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Next: 3.12 Held-Suarez Atmosphere MITgcm Up: 3.11 P coordinate Global Previous: 3.11.2 Discrete Numerical Configuration   Contents

Subsections


3.11.3 Experiment Configuration

The model configuration for this experiment resides under the directory tutorial_examples/global_ocean_circulation/. The experiment files

  • input/data
  • input/data.pkg
  • input/eedata,
  • input/topog.bin,
  • input/deltageopotjmd95.bin,
  • input/lev_s.bin,
  • input/lev_t.bin,
  • input/trenberth_taux.bin,
  • input/trenberth_tauy.bin,
  • input/lev_sst.bin,
  • input/shi_qnet.bin,
  • input/shi_empmr.bin,
  • code/CPP_EEOPTIONS.h
  • code/CPP_OPTIONS.h,
  • code/SIZE.h.
contain the code customizations and parameter settings for these experiments. Below we describe the customizations to these files associated with this experiment.


3.11.3.1 Driving Datasets

Figures (3.3-3.8) show the relaxation temperature ( $ \theta^{\ast}$) and salinity ($ S^{\ast}$) fields, the wind stress components ($ \tau_x$ and $ \tau_y$), the heat flux ($ Q$) and the net fresh water flux ( $ {\cal E} - {\cal P} - {\cal R}$) used in equations 3.50-3.53. The figures also indicate the lateral extent and coastline used in the experiment. Figure (3.9) shows the depth contours of the model domain.

Figure 3.3: Annual mean of relaxation temperature [$ ^{\circ }$C]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/sst}
Figure 3.4: Annual mean of relaxation salinity [PSU]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/sss}
Figure: Annual mean of zonal wind stress component [Nmm$ ^{-2}$]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/tx}
Figure: Annual mean of meridional wind stress component [Nmm$ ^{-2}$]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/ty}
Figure: Annual mean heat flux [Wm$ ^{-2}$]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/qnet}
Figure: Annual mean fresh water flux (Evaporation-Precipitation) [ms$ ^{-1}$]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/emp}
Figure 3.9: Model bathymetry in pressure units [Pa]
\includegraphics[width=.9\textwidth]{part3/case_studies/ogcm_in_pressure/pb0}


3.11.3.2 File input/data

This file, reproduced completely below, specifies the main parameters for the experiment. The parameters that are significant for this configuration are

  • Line 15, 
     viscAr=1.721611620915750E+05,
    this line sets the vertical Laplacian dissipation coefficient to $ 1.72161162091575 \times 10^{5} {\rm Pa^{2}s^{-1}}$. Note that, the factor $ (g\rho)^2$ needs to be included in this line. Boundary conditions for this operator are specified later. This variable is copied into model general vertical coordinate variable viscAr.

    \fbox{ \begin{minipage}{5.0in} {\it S/R CALC\_DIFFUSIVITY}({\it calc\_diffusivity.F}) \end{minipage}}

  • Line 9-10, 
    viscAh=3.E5,
no_slip_sides=.TRUE.
    these lines set the horizontal Laplacian frictional dissipation coefficient to $ 3 \times 10^{5} {\rm m^{2}s^{-1}}$ and specify a no-slip boundary condition for this operator, that is, $ u=0$ along boundaries in $ y$ and $ v=0$ along boundaries in $ x$.

  • Lines 11-13, 
     viscAr =1.721611620915750e5,
#viscAz =1.67E-3,
 no_slip_bottom=.FALSE.,
    These lines set the vertical Laplacian frictional dissipation coefficient to $ 1.721611620915750 \times 10^{5}$ Pa$ ^{2}$s$ ^{-1}$, which corresponds to $ 1.67\times10^{-3}$ m$ ^{2}$s$ ^{-1}$ in the commented line, and specify a free slip boundary condition for this operator, that is, $ \frac{\partial u}{\partial p}=\frac{\partial v}{\partial p}=0$ at $ p=p_{b}^{0}$, where $ p_{b}^{0}$ is the local bottom pressure of the domain at rest. Note that, the factor $ (g\rho)^2$ needs to be included in this line.

  • Line 14, 
     diffKhT=1.E3,
    this line sets the horizontal diffusion coefficient for temperature to $ 1000\,{\rm m^{2}s^{-1}}$. The boundary condition on this operator is $ \frac{\partial}{\partial x}=\frac{\partial}{\partial y}=0$ on all boundaries.

  • Line 15-16, 
     diffKrT=5.154525811125000e3,
#diffKzT=0.5E-4,
    this line sets the vertical diffusion coefficient for temperature to $ 5.154525811125 \times 10^{3}\,{\rm Pa^{2}s^{-1}}$, which corresponds to $ 5\times10^{-4}$ m$ ^{2}$s$ ^{-1}$ in the commented line. Note that, the factor $ (g\rho)^2$ needs to be included in this line. The boundary condition on this operator is $ \frac{\partial}{\partial p}=0$ at both the upper and lower boundaries.

  • Line 17-19, 
     diffKhS=1.E3,
 diffKrS=5.154525811125000e3,
#diffKzS=0.5E-4,
    These lines set the same values for the diffusion coefficients for salinity as for temperature.

  • Line 20-22, 
     implicitDiffusion=.TRUE.,
 ivdc_kappa=1.030905162225000E9,
#ivdc_kappa=10.0,
    Select implicit diffusion as a convection scheme and set coefficient for implicit vertical diffusion to $ 1.030905162225\times10^{9}\,{\rm Pa^{2}s^{-1}}$, which corresponds to $ 10$ m$ ^{2}$ s$ ^{-1}$.

  • Line 23-24, 
     gravity=9.81,
 gravitySign=-1.D0,
    These lines set the gravitational acceleration coefficient to $ 9.81{\rm m}{\rm s}^{-1}$ and define the upward direction relative to the direction of increasing vertical coordinate (in pressure coordinates, up is in the direction of decreasing pressure)
  • Line 25, 
     rhoNil=1035.,
    sets the reference density of sea water to $ 1035$ kg m$ ^{-3}$.
    \fbox{ \begin{minipage}{5.0in} {\it S/R CALC\_PHI\_HYD}~({\it calc\_phi\_hyd.F})... ...\ {\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F}) \end{minipage}}

  • Line 28 
     eosType='JMD95P',
    Selects the full equation of state according to Jackett and McDougall [33]. The only other sensible choice is the equation of state by McDougall et al. [41], 'MDJFW'. All other equations of state do not make sense in this configuration.
    \fbox{ \begin{minipage}{5.0in} {\it S/R FIND\_RHO}~({\it find\_rho.F})\\ {\it S/R FIND\_ALPHA}~({\it find\_alpha.F}) \end{minipage}}

  • Line 28-29, 
     rigidLid=.FALSE., 
 implicitFreeSurface=.TRUE.,
    Selects the barotropic pressure equation to be the implicit free surface formulation.
  • Line 30 
     exactConserv=.TRUE.,
    Select a more accurate conservation of properties at the surface layer by including the horizontal velocity divergence to update the free surface.
  • Line 31-33 
     nonlinFreeSurf=3,
 hFacInf=0.2,
 hFacSup=2.0,
    Select the nonlinear free surface formulation and set lower and upper limits for the free surface excursions.
  • Line 34 
     useRealFreshWaterFlux=.FALSE.,
    Select virtual salt flux boundary condition for salinity. The freshwater flux at the surface only affect the surface salinity, but has no mass flux associated with it

  • Line 35-36, 
     readBinaryPrec=64,
 writeBinaryPrec=64,
    Sets format for reading binary input datasets and writing binary output datasets holding model fields to use 64-bit representation for floating-point numbers.
    \fbox{ \begin{minipage}{5.0in} {\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\ {\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F}) \end{minipage}}

  • Line 42, 
     cg2dMaxIters=200,
    Sets maximum number of iterations the two-dimensional, conjugate gradient solver will use, irrespective of convergence criteria being met.
    \fbox{ \begin{minipage}{5.0in} {\it S/R CG2D}~({\it cg2d.F}) \end{minipage}}

  • Line 43, 
    cg2dTargetResidual=1.E-13,
    Sets the tolerance which the two-dimensional, conjugate gradient solver will use to test for convergence in equation [*] to $ 1 \times 10^{-9}$. Solver will iterate until tolerance falls below this value or until the maximum number of solver iterations is reached.
    \fbox{ \begin{minipage}{5.0in} {\it S/R CG2D}~({\it cg2d.F}) \end{minipage}}

  • Line 48, 
    startTime=0,
    Sets the starting time for the model internal time counter. When set to non-zero this option implicitly requests a checkpoint file be read for initial state. By default the checkpoint file is named according to the integer number of time steps in the startTime value. The internal time counter works in seconds.

  • Line 49-50, 
     endTime=8640000.,
#endTime=62208000000,
    Sets the time (in seconds) at which this simulation will terminate. At the end of a simulation a checkpoint file is automatically written so that a numerical experiment can consist of multiple stages. The commented out setting for endTime is for a 2000 year simulation.

  • Line 51-53, 
     deltaTmom      =   1200.0,
 deltaTtracer   = 172800.0,
 deltaTfreesurf = 172800.0,
    Sets the timestep $ \delta t_{v}$ used in the momentum equations to $ 20~{\rm mins}$ and the timesteps $ \delta t_{\theta}$ in the tracer equations and $ \delta t_{\eta}$ in the implicit free surface equation to $ 48$ hours. See section [*].
    \fbox{ \begin{minipage}{5.0in} {\it S/R TIMESTEP}({\it timestep.F}) \\ {\it S/R... ...rhs.F}) \\ {\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F}) \end{minipage}}

  • Line 55, 
     pChkptFreq  =3110400000.,
    write a pick-up file every 100 years of integration.

  • Line 56-58 
     dumpFreq    = 3110400000.,
 taveFreq    = 3110400000.,
 monitorFreq =   31104000.,
    write model output and time-averaged model output every 100 years, and monitor statisitics every year.

  • Line 59-61 
     periodicExternalForcing=.TRUE.,
 externForcingPeriod=2592000.,
 externForcingCycle=31104000.,
    Allow periodic external forcing, set forcing period, during which one set of data is valid, to 1 month and the repeat cycle to 1 year.
    \fbox{ \begin{minipage}{5.0in} {\it S/R EXTERNAL\_FORCING\_SURF}({\it external\_forcing\_surf.F}) \end{minipage}}
  • Line 62 
     tauThetaClimRelax=5184000.0,
    Set the restoring timescale to 2 months.
    \fbox{ \begin{minipage}{5.0in} {\it S/R EXTERNAL\_FORCING\_SURF}({\it external\_forcing\_surf.F}) \end{minipage}}

  • Line 63 
     abEps=0.1,
    Adams-Bashford factor (see section 2.4)

  • Line 68-69 
     usingCartesianGrid=.FALSE.,
 usingSphericalPolarGrid=.TRUE.,
    Select spherical grid.
  • Line 70-71 
     dXspacing=4.,
 dYspacing=4.,
    Set the horizontal grid spacing in degrees spherical distance.
  • Line 72 
     Ro_SeaLevel=53023122.566084,
    specifies the total height (in $ r$-units, i.e., pressure units) of the sea surface at rest. This is a reference value.
  • Line 73 
     groundAtK1=.TRUE.,
    specifies the reversal of the vertical indexing. The vertical index is 1 at the bottom of the doman and maximal (i.e., 15) at the surface.
  • Line 74-78 
     delR=7103300.720021, \ldots
    set the layer thickness in pressure units, starting with the bottom layer.

  • Line 84-93, 
     bathyFile='topog.box'
 ploadFile='deltageopotjmd95.bin'
 hydrogThetaFile='lev_t.bin',
 hydrogSaltFile ='lev_s.bin',
 zonalWindFile  ='trenberth_taux.bin',
 meridWindFile  ='trenberth_tauy.bin',
 thetaClimFile  ='lev_sst.bin',
 surfQFile      ='shi_qnet.bin',
 EmPmRFile      ='shi_empmr.bin',
    This line specifies the names of the files holding the bathymetry data set, the time-independent geopotential height anomaly at the bottom, initial conditions of temperature and salinity, wind stress forcing fields, sea surface temperature climatology, heat flux, and fresh water flux (evaporation minus precipitation minus run-off) at the surface. See file descriptions in section 3.11.3.

other lines in the file input/data are standard values that are described in the MITgcm Getting Started and MITgcm Parameters notes.

# ==================== # | Model parameters | # ==================== # # Continuous equation parameters &PARM01 tRef=15*20., sRef=15*35., viscAh =3.E5, no_slip_sides=.TRUE., viscAr =1.721611620915750e5, #viscAz =1.67E-3, no_slip_bottom=.FALSE., diffKhT=1.E3, diffKrT=5.154525811125000e3, #diffKzT=0.5E-4, diffKhS=1.E3, diffKrS=5.154525811125000e3, #diffKzS=0.5E-4, implicitDiffusion=.TRUE., ivdc_kappa=1.030905162225000e9, #ivdc_kappa=10.0, gravity=9.81, gravitySign=-1.D0, rhonil=1035., buoyancyRelation='OCEANICP', eosType='JMD95P', rigidLid=.FALSE., implicitFreeSurface=.TRUE., exactConserv=.TRUE., nonlinFreeSurf=3, hFacInf=0.2, hFacSup=2.0, useRealFreshWaterFlux=.FALSE., readBinaryPrec=64, writeBinaryPrec=64, cosPower=0.5, &

# Elliptic solver parameters &PARM02 cg2dMaxIters=200, cg2dTargetResidual=1.E-9, &

# Time stepping parameters &PARM03 startTime = 0., endTime = 8640000., #endTime = 62208000000., deltaTmom = 1200.0, deltaTtracer = 172800.0, deltaTfreesurf = 172800.0, deltaTClock = 172800.0, pChkptFreq = 3110400000., dumpFreq = 3110400000., taveFreq = 3110400000., monitorFreq = 31104000., periodicExternalForcing=.TRUE., externForcingPeriod=2592000., externForcingCycle=31104000., tauThetaClimRelax=5184000.0, abEps=0.1, &

# Gridding parameters &PARM04 usingCartesianGrid=.FALSE., usingSphericalPolarGrid=.TRUE., dXspacing=4., dYspacing=4., Ro_SeaLevel=53023122.566084, groundAtK1=.TRUE., delR=7103300.720021, 6570548.440790, 6041670.010249, 5516436.666057, 4994602.034410, 4475903.435290, 3960063.245801, 3446790.312651, 2935781.405664, 2426722.705046, 1919291.315988, 1413156.804970, 1008846.750166, 705919.025481, 504089.693499, phiMin=-80., &

# Input datasets &PARM05 topoFile ='topog.bin', pLoadFile ='deltageopotjmd95.bin', hydrogThetaFile='lev_t.bin', hydrogSaltFile ='lev_s.bin', zonalWindFile ='trenberth_taux.bin', meridWindFile ='trenberth_tauy.bin', thetaClimFile ='lev_sst.bin', #saltClimFile ='lev_sss.bin', surfQFile ='shi_qnet.bin', EmPmRFile ='shi_empmr.bin', &


3.11.3.3 File input/data.pkg

This file uses standard default values and does not contain customisations for this experiment.


3.11.3.4 File input/eedata

This file uses standard default values and does not contain customisations for this experiment.


3.11.3.5 File input/topog.bin

This file is a two-dimensional ($ x,y$) map of depths. This file is assumed to contain 64-bit binary numbers giving the depth of the model at each grid cell, ordered with the x coordinate varying fastest. The points are ordered from low coordinate to high coordinate for both axes. The units and orientation of the depths in this file are the same as used in the MITgcm code (Pa for this experiment). In this experiment, a depth of 0 Pa indicates a land point wall and a depth of $ > 0 $ Pa indicates open ocean.


3.11.3.6 File input/deltageopotjmd95.box

The file contains 12 identical two dimensional maps ($ x,y$) of geopotential height anomaly at the bottom at rest. The values have been obtained by vertically integrating the hydrostatic equation with the initial density field (from input/lev_t/s.bin). This file has to be consitent with the temperature and salinity field at rest and the choice of equation of state!


3.11.3.7 File input/lev_t/s.bin

The files input/lev_t/s.bin specify the initial conditions for temperature and salinity for every grid point in a three dimensional array ($ x,y,z$). The data are obtain by interpolating Levitus [36] monthly mean values for January onto the model grid. Keep in mind, that the first index corresponds to the bottom layer and highest index to the surface layer.


3.11.3.8 File input/trenberth_taux/y.bin

Each of the input/trenberth_taux/y.bin files specifies 12 two-dimensional ($ x,y,t$) maps of zonal and meridional wind stress values, $ \tau_{x}$ and $ \tau_{y}$, that is monthly mean values from Trenberth [50]. The units used are $ Nm^{-2}$.


3.11.3.9 File input/lev_sst.bin

The file input/lev_sst.bin contains 12 monthly surface temperature climatologies from Levitus [36] in a three dimensional array ($ x,y,t$).


3.11.3.10 File input/shi_qnet/empmr.bin

The files input/shi_qnet/empmr.bin contain 12 monthly surface fluxes of heat (qnet) and freshwater (empmr) by Jiang et al. [34] in three dimensional arrays ($ x,y,t$). Both fluxes are normalized so that of one year there is no net flux into the ocean. The freshwater flux is actually constant in time.


3.11.3.11 File code/SIZE.h

Three lines are customized in this file for the current experiment

  • Line 39, 
     sNx=90,
    this line sets the lateral domain extent in grid points for the axis aligned with the x-coordinate.

  • Line 40, 
     sNy=40,
    this line sets the lateral domain extent in grid points for the axis aligned with the y-coordinate.

  • Line 49, 
     Nr=15,
    this line sets the vertical domain extent in grid points. 

C $Header: /u/gcmpack/manual/part3/case_studies/ogcm_in_pressure/code/SIZE.h,v 1.1 2002/12/17 14:39:53 mlosch Exp $
C $Name:  $
C
C     /==========================================================\
C     | SIZE.h Declare size of underlying computational grid.    |
C     |==========================================================|
C     | The design here support a three-dimensional model grid   |
C     | with indices I,J and K. The three-dimensional domain     |
C     | is comprised of nPx*nSx blocks of size sNx along one axis|
C     | nPy*nSy blocks of size sNy along another axis and one    |
C     | block of size Nz along the final axis.                   |
C     | Blocks have overlap regions of size OLx and OLy along the|
C     | dimensions that are subdivided.                          |
C     \==========================================================/
C     Voodoo numbers controlling data layout.
C     sNx - No. X points in sub-grid.
C     sNy - No. Y points in sub-grid.
C     OLx - Overlap extent in X.
C     OLy - Overlat extent in Y.
C     nSx - No. sub-grids in X.
C     nSy - No. sub-grids in Y.
C     nPx - No. of processes to use in X.
C     nPy - No. of processes to use in Y.
C     Nx  - No. points in X for the total domain.
C     Ny  - No. points in Y for the total domain.
C     Nr  - No. points in Z for full process domain.
      INTEGER sNx
      INTEGER sNy
      INTEGER OLx
      INTEGER OLy
      INTEGER nSx
      INTEGER nSy
      INTEGER nPx
      INTEGER nPy
      INTEGER Nx
      INTEGER Ny
      INTEGER Nr
      PARAMETER (
     &           sNx =  90,
     &           sNy =  40,
     &           OLx =   3,
     &           OLy =   3,
     &           nSx =   1,
     &           nSy =   1,
     &           nPx =   1,
     &           nPy =   1,
     &           Nx  = sNx*nSx*nPx,
     &           Ny  = sNy*nSy*nPy,
     &           Nr  =  15)

C     MAX_OLX  - Set to the maximum overlap region size of any array
C     MAX_OLY    that will be exchanged. Controls the sizing of exch
C                routine buufers.
      INTEGER MAX_OLX
      INTEGER MAX_OLY
      PARAMETER ( MAX_OLX = OLx,
     &            MAX_OLY = OLy )


3.11.3.12 File code/CPP_OPTIONS.h

This file uses mostly standard default values except for:

  • #define ATMOSPHERIC_LOADING
    enable pressure loading which is abused to include the initial geopotential height anomaly
  • #define EXACT_CONSERV
    enable more accurate conservation properties to include the horizontal mass divergence in the free surface
  • #define NONLIN_FRSURF
    enable the nonlinear free surface


3.11.3.13 File code/CPP_EEOPTIONS.h

This file uses standard default values and does not contain customisations for this experiment.

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Next: 3.12 Held-Suarez Atmosphere MITgcm Up: 3.11 P coordinate Global Previous: 3.11.2 Discrete Numerical Configuration   Contents
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