Difference between revisions of "FJORD TIDAL CASE"

Revision as of 14:12, 7 August 2017

Fjord Tidal Test Case

There are a few ways to setup tidal forcing in ROMS (...learn more about tides in ROMS). This tutorial will explain the simplest way, which is to prescribe (analytically) tidal variations in sea-surface height at a open boundary (this uses a FLATHER/CHAPMAN combination). I learned this trick from hetland in this forum post (at the bottom).

RESTRICTIONS: This technique is ONLY applicable to embayments with a relatively small open boundary (say < 10 km). In this cases, the tidal height along the open boundary is essentially uniform and can be prescribed analytically.

PREREQUISITES: This tutorial assumes that you have (1) downloaded ROMS, (2) installed it in your computer (or cluster), and (3) tested it by compiling and running one of the included test cases. If you haven't done all the above, check the "Getting Started" and "Tutorials" WikiROMS sections.

WATCH HERE a YouTube Video with a simulation product of this tutorial. The plotted colormap is current velocity in the u direction.

Geographical Preamble

This application is for Ship Harbour, an estuarine fjord in Nova Scotia, Canada. Click here to see the location in Google. Tides are semidiurnal and tidal range is 1.4 m on average and 2 m on spring tides. Ship Harbour is a long embayment (~7 km) with an open (EAST) boundary of ~1 km, therefore it is an ideal candidate for the type of analytical tidal forcing taught in this tutorial. For now I will only include tidal forcing, however, there is a river at the uppermost end of the estuary, which discharges freshwater at an annual average rate of 18 m³ s^-1. I plan to write another tutorial on how to add a river, but for now is only tides.

Grid Generation

The first step to set up a realistic application is to set up a realistic grid. There are several software packages to generate ROMS grids; SEAGRID and GRIDGEN being the most popular ones. I used the much-less-fancy EASYGRID, which is a bit easier to get up and running.

DOWNLOAD HERE the grid and initialization files required for this tutorial. Alternatively, you can create your own grid and initialization files for this tutorial using the grid-generation software of your choice. You can download the bathymetry and coastline data for Ship Harbour Fjord HERE.

NOTE: I also wrote a tutorial for grid generation using EASYGRID. The output of that tutorial are the grid and initialization files used in this tutorial (see above). So if you want to start from scratch, you may want to begin with that tutorial.

Compiling ROMS with tides

Before you compile ROMS, you need to create a header (.h) file with the appropriate cpp definitions that turn ON the analytical tides. Also, you need to modify some analytical Fortran files, where you are going to specify how to create the analytical tide.

Creating header (.h) file

Create a file named fjord.h and copy-paste the cpp definitions below:

/*
**
** Options for Tidal Fjord.
**
** Application flag:   FJORD
** Input script:       ocean_fjord.in
*/
#define UV_ADV                 /* use to turn ON or OFF advection terms  */
#define UV_COR                 /* use to turn ON or OFF Coriolis term    */
#define UV_QDRAG               /* use to turn ON or OFF quadratic bottom friction */
#define UV_VIS4                /* use to turn ON or OFF harmonic horizontal mixing */
#define MIX_S_UV               /* momentum mixing on s-surfaces */
#define DJ_GRADPS              /* use if splines density Jacobian (Shchepetkin, 2000) */
#define TS_U3HADVECTION        /* use if 3rd-order upstream horiz. advection */
#define TS_C4VADVECTION        /* use if 4th-order centered vertical advection */
#define SOLVE3D                /* use if solving 3D primitive equations */
#define SPLINES                /* use to activate parabolic splines reconstruction */
/* */
#define ANA_SMFLUX             /* use if analytical surface momentum stress */
#define ANA_STFLUX             /* use if analytical surface temperature flux */
#define ANA_SSFLUX             /* use if analytical surface salinity flux */
#define ANA_BSFLUX             /* use if analytical bottom salinity flux */
#define ANA_BTFLUX             /* use if analytical bottom temperature flux */
#define MASKING                /* use if analytical masking is enabled */
#define EAST_FSCHAPMAN         /* use if free-surface Chapman condition*/
#define EAST_M2FLATHER         /* use if 2D momentum Flather condition*/
#define EAST_M3RADIATION       /* use if 3D momentum radiation condition*/
#define EAST_TRADIATION        /* use if tracers radiation condition*/
#define ANA_FSOBC              /* use if analytical free-surface boundary conditions*/
#define ANA_M2OBC              /* use if analytical 2D momentum boundary conditions*/

The last 6 cpp definitions are the responsible for the analytical tidal forcing. I used the basin.h header file as a starting template... the first 10 cpp definitions are from it.
If your open boundary is not EAST... change EAST_FSCHAPMAN, EAST_M2FLATHER, EAST_M3RADIATION and EAST_TRADIATION to represent your open boundary (e.g. WEST__FSCHAPMAN for a west open boundary... etc.).

Modify ana_fsobc.h

You will have to edit the file ana_fsobc.h (located in trunk/ROMS/Functionals) to tell ROMS to estimate surface height analytically (at the open boundary) when running the FJORD case. Below is a snippet of the end of the file... you have to ADD the green code.

#elif defined TEST_CHAN
     IF (WESTERN_EDGE) THEN
       cff=0.0_r8
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_west(j)=cff
       END DO
     END IF
     IF (EASTERN_EDGE) THEN
       cff=-0.4040_r8*MIN(time(ng)/150000.0_r8,1.0_r8)
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_east(j)=cff
       END DO
     END IF
#elif defined WEDDELL
     IF (WESTERN_EDGE) THEN
       fac=TANH((tdays(ng)-dstart)/1.0_r8)
       omega=2.0_r8*pi*time(ng)/(12.42_r8*3600.0_r8)  !  M2 Tide period
       val=0.53_r8+(0.53_r8-0.48_r8)/REAL(Iend+1,r8)
       phase=(277.0_r8+(277.0_r8-240.0_r8)/REAL(Iend+1,r8))*deg2rad
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_west(j)=fac*val*COS(omega-phase)
       END DO
     END IF
     IF (EASTERN_EDGE) THEN
       fac=TANH((tdays(ng)-dstart)/1.0_r8)
       omega=2.0_r8*pi*time(ng)/(12.42_r8*3600.0_r8)  !  M2 Tide period
       val=0.53_r8+(0.53_r8-0.48_r8)
       phase=(277.0_r8+(277.0_r8-240.0_r8))*deg2rad
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_east(j)=fac*val*COS(omega-phase)
       END DO
     END IF
#elif defined FJORD
     IF (EASTERN_EDGE) THEN
       fac=TANH((tdays(ng)-dstart)/1.0_r8)
       omega=2.0_r8*pi*time(ng)/(12.42_r8*3600.0_r8)  !  M2 Tide period
       val=0.53_r8+(0.53_r8-0.48_r8)
       phase=(277.0_r8+(277.0_r8-240.0_r8))*deg2rad
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_east(j)=fac*val*COS(omega-phase)
       END DO
     END IF      
#else
     IF (EASTERN_EDGE) THEN
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_east(j)=0.0_r8
       END DO
     END IF
     IF (WESTERN_EDGE) THEN
       DO j=JstrR,JendR
         BOUNDARY(ng)%zeta_west(j)=0.0_r8
       END DO
     END IF
     IF (SOUTHERN_EDGE) THEN
       DO i=IstrR,IendR
         BOUNDARY(ng)%zeta_south(i)=0.0_r8
       END DO
     END IF
     IF (NORTHERN_EDGE) THEN
       DO i=IstrR,IendR
         BOUNDARY(ng)%zeta_north(i)=0.0_r8
       END DO
     END IF
#endif
     RETURN
     END SUBROUTINE ana_fsobc_tile

Modify ana_m2obc.h

You will have to edit the file ana_m2obc.h (located in trunk/ROMS/Functionals) to tell ROMS to estimate currents analytically (at the open boundary) when running the FJORD case. Below is a snippet of the end of the file... you have to ADD the green code.

#elif defined WEDDELL
     IF (WESTERN_EDGE) THEN
       fac=TANH((tdays(ng)-dstart)/1.0_r8)
       omega=2.0_r8*pi*time(ng)/(12.42_r8*3600.0_r8)  !  M2 Tide period
       minor=0.0143_r8+(0.0143_r8+0.010_r8)/REAL(Iend+1,r8)
       major=0.1144_r8+(0.1144_r8-0.013_r8)/REAL(Iend+1,r8)
       phase=(318.0_r8+(318.0_r8-355.0_r8)/REAL(Iend+1,r8))*deg2rad
       angle=(125.0_r8+(125.0_r8- 25.0_r8)/REAL(Iend+1,r8))*deg2rad
       DO j=JstrR,JendR
         val=0.5_r8*(angler(Istr-1,j)+angler(Istr,j))
         BOUNDARY(ng)%ubar_west(j)=fac*(major*COS(angle-val)*          &
    &                                         COS(omega-phase)-        &
    &                                   minor*SIN(angle-val)*          &
    &                                         SIN(omega-phase))
       END DO
       DO j=Jstr,JendR
         val=0.5_r8*(angler(Istr-1,j-1)+angler(Istr-1,j))
         BOUNDARY(ng)%vbar_west(j)=fac*(major*SIN(angle-val)*          &
    &                                         COS(omega-phase)-        &
    &                                   minor*SIN(angle-val)*          &
    &                                         COS(omega-phase))
       END DO
     END IF
     IF (EASTERN_EDGE) THEN
       fac=TANH((tdays(ng)-dstart)/1.0_r8)
       omega=2.0_r8*pi*time(ng)/(12.42_r8*3600.0_r8)  !  M2 Tide period
       minor=0.0143_r8+(0.0143_r8+0.010_r8)
       major=0.1144_r8+(0.1144_r8-0.013_r8)
       phase=(318.0_r8+(318.0_r8-355.0_r8))*deg2rad
       angle=(125.0_r8+(125.0_r8- 25.0_r8))*deg2rad
       DO j=JstrR,JendR
         val=0.5_r8*(angler(Iend,j)+angler(Iend+1,j))
         BOUNDARY(ng)%ubar_east(j)=fac*(major*COS(angle-val)*          &
    &                                         COS(omega-phase)-        &
    &                                   minor*SIN(angle-val)*          &
    &                                         SIN(omega-phase))
       END DO
       DO j=Jstr,JendR
         val=0.5_r8*(angler(Iend+1,j-1)+angler(Iend+1,j))
         BOUNDARY(ng)%vbar_east(j)=fac*(major*SIN(angle-val)*          &
    &                                         COS(omega-phase)-        &
    &                                   minor*SIN(angle-val)*          &
    &                                         COS(omega-phase))
       END DO
     END IF
#elif defined FJORD
     IF (EASTERN_EDGE) THEN
       fac=TANH((tdays(ng)-dstart)/1.0_r8)
       omega=2.0_r8*pi*time(ng)/(12.42_r8*3600.0_r8)  !  M2 Tide period
       minor=0.0143_r8+(0.0143_r8+0.010_r8)
       major=0.1144_r8+(0.1144_r8-0.013_r8)
       phase=(318.0_r8+(318.0_r8-355.0_r8))*deg2rad
       angle=(125.0_r8+(125.0_r8- 25.0_r8))*deg2rad
       DO j=JstrR,JendR
         val=0.5_r8*(angler(Iend,j)+angler(Iend+1,j))
         BOUNDARY(ng)%ubar_east(j)=fac*(major*COS(angle-val)*          &
    &                                         COS(omega-phase)-        &
    &                                   minor*SIN(angle-val)*          &
    &                                         SIN(omega-phase))
       END DO
       DO j=Jstr,JendR
         val=0.5_r8*(angler(Iend+1,j-1)+angler(Iend+1,j))
         BOUNDARY(ng)%vbar_east(j)=fac*(major*SIN(angle-val)*          &
    &                                         COS(omega-phase)-        &
    &                                   minor*SIN(angle-val)*          &
    &                                         COS(omega-phase))
       END DO
     END IF      
#else
     IF (EASTERN_EDGE) THEN
       DO j=JstrR,JendR
         BOUNDARY(ng)%ubar_east(j)=0.0_r8
       END DO
       DO j=Jstr,JendR
         BOUNDARY(ng)%vbar_east(j)=0.0_r8
       END DO
     END IF
     IF (WESTERN_EDGE) THEN
       DO j=JstrR,JendR
         BOUNDARY(ng)%ubar_west(j)=0.0_r8
       END DO
       DO j=Jstr,JendR
         BOUNDARY(ng)%vbar_west(j)=0.0_r8
       END DO
     END IF
     IF (SOUTHERN_EDGE) THEN
       DO i=Istr,IendR
         BOUNDARY(ng)%ubar_south(i)=0.0_r8
       END DO
       DO i=IstrR,IendR
         BOUNDARY(ng)%vbar_south(i)=0.0_r8
       END DO
     END IF
     IF (NORTHERN_EDGE) THEN
       DO i=Istr,IendR
         BOUNDARY(ng)%ubar_north(i)=0.0_r8
       END DO
       DO i=IstrR,IendR
         BOUNDARY(ng)%vbar_north(i)=0.0_r8
       END DO
     END IF
#endif
     RETURN
     END SUBROUTINE ana_m2obc_tile

Now you are ready to compile ROMS!
Same as you did with the test cases... now you have to compile ROMS using the newly created fjord.h header file. If you are unsure of how to compile ROMS, you may want to take a look to the build.sh / build.bash page and to the example within the "contributions" section of that page.

Creating ocean_fjord.in

Once ROMS has been compiled and you have your oceanS (or oceanM) executable file, you need to created an input file to run ROMS. You may want to make a copy of ocean_basin.in (trunk/ROMS/External) and use it as a starting template. Don't forget to rename the copy as ocean_fjord.in

Below are snippets of ocean_basin.in. In GREEN are the parts that you need to change in the copy (ocean_fjord.in). Parts in RED also need to be changed in the copy, but the actual replaced text will depend on your own configuration.

Application Title & RHO-grid dimensions

! Application title.
!
      TITLE = Tidal Fjord
!
! C-preprocessing Flag.
!
   MyAppCPP = FJORD
!
! Input variable information file name.  This file needs to be processed
! first so all information arrays can be initialized properly.
!
    VARNAME = ../PATH2VARINFO/varinfo.dat
!
! Grid dimension parameters. See notes below in the Glossary for how to set
! these parameters correctly.
!
         Lm == 90             ! Number of I-direction INTERIOR RHO-points
         Mm == 24             ! Number of J-direction INTERIOR RHO-points
          N == 10             ! Number of vertical levels

NOTE: The values of Lm, Mm and N are output to the screen when creating the grid file using EASYGRID.

Parallelizations parameters

If Running ROMS in parallel, use the configuration below... otherwise you may leave NtileI == 1 and NtileJ == 1

! Domain decomposition parameters for serial, distributed-memory or
! shared-memory configurations used to determine tile horizontal range
! indices (Istr,Iend) and (Jstr,Jend), [1:Ngrids].
!
     NtileI == 4                               ! I-direction partition
     NtileJ == 1                               ! J-direction partition

Time steps

! Time-Stepping parameters.
!
     NTIMES == 1866241                 ! 3 days
         DT == 10
    NDTFAST == 20

NOTE: The values of DT is also output to the screen when creating the grid file using EASYGRID.

Other parameters

These changes are just to speed up simulations.

! Number of eigenvalues (NEV) and eigenvectors (NCV) to compute for the
! Lanczos/Arnoldi problem in the Generalized Stability Theory (GST)
! analysis. NCV must be greater than NEV (see documentation below).
!
        NEV =  2                              ! Number of eigenvalues
        NCV =  10                             ! Number of eigenvectors
!
! Input/Output parameters.
!
      NRREC == 0
  LcycleRST == T
       NRST == 360                            ! Every 1 hour
       NSTA == 360                            ! Every 1 hour
       NFLT == 360                            ! Every 1 hour
      NINFO == 360                            ! Every 1 hour
!
! Output history, average, diagnostic files parameters.
!
    LDEFOUT == T
       NHIS == 60            ! Every 10 minutes
    NDEFHIS == 0             
     NTSAVG == 1
       NAVG == 60            ! Every 10 minutes
    NDEFAVG == 0
     NTSDIA == 1
       NDIA == 60            ! Every 10 minutes
    NDEFDIA == 0

Diffusion coefficients

I'm not sure why, but the values below work ok, while other values make ROMS to blow up

! Harmonic/biharmonic horizontal diffusion of tracer: [1:NAT+NPT,Ngrids].
!
       TNU2 == 20.0d0  20.0d0                  ! m2/s
       TNU4 == 2*0.0d0                         ! m4/s
!
! Harmononic/biharmonic, horizontal viscosity coefficient: [Ngrids].
!
      VISC2 == 100.0d0                         ! m2/s
      VISC4 == 0.0d0                           ! m4/s
!
! Vertical mixing coefficients for active tracers: [1:NAT+NPT,Ngrids]
!
    AKT_BAK == 1.0d-6 1.0d-6                   ! m2/s

Vertical S-coordinates parameters

Adjust parameters for the depth of the our fjord

! Vertical S-coordinates parameters, [1:Ngrids].
!
    THETA_S == 5.0d0                      ! 0 < THETA_S < 20
    THETA_B == 0.4d0                      ! 0 < THETA_B < 1
     TCLINE == 30.0d0                     ! m

Time-stamp at start and reference time

! Time-stamp assigned for model initialization, reference time
! origin for tidal forcing, and model reference time for output
! NetCDF units attribute.
!
       DSTART =  52791.0d0                ! days
   TIDE_START =  52791.0d0                ! days
     TIME_REF =  18581117.0               ! yyyymmdd.dd

Logical switches

! Logical switches (TRUE/FALSE) to specify the state surface forcing
! variable whose stochastic optimals is required.
!
SOstate(isUstr) == F                       ! surface u-stress
SOstate(isVstr) == F                       ! surface v-stress

To speed up simulations

Hout(inert) == F                           ! inert passive tracers

Hout(idBott) == F F F F F F F F F F F F F F F F

Input files

Write path to the GRID and INITIALIZATION input files. !Comment-out the ones that we don't need.

! Input NetCDF file names, [1:Ngrids].
!
    GRDNAME == ../PATH2yourFILE/Fjord_grd.nc
    ININAME == ../PATH2yourFILE/Fjord_ini.nc
!     ITLNAME == ocean_itl.nc
!     IRPNAME == ocean_irp.nc
!     IADNAME == ocean_iad.nc
!     CLMNAME == ocean_clm.nc
!     BRYNAME == ocean_bry.nc
!     FWDNAME == ocean_fwd.nc
!     ADSNAME == ocean_ads.nc

Forcing files

No forcing. !Comment-out the what we don't need.

!   NFFILES == 1                          ! number of forcing files
!
!   FRCNAME == ocean_frc.nc               ! forcing file 1, grid 1

Output files

Finally, the output file names (may want to change all, eventhough only his, avg and rst will be used)

! Output NetCDF file names, [1:Ngrids].
!
    GSTNAME == Fjord_ocean_gst.nc
    RSTNAME == Fjord_ocean_rst.nc
    HISNAME == Fjord_ocean_his.nc
    TLMNAME == Fjord_ocean_tlm.nc
    TLFNAME == Fjord_ocean_tlf.nc
    ADJNAME == Fjord_ocean_adj.nc
    AVGNAME == Fjord_ocean_avg.nc
    DIANAME == Fjord_ocean_dia.nc
    STANAME == Fjord_ocean_sta.nc
    FLTNAME == Fjord_ocean_flt.nc

Running ROMS

Similar to the "Getting Started" tutorial...

To run ROMS in serial, just type:

oceanS < ROMS/External/ocean_fjord.in > & log &

or to run in parallel (distributed-memory) on four processors:

mpirun -np 4 oceanM ROMS/External/ocean_fjord.in > & log &