, revision 550, was frozen and tagged as ROMS 3.4. This version is quite stable and includes several improvements to all 4D-Var and (4D-Var)T data assimilation algorithms. The major developments and improvements are summarized below. Additional detailed information can be found in the ROMS repository :arrow: trac ticket system. Please check the upgrade type tickets.

Many thanks to Andy Moore for his great help in the development and testing of all 4D-Var and (4D-Var)T data assimilation algorithms.

What is New:

  • The test :arrow: svn repository was updated to include several idealized and realistic ROMS applications. Notice that the repository includes several :arrow: sub-directories. Each sub-directory contains the necessary header file (my_application.h), input scripts (ocean.in, and others), build scripts (build.bash, build.sh), and, if applicable, configuration scripts (job_*.in). These test cases show the versatility of the build script and how users can play with different combinations of C-preprocessing options, ROMS source code, parallel/serial applications, and various MPI libraries (mpich, mpich2, OpenMPI). Notice that each application header file is very clean (no #undef directives) and the important CPP options are actually defined in the build script, for example in the default upwelling test case we have:
    Code:
     export      MY_CPP_FLAGS="-DAVERAGES"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDIAGNOSTICS_TS"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDIAGNOSTICS_UV"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DSTATIONS"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DFLOATS"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DFLOAT_VWALK"

    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDEBUGGING"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DOUT_DOUBLE"

     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DEW_PERIODIC"

     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DUV_VIS2"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DUV_VIS4"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DMIX_S_UV"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DMIX_GEO_UV"

    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DUV_LOGDRAG"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DUV_LDRAG"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DUV_QDRAG"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DUV_DRAG_GRID"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DANA_DRAG"

     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DTS_U3HADVECTION"
     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DTS_C4VADVECTION"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DTS_MPDATA"

     export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DBIO_FENNEL"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DECOSIM"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DNEMURO"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DNPZD_FRANKS"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DNPZD_IRON"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DNPZD_POWELL"

    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DGLS_MIXING"
    #export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DMY25_MIXING"

    Notice that it is much easier to comment options in the build script that using the define/undef directive in the header file.

  • To checkout the test cases repository use:
    Code:
    svn checkout --username joe_roms https://www.myroms.org/svn/src/test my_test

  • We added test cases for the 4D-Var and (4D-Var)T data assimilation algorithms using California Current System, 1/3 resolution, WC13 application. You will find a directory for each 4D-Var algorithm:
    Code:
    /WC13                       Main California Current System 4D-Var applications
          /ARRAY_MODES          Stabilized representer matrix array modes and clipping
          /Data                 Input data directory
          /Functionals          Analytical expression header file
          /I4DVAR               Primal form of incremental, strong constraint 4D-Var, I4D-Var
          /I4DVAR_impact        I4D-Var observation impact
          /Normalization        4D-Var error covariance normalization coefficients
          /plotting             4D-Var plotting scripts (Matlab and ROMS plotting package)
          /PSAS                 Dual form of 4D-Var, Physical-space Statistical Analysis System, 4D-PSAS
          /PSAS_impact          4D-PSAS observation impact
          /PSAS_sensitivity     4D-PSAS observation sensitivity (adjoint of 4D-PSAS)
          /R4DVAR               Dual form of 4D-Var, indirect representer method, R4D-Var
          /R4DVAR_impact        R4D-Var observation impact
          /R4DVAR_sensitivity   R4D-Var observation sensitivity (adjoint of R4D-Var)

    We provided a lot of documentation about how to use these algorithms in :arrow: WikiROMS with several 4D-Var tutorials. The tutorials are part of the ROMS data assimilation workshop that Andy Moore and I offered in July 2010 at the University of California, Santa Cruz.

  • Added test cases for the adjoint-based Generalized Stability Theory (GST) algorithms using the idealized double gyre example. You will find a directory for each GST algorithm:
    Code:
    /double_gyre                Main double gyre test case
                /Data           Input NetCDF file
                /Forward        Nonlinear forward trajectory
                /AFTE           Adjoint Finite Time Eigenmodes
                /FTE            Finite time Eigenmodes
                /FSV            Forcing Singular Vectors
                /OP             Optimal Perturbations
                /SOsemi         Stochastic Optimals, seminorn

  • Added grid, initial conditions, and forcing NetCDF files for the BIO_TOY test case. It includes initial conditions for BIO_FENNEL, ECOSIM, NEMURO, and all NPZD models (NPZD_FRANKS, NPZD_IRON, and NPZD_POWELL). All the NetCDF files are now under svn control and located in the bio_toy/Data sub-directory. The grid is a 5x5 double periodic domain sampled from the North Eastern North Atlantic (NENA) application. There is an initial conditions file corresponding to each ecosystem model. The fields are horizontally uniform rendering ROMS into 1D vertical model. Currently, we have the following files:
    Code:
    bio_toy/Data/bio_toy_grd.nc            grid
    bio_toy/Data/bio_toy_frc.nc            forcing
    bio_toy/Data/bio_toy_ini_fennel.nc     BIO_FENNEL
    bio_toy/Data/bio_toy_ini_ecosim.nc     ECOSIM
    bio_toy/Data/bio_toy_ini_nemuro.nc     NEMURO
    bio_toy/Data/bio_toy_ini_npzd.nc       any NPZD model

    The forcing data is from a typical year (days 0.5 to 364.5) ECMWF 40-year re-analysis. The time coordinate has the cycle_length attribute with a 365 value. Therefore, this application can be run for several years with a perpetual annual forcing cycle.

  • The build script (ROMS/Bin/build.bash and ROMS/Bin/build.sh) was improved and updated. Most of the user tunable parameters are close to each other and better documented:
    Code:
    # Other user defined environmental variables. See the ROMS makefile for
    # details on other options the user might want to set here. Be sure to
    # leave the switches meant to be off set to an empty string or commented
    # out. Any string value (including off) will evaluate to TRUE in
    # conditional if-statements.

     export           USE_MPI=on            # distributed-memory parallelism
     export        USE_MPIF90=on            # compile with mpif90 script
    #export        which_MPI=mpich         # compile with MPICH library
    #export        which_MPI=mpich2        # compile with MPICH2 library
     export         which_MPI=openmpi       # compile with OpenMPI library

    #export        USE_OpenMP=on           # shared-memory parallelism

     export              FORT=ifort
    #export              FORT=gfortran
    #export              FORT=pgi

    #export         USE_DEBUG=on           # use Fortran debugging flags
     export         USE_LARGE=on            # activate 64-bit compilation
    #export       USE_NETCDF4=on           # compile with NetCDF-4 library
    #export   USE_PARALLEL_IO=on           # Parallel I/O with Netcdf-4/HDF5

    #export       USE_MY_LIBS=on           # use my library paths below
    Notice the new local variable which_MPI to specify which MPI library to use during compilation. You need choose only one and comment the other values. The value of local variable USE_MY_LIBS is commented out by default. If you want to use this nice capability, you need to change the paths of the required libraries in your particular computer. Recall that you may want to have different copies of the build script for a particular computer.

  • Now we are using the NetCDF-4 configuration script nc-config which is available since NetCDF version 4.0.1. This script reports all the required libraries according to the NetCDF-4 installation options (openDAP, NetCDF4/HDF5 file format). For Example, the logic for the ifort compiler in build.bash is now:
    Code:
    if [ -n "${USE_MY_LIBS:+1}" ]; then
      case "$FORT" in
        ifort )
          export             ESMF_OS=Linux
          export       ESMF_COMPILER=ifort
          export           ESMF_BOPT=O
          export            ESMF_ABI=64
          export           ESMF_COMM=mpich
          export           ESMF_SITE=default

          export       ARPACK_LIBDIR=/opt/intelsoft/serial/ARPACK
          if [ -n "${USE_MPI:+1}" ]; then
            if [ "${which_MPI}" = "mpich" ]; then
              export        ESMF_DIR=/opt/intelsoft/mpich/esmf
              export      MCT_INCDIR=/opt/intelsoft/mpich/mct/include
              export      MCT_LIBDIR=/opt/intelsoft/mpich/mct/lib
              export  PARPACK_LIBDIR=/opt/intelsoft/mpich/PARPACK
            elif [ "${which_MPI}" = "mpich2" ]; then
              export        ESMF_DIR=/opt/intelsoft/mpich2/esmf
              export      MCT_INCDIR=/opt/intelsoft/mpich2/mct/include
              export      MCT_LIBDIR=/opt/intelsoft/mpich2/mct/lib
              export  PARPACK_LIBDIR=/opt/intelsoft/mpich2/PARPACK
            elif [ "${which_MPI}" = "openmpi" ]; then
              export        ESMF_DIR=/opt/intelsoft/openmpi/esmf
              export      MCT_INCDIR=/opt/intelsoft/openmpi/mct/include
              export      MCT_LIBDIR=/opt/intelsoft/openmpi/mct/lib
              export  PARPACK_LIBDIR=/opt/intelsoft/openmpi/PARPACK
            fi
          fi

          if [ -n "${USE_NETCDF4:+1}" ]; then
            if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
              if [ "${which_MPI}" = "mpich" ]; then
                export     NC_CONFIG=/opt/intelsoft/mpich/netcdf4/bin/nc-config
                export NETCDF_INCDIR=/opt/intelsoft/mpich/netcdf4/include
              elif [ "${which_MPI}" = "mpich2" ]; then
                export     NC_CONFIG=/opt/intelsoft/mpich2/netcdf4/bin/nc-config
                export NETCDF_INCDIR=/opt/intelsoft/mpich2/netcdf4/include
              elif [ "${which_MPI}" = "openmpi" ]; then
                export     NC_CONFIG=/opt/intelsoft/openmpi/netcdf4/bin/nc-config
                export NETCDF_INCDIR=/opt/intelsoft/openmpi/netcdf4/include
              fi
            else
              export       NC_CONFIG=/opt/intelsoft/serial/netcdf4/bin/nc-config
              export   NETCDF_INCDIR=/opt/intelsoft/serial/netcdf4/include
            fi
          else
            export     NETCDF_INCDIR=/opt/intelsoft/serial/netcdf3/include
            export     NETCDF_LIBDIR=/opt/intelsoft/serial/netcdf3/lib
          fi
          ;;
        ...
    Again, all the above logic is processed when the environmental variable USE_MY_LIBS is not empty and has any non-blank value. This change required an update to all the make configuration (*.mk) files in the Compilers directory. This cleaned the logic nicely. Notice that nc-config is not available for NetCDF 3.x. Many thanks to Mark Hadfield for :arrow: suggesting this change.

    We highly recommend using the build script when compiling and linking ROMS. Advanced users that run on various computer architecture may want to have their own Compilers sub-directory somewhere else. I have my customized make configuration files in $HOME/Compilers. So I tell the build script to use those configuration files instead:
    Code:
    #export         COMPILERS=${MY_ROMS_SRC}/Compilers
     export          COMPILERS=${HOME}/Compilers
  • The time-averaged, diagnostic terms for the momentum (DIAGNOSTICS_UV) and tracer (DIAGNOSTICS_TS) equations were expanded to include components in the ξ- and η-directions for horizontal advection and horizontal viscosity/diffusion. For technical information on implementation check following :arrow: trac ticket.

    • The momentum advection output variables are:
      Code:
      ubar_hadv, vbar_hadv     2D momentum horizontal   advection
      ubar_xadv, vbar_xadv     2D momentum horizontal ξ-advection
      ubar_yadv, vbar_yadv     2D momentum horizontal η-advection

      u_hadv,    v_hadv        3D momentum horizontal   advection
      u_xadv,    v_xadv        3D momentum horizontal ξ-advection
      u_yadv,    v_yadv        3D momentum horizontal η-advection
      u_vadv,    v_vadv        3D momentum vertical     advection

    • The momentum viscosity (stress tensor) output variables are:
      Code:
      ubar_hvisc, vbar_hvisc   2D momentum horizontal   viscosity
      ubar_xvisc, vbar_xvisc   2D momentum horizontal ξ-viscosity
      ubar_yvisc, vbar_yvisc   2D momentum horizontal η-viscosity

      u_hvisc,    v_hvisc      3D momentum horizontal   viscosity
      u_xvisc,    v_xvisc      3D momentum horizontal ξ-viscosity
      u_yvisc,    v_yvisc      3D momentum horizontal η-viscosity
      u_vvisc,    v_vvisc      3D momentum vertical     viscosity

    • The tracer advection output variables are: (Tname is typically, temp, salt, ...)
      Code:
      Tname_hadv               tracer horizontal   advection
      Tname_xadv               tracer horizontal ξ-advection
      Tname_yadv               tracer horizontal η-advection
      Tname_vadv               tracer vertical     advection

    • The tracer diffusion output variables are: (Tname is typically, temp, salt, ...)
      Code:
      Tname_hdiff              tracer horizontal   diffusion
      Tname_xdiff              tracer horizontal ξ-diffusion
      Tname_ydiff              tracer horizontal η-diffusion
      Tname_sdiff              tracer horizontal s-diffusion (rotated tensor)
      Tname_vdiff              tracer vertical     diffusion

    • Vorticity diagnostics output variables (new fields computed in new routine vorticity.F):
      Code:
      rvorticity_bar           2D relative  vorticity
      pvorticity_bar           2D potential vorticity

      rvorticity               3D relative  vorticity
      pvorticity               3D potential vorticity

  • The logic for writing time-averaged fields (AVERAGES) and diagnostic terms (DIAGNOSTICS_TS, DIAGNOSTICS_UV) into respective output NetCDF files was redesigned to provide more flexibility and facilitate expansion in the future. A new set of logical switches (T/F) Aout were added to control the time-averaged fields written into the output AVGNAME NetCDF file. These switches are set in the standard input script, ocean.in:
    Code:
    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged
    ! fields into AVERAGE output file.

    Aout(idUvel) == T       ! u                  3D U-velocity
    Aout(idVvel) == T       ! v                  3D V-velocity
    Aout(idWvel) == T       ! w                  3D W-velocity
    Aout(idOvel) == T       ! omega              omega vertical velocity
    Aout(idUbar) == T       ! ubar               2D U-velocity
    Aout(idVbar) == T       ! vbar               2D V-velocity
    Aout(idFsur) == T       ! zeta               free-surface

    Aout(idTvar) == T T     ! temp, salt         temperature and salinity

    Aout(idUsms) == F       ! sustr              surface U-stress
    Aout(idVsms) == F       ! svstr              surface V-stress
    Aout(idUbms) == F       ! bustr              bottom U-stress
    Aout(idVbms) == F       ! bvstr              bottom V-stress

    Aout(idW2xx) == F       ! Sxx_bar            2D radiation stress, Sxx component
    Aout(idW2xy) == F       ! Sxy_bar            2D radiation stress, Sxy component
    Aout(idW2yy) == F       ! Syy_bar            2D radiation stress, Syy component
    Aout(idU2rs) == F       ! Ubar_Rstress       2D radiation U-stress
    Aout(idV2rs) == F       ! Vbar_Rstress       2D radiation V-stress
    Aout(idU2Sd) == F       ! ubar_stokes        2D U-Stokes velocity
    Aout(idV2Sd) == F       ! vbar_stokes        2D V-Stokes velocity

    Aout(idW3xx) == F       ! Sxx                3D radiation stress, Sxx component
    Aout(idW3xy) == F       ! Sxy                3D radiation stress, Sxy component
    Aout(idW3yy) == F       ! Syy                3D radiation stress, Syy component
    Aout(idW3zx) == F       ! Szx                3D radiation stress, Szx component
    Aout(idW3zy) == F       ! Szy                3D radiation stress, Szy component
    Aout(idU3rs) == F       ! u_Rstress          3D U-radiation stress
    Aout(idV3rs) == F       ! v_Rstress          3D V-radiation stress
    Aout(idU3Sd) == F       ! u_stokes           3D U-Stokes velocity
    Aout(idV3Sd) == F       ! v_stokes           3D V-Stokes velocity

    Aout(idPair) == F       ! Pair               surface air pressure
    Aout(idUair) == F       ! Uair               surface U-wind component
    Aout(idVair) == F       ! Vair               surface V-wind component

    Aout(idTsur) == F F     ! shflux, ssflux     surface net heat and salt flux
    Aout(idLhea) == F       ! latent             latent heat flux
    Aout(idShea) == F       ! sensible           sensible heat flux
    Aout(idLrad) == F       ! lwrad              longwave radiation flux
    Aout(idSrad) == F       ! swrad              shortwave radiation flux
    Aout(idevap) == F       ! evaporation        evaporation rate
    Aout(idrain) == F       ! rain               precipitation rate

    Aout(idDano) == F       ! rho                density anomaly
    Aout(idVvis) == F       ! AKv                vertical viscosity
    Aout(idTdif) == F       ! AKt                vertical T-diffusion
    Aout(idSdif) == F       ! AKs                vertical Salinity diffusion
    Aout(idHsbl) == F       ! Hsbl               depth of surface boundary layer
    Aout(idHbbl) == F       ! Hbbl               depth of bottom boundary layer

    Aout(idHUav) == F       ! Huon               u-volume flux, Huon
    Aout(idHVav) == F       ! Hvom               v-volume flux, Hvom
    Aout(idUUav) == F       ! uu                 quadratic <u*u> term
    Aout(idUVav) == F       ! uv                 quadratic <u*v> term
    Aout(idVVav) == F       ! vv                 quadratic <v*v> term
    Aout(idU2av) == F       ! ubar2              quadratic <ubar*ubar> term
    Aout(idV2av) == F       ! vbar2              quadratic <vbar*vbar> term
    Aout(idZZav) == F       ! zeta2              quadratic <zeta*zeta> term

    Aout(idTTav) == F F     ! temp2, salt2       quadratic <t*t> T/S terms
    Aout(idUTav) == F F     ! utemp, usalt       quadratic <u*t> T/S terms
    Aout(idVTav) == F F     ! vtemp, vsalt       quadratic <v*t> T/S terms
    Aout(iHUTav) == F F     ! Huontemp, ...      T/S volume flux, <Huon*t>
    Aout(iHVTav) == F F     ! Hvomtemp, ...      T/S volume flux, <Hvom*t>

    ! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
    ! tracers other than biological and sediment tracers into the AVERAGE file.

     Aout(inert) == T       ! dye_01, ...        inert passive tracers

    The strategy here is to provide the user with switches to control which variables are written into the AVGNAME output file. The time-averages require global arrays to hold the accumulated sums. This increases the memory requirements of the model. This update only allocates those fields that are requested. Otherwise, the pointer for the array in the AVERAGE(ng)%avg... structure remains unassociated and does not use memory. For example, in mod_average.F we now have:
    Code:
           IF (Aout(idFsur,ng)) THEN
             allocate ( AVERAGE(ng) % avgzeta(LBi:UBi,LBj:UBj) )
           END IF

    Since we control the time-averaged fields with switches, there is no longer a need for the following C-preprocessing options: AVERAGES_AKV, AVERAGES_AKS, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC. These options are eliminated. The only option that is required to write any of these fields is AVERAGES. This is nice because we do not have to recompile if new fields are needed later.

  • The routine set_avg_tile was completely redesigned to use these control swithes. Notice that arrays are no longer passed as arguments. This facilitates adding new fields in the future.
    Code:
          CALL set_avg_tile (ng, tile,                                      &
         &                   LBi, UBi, LBj, UBj,                            &
         &                   IminS, ImaxS, JminS, JmaxS,                    &
    # ifdef SOLVE3D
         &                   NOUT,                                          &
    # endif
         &                   KOUT)

    ...

            IF (Aout(idFsur,ng)) THEN
              DO j=JstrR,JendR
                DO i=IstrR,IendR
                  AVERAGE(ng)%avgzeta(i,j)=AVERAGE(ng)%avgzeta(i,j)+        &
         &                                 OCEAN(ng)%zeta(i,j,Kout)
                END DO
              END DO
            END IF

  • We still need the option AVERAGES_DETIDE to process time-averaged, detided fields. Notice that we also control the processing of these fields with the Aout switches. Also, I added the capability to detide temperature and salinity since we have better control of the memory requirements.
    Code:
    Aout(idu3dD) == F       ! u_detided          detided 3D U-velocity
    Aout(idv3dD) == F       ! v_detided          detided 3D V-velocity
    Aout(idu2dD) == F       ! ubar_detided       detided 2D U-velocity
    Aout(idv2dD) == F       ! vbar_detided       detided 2D V-velocity
    Aout(idFsuD) == F       ! zeta_detided       detided free-surface

    Aout(idTrcD) == F F     ! temp_detided, ...  detided temperature and salinity


  • The time-averaged vorticity fields were moved from DIANAME to AVGNAME. This is a better place for such fields:
    Code:
    Aout(id2dRV) == F       ! pvorticity_bar     2D relative vorticity
    Aout(id3dRV) == F       ! pvorticity         3D relative vorticity
    Aout(id2dPV) == F       ! rvorticity_bar     2D potential vorticity
    Aout(id3dPV) == F       ! rvorticity         3D potential vorticity

  • A new set of logical switches (T/F) Dout were added to control the time-averaged diagnostic terms written into the output DIANAME NetCDF file. These switches are set in standard input script, ocean.in:
    Code:
    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
    ! 2D momentum (ubar,vbar) diagnostic terms into DIAGNOSTIC output file.

    Dout(M2rate) == T       ! ubar_accel, ...    acceleration
    Dout(M2pgrd) == T       ! ubar_prsgrd, ...   pressure gradient
    Dout(M2fcor) == T       ! ubar_cor, ...      Coriolis force
    Dout(M2hadv) == T       ! ubar_hadv, ...     horizontal total advection
    Dout(M2xadv) == T       ! ubar_xadv, ...     horizontal XI-advection
    Dout(M2yadv) == T       ! ubar_yadv, ...     horizontal ETA-advection
    Dout(M2hrad) == T       ! ubar_hrad, ...     horizontal total radiation stress
    Dout(M2hvis) == T       ! ubar_hvisc, ...    horizontal total viscosity
    Dout(M2xvis) == T       ! ubar_xvisc, ...    horizontal XI-viscosity
    Dout(M2yvis) == T       ! ubar_yvisc, ...    horizontal ETA-viscosity
    Dout(M2sstr) == T       ! ubar_sstr, ...     surface stress
    Dout(M2bstr) == T       ! ubar_bstr, ...     bottom stress

    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
    ! 3D momentum (u,v) diagnostic terms into DIAGNOSTIC output file.

    Dout(M3rate) == T       ! u_accel, ...       acceleration
    Dout(M3pgrd) == T       ! u_prsgrd, ...      pressure gradient
    Dout(M3fcor) == T       ! u_cor, ...         Coriolis force
    Dout(M3hadv) == T       ! u_hadv, ...        horizontal total advection
    Dout(M3xadv) == T       ! u_xadv, ...        horizontal XI-advection
    Dout(M3yadv) == T       ! u_yadv, ...        horizontal ETA-advection
    Dout(M3vadv) == T       ! u_vadv, ...        vertical advection
    Dout(M3hrad) == T       ! u_hrad, ...        horizontal total radiation stress
    Dout(M3vrad) == T       ! u_vrad, ...        vertical radiation stress
    Dout(M3hvis) == T       ! u_hvisc, ...       horizontal total viscosity
    Dout(M3xvis) == T       ! u_xvisc, ...       horizontal XI-viscosity
    Dout(M3yvis) == T       ! u_yvisc, ...       horizontal ETA-viscosity
    Dout(M3vvis) == T       ! u_vvisc, ...       vertical viscosity

    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
    ! active (temperature and salinity) and passive (inert) tracer diagnostic
    ! terms into DIAGNOSTIC output file: [1:NAT+NPT,Ngrids].

    Dout(iTrate) == T T     ! temp_rate, ...     time rate of change
    Dout(iThadv) == T T     ! temp_hadv, ...     horizontal total advection
    Dout(iTxadv) == T T     ! temp_xadv, ...     horizontal XI-advection
    Dout(iTyadv) == T T     ! temp_yadv, ...     horizontal ETA-advection
    Dout(iTvadv) == T T     ! temp_vadv, ...     vertical advection
    Dout(iThdif) == T T     ! temp_hdiff, ...    horizontal total diffusion
    Dout(iTxdif) == T T     ! temp_xdiff, ...    horizontal XI-diffusion
    Dout(iTydif) == T T     ! temp_ydiff, ...    horizontal ETA-diffusion
    Dout(iTsdif) == T T     ! temp_sdiff, ...    horizontal S-diffusion
    Dout(iTvdif) == T T     ! temp_vdiff, ...    vertical diffusion

    Similar Aout and Dout switches are added to all the biology and sediment models input scripts. For example, in bio_Fennel.in now we have:
    Code:
    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
    ! into AVERAGE output file: [1:NBT,Ngrids].

    Aout(idTvar) == 12*T                  ! biological tracer

    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
    ! biological tracer diagnostic terms into DIAGNOSTIC output file:
    ! [1:NBT,Ngrids].

    Dout(iTrate) == 12*T                  ! time rate of change
    Dout(iThadv) == 12*T                  ! horizontal total advection
    Dout(iTxadv) == 12*T                  ! horizontal XI-advection
    Dout(iTyadv) == 12*T                  ! horizontal ETA-advection
    Dout(iTvadv) == 12*T                  ! vertival advection
    Dout(iThdif) == 12*T                  ! horizontal total diffusion
    Dout(iTxdif) == 12*T                  ! horizontal XI-diffusion
    Dout(iTydif) == 12*T                  ! horizontal ETA-diffusion
    Dout(iTsdif) == 12*T                  ! horizontal S-diffusion
    Dout(iTvdif) == 12*T                  ! vertical diffusion

    ! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
    ! biological processes diagnostics terms into DIAGNOSTIC output file [Ngrids].

     Dout(iCOfx) == T                     ! air-sea CO2 flux
     Dout(iDNIT) == T                     ! denitrification flux
     Dout(ipCO2) == T                     ! CO2 partial pressure
     Dout(iO2fx) == T                     ! air-sea O2 flux
     Dout(iPPro) == T                     ! primary production
     Dout(iNO3u) == T                     ! NO3 uptake

    Notice that diagnostics activated with DIGNOSTICS_BIO in Fennel's model are also controlled with the Dout instead of the Hout switches above. They need to be scaled before writing in wrt_diag.F:
    Code:
          DO ivar=1,NDbio2d
            ifield=iDbio2(ivar)
            IF (Dout(ifield,ng)) THEN
              IF (ivar.eq.ipCO2) THEN
                scale=1.0_r8
              ELSE
                scale=1.0_r8/(REAL(nDIA(ng),r8)*dtBIO)   ! mmole m-2 day-1
              END IF
              ...
            END IF
          END DO

  • A new C-preprocessing option FLOAT_STICKY was added to reflect floats that hit the surface and stick floats that hit the bottom. This is needed to avoid overshoots and spurious unmixing near the boundary when vertical random walk (FLOAT_VWALK) is activated. Many thanks to Mark Hadfield for contributing this option.

  • A new vertical stretching function, Vstretching = 4, was added and it is denoted as Shchepetkin (2010). This is a major improvement to his 2005 function, Vstretching = 2. The new function, C(s), has a double stretching transformation:
    Code:
       C(s) = [1 - COSH(theta_s * s)] / [COSH(theta_s) - 1]

    with bottom refinement:

       C(s) = [EXP(theta_b * C(s)) - 1] / [1 - EXP(-theta_b)]
    Notice that the bottom function is the second stretching of an already stretched transform. The resulting function is continuous with respect the control parameters theta_s and theta_b with a meaningful range of:
    Code:
       0 <  theta_s <= 10.0
       0 <= theta_b <=  4.0
    Due to its functionality and properties Vtransform = 2 and Vstretching = 4 are now the default values for ROMS. Many thanks to Sasha Shchepetkin for designing this nice and continuous transformation.

    Notice that with Vtransform = 2 the true sigma-coordinate system is recovered as hc goes to infinity. This is useful when configuring applications with flat bathymetry and uniform level thickness. Practically, you can achieve this by setting the following in ocean.in:
    Code:
       THETA_S = 0.0d0
       THETA_B = 0.0d0
       TCLINE  = 1.0d+17       (a large number)
    Please check :arrow: WikiROMS for updated documentation and plots. For example, in the coarse resolution, North Atlantic application (DAMEE_4) we get:

    Image

  • The following testcases were changed to have the default transformation Vtransform = 2 and Vstretching = 4:
    Code:
                           OLD (1,1)                      NEW (2,4)
                   theta_s  theta_b  Tcline      theta_s   theta_b  Tcline
                  ---------------------------------------------------------

    BASIN            3.3      0.0     1400         3.3       0.0     1400
    BENCHMARK        5.0      0.4      200         0.0       0.0      400                     
    BL_TEST          3.2      0.2        5         5.0       1.5       20
    CANYON2D        1d-4      0.0       90         0.0       0.0    1d+16
    DOUBLE_GYRE      1.0      1.0       50         0.0       0.0    1d+16
    FLT_TEST2D       3.0      0.4      100         0.0       0.0    1d+16
    FLT_TEST3D       3.0      0.4      100         0.0       0.0    1d+16
    GRAV_ADJ        1d-4      0.0       50         0.0       0.0    1d+16
    KELVIN           3.0      0.0       50         0.0       0.0    1d+16
    LMD_TEST        1d-4      0.0       50         0.0       0.0    1d+16
    RIVERPLUME1      3.0      0.4       50         3.0       0.0       30
    RIVERPLUME2      3.0      0.4       50         3.0       0.0       30
    SEAMOUNT         5.0      0.4       50         6.5       2.0      100
    SOLITON         1d-4      0.0       50         0.0       0.0    1d+16
    UPWELLING        3.0      0.0       50         3.0       0.0       25
    WINDBASIN       1d-4      0.0       50         1.0       0.0       50

  • A new driver array_modes_w4dvar.h was added to compute either the requested array mode eigenvector (ARRAY_MODES) or clipped spectrum analysis (CLIPPING) of the stabilized representer matrix during weak constraint, variational data assimilation. The array mode analysis can be used to assess the observing system, prior covariance hypothesis, and the stability of the generalized inverse. The following new CPP options are added:
    Code:
    ARRAY_MODES         use if computing W4DVAR representer matrix array modes
    ARRAY_MODES_SPLIT   use to separate analysis due to IC, forcing, and OBC
    CLIPPING            use if computing W4DVAR representer matrix clipping analysis
    CLIPPING_SPLIT      use to separate analysis due to IC, forcing, and OBC
    RECOMPUTE_4DVAR     use if recomputing W4DVAR in analysis algorithms
    A new parameter, Nvct, was added to the s4dvar.in input script. If ARRAY_MODES is activated, Nvct eigenvectors of the stabilized representer matrix will be processed (Nvct=1 is the least important, and Nvct=Ninner is the most important). If CLIPPING is activated, only eigenvector Nvct=Ninner will be processed and the rest will be disgarded.

  • A new C-preprocessing option, MINRES, was added to accelerate the convergence of the dual formulation data assimilation algorithms (R4D-Var and 4D-PSAS) using the Minimal Residual Method (MinRes) proposed by El Akkraoui and Gauthier (2010, QJRMS, 136, 107-115). This method is described by Paige and Saunders (Sparse Indefinite Systems of Linear Equations, 1975, SIAM Journal on Numerical Analysis, 617-619). Specifically we use equations 6.10 and 6.11 of this paper. This is a remarkable algorithm and makes R4D-Var and 4D-PSAS practical in strong- and weak-constraint applications. The convergence rate is similar to that of the primal form I4D-Var. This is illustrated in the following plot:

    Image

    This algorithm also works for the associated observation sensitivity and observation impact. We still need to work on the posterior analysis routines posterior.F and posterior_var.F. These routines will be updated to MINRES later. Many thanks to Andy Moore for his help in coding and testing this new algorithm. Also many thanks to Amal El Akkraoui for bringing this minimization algorithm to our attention at the last International Adjoint Workshop.

  • All the Generalized Stability Theory (GST), adjoint-based algorithms were updated:
    Code:
        afte_ocean.h      Adjoint Finite Time Eigenmodes (AFT_EIGENMODES)
        fte_ocean.h       Finite Time Eigenmodes (FT_EIGENMODES)
        fsv_ocean.h       Forcing Singular Vectors (FORCING_SV)
        op_ocean.h        Optimal Perturbations (OPT_PERTURBATION)
        so_semi_ocean.h   Stochastic Optimals, Seminorm (SO_SEMI)
    The check-pointing CPP option, CHECKPOINTING, is no longer an internal flag. It is removed from globaldefs.h and the User needs to activate it explicitly in order to create/use the GST restart NetCDF file. Recall the the restart switch LrstGST is activated in the standard input ocean.in file. I removed all the calls to the BLAS library routines daxpy and dnrm2, which is used to computed the Eucledean norm in the GST algorithms. The BLAS library only works in parallel with the PGI compiler. We were getting the wrong norms with the ifort and gfortran compilers. This is due to the legacy code style in this library that dimensions arrays as x(1) instead of x(n). The MPI reduction operations were giving incorrect values. In addition, these routines and others have deprecated arithmetic GO TO and were getting a lot of warnings during compilation. Some of these legacy libraries need to be updated for future compilers that do not support old f77 dimension style. To avoid problems in the future, I wrote my own Eucledean norm routines for real vectors (r_norm2) and complex vectors (c_norm2).

  • The output Ritz vectors from the GST algorithms can be written in separate NetCDF files when the new standard input logical switch LmultiGST is activated:
    Code:
    ! GST output and check pointing restart parameters.

       LmultiGST =  F                               ! one eigenvector per file
         LrstGST =  F                               ! GST restart switch
      MaxIterGST =  500                             ! maximun number of iterations
            NGST =  10                              ! check-pointing interval
    The eigenvectors for the AFT_EIGENMODES or FT_EIGENMODES are usually complex. In this case, both the real and imaginary eigenvectors are stored in the same file when LmultiGST is activated. Notice that all the eigenvectors have an output record for the initial or final perturbation, except the eigenvectors that have only the adjoint model as a propagator (AFT_EIGENMODES and SO_SEMI). This is a function of the running time window.

  • The subroutine mp_ncwrite in distributed.F, which used to write 1D/2D state arrays in the GST algorithms, is split into mp_ncwrite1d and mp_ncwrite2d.

  • The Forcing Singular Vectors and Stochastic Optimals Vectors are expanded to include the full state (zeta, u, v, temp, salt, ...) and/or surface forcing (sustr, svstr, shflx, ssflux, ...). Several new logical switches were added to the standard input ocean.in to set the desired state vector:
    Code:
    ! Logical switches (TRUE/FALSE) to specify the state variables for
    ! which Forcing Singular Vectors or Stochastic Optimals is required.

    Fstate(isFsur) == F                        ! free-surface
    Fstate(isUbar) == F                        ! 2D U-momentum
    Fstate(isVbar) == F                        ! 2D V-momentum
    Fstate(isUvel) == F                        ! 3D U-momentum
    Fstate(isVvel) == F                        ! 3D V-momentum
    Fstate(isTvar) == F F                      ! NT tracers

    Fstate(isUstr) == T                        ! surface U-stress
    Fstate(isVstr) == T                        ! surface V-stress
    Fstate(isTsur) == F F                      ! NT surface tracers flux

  • Added spatially varying bottom roughness length (ZoBot(i,j); m), linear bottom drag coefficients (rdrag(i,j); m/s), or quadratic bottom drag coefficients (rdrag2(i,j); non-dimensional). This can be activated with new C-preprocessing option UV_DRAG_GRID. These spatially varying bottom friction parameters can be specified with either analytical expressions using new C-preprocessing option ANA_DRAG in new routine ana_drag.h or read from application GRID NetCDF file. These parameters are defined at RHO-points and processed according to the momentum bottom friction options UV_LOGDRAG (ZoBot), UV_LDRAG (rdrag), or UV_QDRAG (rdrag2). If reading these variables from the GRID NetCDF, you need to have the following metadata:
    Code:
            double ZoBot(eta_rho, xi_rho) ;
                    ZoBot:long_name = "time invariant, bottom roughness length" ;
                    ZoBot:units = "meter ;
                    ZoBot:coordinates = "lon_rho lat_rho" ;

            double rdrag(eta_rho, xi_rho) ;
                    rdrag:long_name = "linear bottom drag coefficient" ;
                    rdrag:units = "meter second-1 ;
                    rdrag:coordinates = "lon_rho lat_rho" ;

            double rdrag2(eta_rho, xi_rho) ;
                    rdrag2:long_name = "quadratic bottom drag coefficient" ;
                    rdrag2:coordinates = "lon_rho lat_rho" ;
    Notice that only one of these variables is needed according to the C-preprocessing option UV_LOGDRAG, UV_LDRAG, or UV_QDRAG, respectively. It is also possible to use spatially varying ZoBot when SEDIMENT and/or internal BBL_MODEL options are/is activated. The user is allowed to have different NetCDF variable names for these bottom friction parameters. This can be done in the metadata file varinfo.dat. Any of these time-independent variables are written to the header of output NetCDF files when UV_DRAG_GRID is activated.

    Notice that the sediment variable bottom(i,j,izdef) is initialized to ZoBot. However, bottom(i,j,izdef) changes in time due to sediment processes. There is a difference in these variables due to the time dependency which affect the adjoint model.

  • The standard output information has been expanded to include the maximum Courant number values and its location. The Courant number in 3D applications is defined at RHO-points as:
    Code:
        C = Cu + Cv + Cw

    where

        Cu = ABS(u(i,j,k) + u(i+1,j,k)) * dt * pm(i,j)

        Cv = ABS(v(i,j,k) + v(i,j+1,k)) * dt * pn(i,j)

        Cw = ABS(wvel(i,j,k-1) + wvel(i,j,k)) * dt * Hz(i,j,k)
    The (i,j,k) location where the maximum of C occurs is also reported. Finally, the maximum value of the horizontal speed, SQRT(u*u + v*v), is also reported. This information may be useful to monitor the model CFL condition. It also indicates the places in the grid where the CFL is violated during model blow-up. For example, we get in standard output:
    Code:
       STEP   Day HH:MM:SS  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
              C => (i,j,k)       Cu            Cv            Cw         Max Speed

        960    40 00:00:00  8.657897E-04  1.948261E+04  1.948261E+04  2.182663E+17
              (096,125,01)  9.919103E-03  4.299619E-03  1.211318E-02  1.049095E+00

    Notice that this information is written after the global energy and volume diagnostics. The total value of C is not written in 3D applications, but it can be obtained by summing the values of Cu, Cv, and Cw. This information also gives you the clue of which component of C is getting is the largest. In some applications with rotated tensors the value of Cw may get large and the time-step needs to be reduced to avoid the model to blow-up.

    The total value of C is reported in 2D application, since we have an information column available (no Cw value is possible):
    Code:
       STEP   Day HH:MM:SS  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
              C => (i,j,k)       Cu            Cv           C Max       Max Speed

  • Added the capability for writing surface pressure (Pair) and surface wind components (Uair, Vair) to history, averages, and station output NetCDF files. This is done for convenience during post-processing of the model output. For example, it can be used to plot the dependency between surface elevation, pressure, and winds at a particular station location. The winds are written as provided at input, ROMS curvilinear coordinates (XI, ETA) and rotated angles, if applicable. This can be activated in the standard input file ocean.in by turning on the following new switches:
    Code:
    Hout(idPair) == T                          ! surface air pressure
    Hout(idUair) == T                          ! surface U-wind component
    Hout(idVair) == T                          ! surface V-wind component

    ...

    Aout(idPair) == T                          ! surface air pressure
    Aout(idUair) == T                          ! surface U-wind component
    Aout(idVair) == T                          ! surface V-wind component
    and station.in input script:
    Code:
    Sout(idPair) == T                          ! surface air pressure
    Sout(idUair) == T                          ! surface U-wind component
    Sout(idVair) == T                          ! surface V-wind component


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