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3.6 Doing it yourself: customizing the model configuration

When you are ready to run the model in the configuration you want, the easiest thing is to use and adapt the setup of the case studies experiment (described previously) that is the closest to your configuration. Then, the amount of setup will be minimized. In this section, we focus on the setup relative to the ``numerical model'' part of the code (the setup relative to the ``execution environment'' part is covered in the parallel implementation section) and on the variables and parameters that you are likely to change.

The CPP keys relative to the ``numerical model'' part of the code are all defined and set in the file CPP_OPTIONS.h in the directory model/inc or in one of the code directories of the case study experiments under verification. The model parameters are defined and declared in the file model/inc/PARAMS.h and their default values are set in the routine model/src/set_defaults.F. The default values can be modified in the namelist file data which needs to be located in the directory where you will run the model. The parameters are initialized in the routine model/src/ini_parms.F. Look at this routine to see in what part of the namelist the parameters are located. Here is a complete list of the model parameters related to the main model (namelist parameters for the packages are located in the package descriptions), their meaning, and their default values:


Name value Description Reference
       
buoyancyRelation   buoyancyRelation = OCEANIC
fluidIsAir F fluid major constituent is Air
fluidIsWater T fuild major constituent is Water
usingPCoords F use p (or p
usingZCoords T use z (or z
tRef 2.0E+01 at K= top Reference temperature profile ( oC or K )
sRef 3.0E+01 at K= top Reference salinity profile ( psu )
viscAh 0.0E+00 Lateral eddy viscosity ( $ m^2/s$ )
viscAhMax 1.0E+21 Maximum lateral eddy viscosity ( $ m^2/s$ )
viscAhGrid 0.0E+00 Grid dependent lateral eddy viscosity ( non-dim. )
useFullLeith F Use Full Form of Leith Viscosity on/off flag
useStrainTensionVisc F Use StrainTension Form of Viscous Operator on/off flag
useAreaViscLength F Use area for visc length instead of geom. mean
viscC2leith 0.0E+00 Leith harmonic visc. factor (on grad(vort),non-dim.)
viscC2leithD 0.0E+00 Leith harmonic viscosity factor (on grad(div),non-dim.)
viscC2smag 0.0E+00 Smagorinsky harmonic viscosity factor (non-dim.)
viscA4 0.0E+00 Lateral biharmonic viscosity ( $ m^4/s$ )
viscA4Max 1.0E+21 Maximum biharmonic viscosity ( $ m^2/s$ )
viscA4Grid 0.0E+00 Grid dependent biharmonic viscosity ( non-dim. )
viscC4leith 0.0E+00 Leith biharm viscosity factor (on grad(vort), non-dim.)
viscC4leithD 0.0E+00 Leith biharm viscosity factor (on grad(div), non-dim.)
viscC4Smag 0.0E+00 Smagorinsky biharm viscosity factor (non-dim)
no_slip_sides T Viscous BCs: No-slip sides
sideDragFactor 2.0E+00 side-drag scaling factor (non-dim)
viscAr 0.0E+00 Vertical eddy viscosity ( units of $ r^2/s$ )
no_slip_bottom T Viscous BCs: No-slip bottom
bottomDragLinear 0.0E+00 linear bottom-drag coefficient ( m/s )
bottomDragQuadratic 0.0E+00 quadratic bottom-drag coeff. ( 1 )
diffKhT 0.0E+00 Laplacian diffusion of heat laterally ( $ m^2/s$ )
diffK4T 0.0E+00 Bihaarmonic diffusion of heat laterally ( $ m^4/s$ )
diffKhS 0.0E+00 Laplacian diffusion of salt laterally ( $ m^2/s$ )
diffK4S 0.0E+00 Bihaarmonic diffusion of salt laterally ( $ m^4/s$ )
diffKrNrT 0.0E+00 at K= top vertical profile of vertical diffusion of Temp ( $ m^2/s$ )
diffKrNrS 0.0E+00 at K= top vertical profile of vertical diffusion of Salt ( $ m^2/s$ )
diffKrBL79surf 0.0E+00 Surface diffusion for Bryan and Lewis 1979 ( $ m^2/s$ )
diffKrBL79deep 0.0E+00 Deep diffusion for Bryan and Lewis 1979 ( $ m^2/s$ )
diffKrBL79scl 2.0E+02 Depth scale for Bryan and Lewis 1979 ( m )
diffKrBL79Ho -2.0E+03 Turning depth for Bryan and Lewis 1979 ( m )
eosType LINEAR Equation of State
tAlpha 2.0E-04 Linear EOS thermal expansion coefficient ( 1/oC )


Name value Description Reference
       
sBeta 7.4E-04 Linear EOS haline contraction coef ( 1/psu )
rhonil 9.998E+02 Reference density ( $ kg/m^3$ )
rhoConst 9.998E+02 Reference density ( $ kg/m^3$ )
rhoConstFresh 9.998E+02 Reference density ( $ kg/m^3$ )
gravity 9.81E+00 Gravitational acceleration ( $ m/s^2$ )
gBaro 9.81E+00 Barotropic gravity ( $ m/s^2$ )
rotationPeriod 8.6164E+04 Rotation Period ( s )
omega 7.292123516990375E-05 Angular velocity ( rad/s )
f0 1.0E-04 Reference coriolis parameter ( 1/s )
beta 9.999999999999999E-12 Beta ( 1/(m.s) )
freeSurfFac 1.0E+00 Implicit free surface factor
implicitFreeSurface T Implicit free surface on/off flag
rigidLid F Rigid lid on/off flag
implicSurfPress 1.0E+00 Surface Pressure implicit factor (0-1)
implicDiv2Dflow 1.0E+00 Barot. Flow Div. implicit factor (0-1)
exactConserv F Exact Volume Conservation on/off flag
uniformLin_PhiSurf T use uniform Bo_surf on/off flag
nonlinFreeSurf 0 Non-linear Free Surf. options (-1,0,1,2,3)
hFacInf 2.0E-01 lower threshold for hFac (nonlinFreeSurf only)
hFacSup 2.0E+00 upper threshold for hFac (nonlinFreeSurf only)
select_rStar 0 r
useRealFreshWaterFlux F Real Fresh Water Flux on/off flag
convertFW2Salt 3.5E+01 convert F.W. Flux to Salt Flux (-1=use local S)
use3Dsolver F use 3-D pressure solver on/off flag
nonHydrostatic F Non-Hydrostatic on/off flag
nh_Am2 1.0E+00 Non-Hydrostatic terms scaling factor
quasiHydrostatic F Quasi-Hydrostatic on/off flag
momStepping T Momentum equation on/off flag
vectorInvariantMomentum F Vector-Invariant Momentum on/off
momAdvection T Momentum advection on/off flag
momViscosity T Momentum viscosity on/off flag
momImplVertAdv F Momentum implicit vert. advection on/off
implicitViscosity F Implicit viscosity on/off flag
metricTerms F metric-Terms on/off flag
useNHMTerms F Non-Hydrostatic Metric-Terms on/off
useCoriolis T Coriolis on/off flag
useCDscheme F CD scheme on/off flag
useJamartWetPoints F Coriolis WetPoints method flag
useJamartMomAdv F V.I. Non-linear terms Jamart flag


Name value Description Reference
       
SadournyCoriolis F Sadourny Coriolis discr. flag
upwindVorticity F Upwind bias vorticity flag
useAbsVorticity F Work with f
highOrderVorticity F High order interp. of vort. flag
upwindShear F Upwind vertical Shear advection flag
selectKEscheme 0 Kinetic Energy scheme selector
momForcing T Momentum forcing on/off flag
momPressureForcing T Momentum pressure term on/off flag
implicitIntGravWave F Implicit Internal Gravity Wave flag
staggerTimeStep F Stagger time stepping on/off flag
multiDimAdvection T enable/disable Multi-Dim Advection
useMultiDimAdvec F Multi-Dim Advection is/is-not used
implicitDiffusion F Implicit Diffusion on/off flag
tempStepping T Temperature equation on/off flag
tempAdvection T Temperature advection on/off flag
tempImplVertAdv F Temp. implicit vert. advection on/off
tempForcing T Temperature forcing on/off flag
saltStepping T Salinity equation on/off flag
saltAdvection T Salinity advection on/off flag
saltImplVertAdv F Sali. implicit vert. advection on/off
saltForcing T Salinity forcing on/off flag
readBinaryPrec 32 Precision used for reading binary files
writeBinaryPrec 32 Precision used for writing binary files
globalFiles F write "global" (=not per tile) files
useSingleCpuIO F only master MPI process does I/O
debugMode F Debug Mode on/off flag
debLevA 1 1rst level of debugging
debLevB 2 2nd level of debugging
debugLevel 1 select debugging level
cg2dMaxIters 150 Upper limit on 2d con. grad iterations
cg2dChkResFreq 1 2d con. grad convergence test frequency
cg2dTargetResidual 1.0E-07 2d con. grad target residual
cg2dTargetResWunit -1.0E+00 CG2d target residual [W units]
cg2dPreCondFreq 1 Freq. for updating cg2d preconditioner
nIter0 0 Run starting timestep number
nTimeSteps 0 Number of timesteps
deltatTmom 6.0E+01 Momentum equation timestep ( s )
deltaTfreesurf 6.0E+01 FreeSurface equation timestep ( s )
dTtracerLev 6.0E+01 at K= top Tracer equation timestep ( s )
deltatTClock 6.0E+01 Model clock timestep ( s )


Name value Description Reference
       
cAdjFreq 0.0E+00 Convective adjustment interval ( s )
momForcingOutAB 0 =1: take Momentum Forcing out of Adams-Bash.
tracForcingOutAB 0 =1: take T,S,pTr Forcing out of Adams-Bash.
momDissip_In_AB T put Dissipation Tendency in Adams-Bash.
doAB_onGtGs T apply AB on Tendencies (rather than on T,S)
abEps 1.0E-02 Adams-Bashforth-2 stabilizing weight
baseTime 0.0E+00 Model base time ( s ).
startTime 0.0E+00 Run start time ( s ).
endTime 0.0E+00 Integration ending time ( s ).
pChkPtFreq 0.0E+00 Permanent restart/checkpoint file interval ( s ).
chkPtFreq 0.0E+00 Rolling restart/checkpoint file interval ( s ).
pickup_write_mdsio T Model IO flag.
pickup_read_mdsio T Model IO flag.
pickup_write_immed F Model IO flag.
dumpFreq 0.0E+00 Model state write out interval ( s ).
dumpInitAndLast T write out Initial and Last iter. model state
snapshot_mdsio T Model IO flag.
monitorFreq 6.0E+01 Monitor output interval ( s ).
monitor_stdio T Model IO flag.
externForcingPeriod 0.0E+00 forcing period (s)
externForcingCycle 0.0E+00 period of the cyle (s).
tauThetaClimRelax 0.0E+00 relaxation time scale (s)
tauSaltClimRelax 0.0E+00 relaxation time scale (s)
latBandClimRelax 3.703701E+05 max. Lat. where relaxation
usingCartesianGrid T Cartesian coordinates flag ( True / False )
usingSphericalPolarGrid F Spherical coordinates flag ( True / False )
usingCylindricalGrid F Spherical coordinates flag ( True / False )
Ro_SeaLevel 0.0E+00 r(1) ( units of r )
rkSign -1.0E+00 index orientation relative to vertical coordinate
horiVertRatio 1.0E+00 Ratio on units : Horiz - Vertical
drC 5.0E+03 at K=1 C spacing ( units of r )
drF 1.0E+04 at K= top W spacing ( units of r )
delX 1.234567E+05 at I= east U spacing ( m - cartesian, degrees - spherical )
delY 1.234567E+05 at J=1 V spacing ( m - cartesian, degrees - spherical )
ygOrigin 0.0E+00 South edge Y-axis origin (cartesian: m, spherical: deg.)

xgOrigin 0.0E+00 West edge X-axis origin (cartesian: m, spherical: deg.)
rSphere 6.37E+06 Radius ( ignored - cartesian, m - spherical )
xcoord 6.172835E+04 at I=1 P-point X coord ( m - cartesian, degrees - spherical )
ycoord 6.172835E+04 at J=1 P-point Y coord ( m - cartesian, degrees - spherical )
rcoord -5.0E+03 at K=1 P-point R coordinate ( units of r )
rF 0.0E+00 at K=1 W-Interf. R coordinate ( units of r )
dBdrRef 0.0E+00 at K= top Vertical gradient of reference boyancy [ $ (m/s/r)^2)$ ]


Name value Description Reference
       
dxF 1.234567E+05 at K= top dxF(:,1,:,1) ( m - cartesian, degrees - spherical )
dyF 1.234567E+05 at I= east dyF(:,1,:,1) ( m - cartesian, degrees - spherical )
dxG 1.234567E+05 at I= east dxG(:,1,:,1) ( m - cartesian, degrees - spherical )
dyG 1.234567E+05 at I= east dyG(:,1,:,1) ( m - cartesian, degrees - spherical )
dxC 1.234567E+05 at I= east dxC(:,1,:,1) ( m - cartesian, degrees - spherical )
dyC 1.234567E+05 at I= east dyC(:,1,:,1) ( m - cartesian, degrees - spherical )
dxV 1.234567E+05 at I= east dxV(:,1,:,1) ( m - cartesian, degrees - spherical )
dyU 1.234567E+05 at I= east dyU(:,1,:,1) ( m - cartesian, degrees - spherical )
rA 1.524155677489E+10 at I= east rA(:,1,:,1) ( m - cartesian, degrees - spherical )
rAw 1.524155677489E+10 at K= top rAw(:,1,:,1) ( m - cartesian, degrees - spherical )
rAs 1.524155677489E+10 at K= top rAs(:,1,:,1) ( m - cartesian, degrees - spherical )


Name Default value Description Reference
       
tempAdvScheme 2 Temp. Horiz.Advection scheme selector
tempVertAdvScheme 2 Temp. Vert. Advection scheme selector
tempMultiDimAdvec F use Muti-Dim Advec method for Temp
tempAdamsBashforth T use Adams-Bashforth time-stepping for Temp
saltAdvScheme 2 Salt. Horiz.advection scheme selector
saltVertAdvScheme 2 Salt. Vert. Advection scheme selector
saltMultiDimAdvec F use Muti-Dim Advec method for Salt
saltAdamsBashforth T use Adams-Bashforth time-stepping for Salt

In what follows the parameters are grouped into categories related to the computational domain, the equations solved in the model, and the simulation controls.


Subsections
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Next: 3.6.1 Parameters: Computational domain, Up: 3. Getting Started with Previous: 3.5.2 Looking at the   Contents
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