| 79 |  |  | 
| 80 | \end{enumerate} | \end{enumerate} | 
| 81 |  |  | 
| 82 | \subsubsection{Checkout from CVS} | \subsection{Method 1 - Checkout from CVS} | 
| 83 | \label{sect:cvs_checkout} | \label{sect:cvs_checkout} | 
| 84 |  |  | 
| 85 | If CVS is available on your system, we strongly encourage you to use it. CVS | If CVS is available on your system, we strongly encourage you to use it. CVS | 
| 169 | \end{verbatim} | \end{verbatim} | 
| 170 |  |  | 
| 171 |  |  | 
| 172 | \subsubsection{Conventional download method} | \subsection{Method 2 - Tar file download} | 
| 173 | \label{sect:conventionalDownload} | \label{sect:conventionalDownload} | 
| 174 |  |  | 
| 175 | If you do not have CVS on your system, you can download the model as a | If you do not have CVS on your system, you can download the model as a | 
| 1059 | >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end | >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end | 
| 1060 | \end{verbatim} | \end{verbatim} | 
| 1061 |  |  | 
|  | \section[Customizing MITgcm]{Doing it yourself: customizing the code} |  | 
|  |  |  | 
|  | 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. |  | 
|  |  |  | 
|  | \subsection{Configuration and setup} |  | 
|  |  |  | 
|  | The CPP keys relative to the ``numerical model'' part of the code are |  | 
|  | all defined and set in the file \textit{CPP\_OPTIONS.h }in the |  | 
|  | directory \textit{ model/inc }or in one of the \textit{code |  | 
|  | }directories of the case study experiments under |  | 
|  | \textit{verification.} The model parameters are defined and declared |  | 
|  | in the file \textit{model/inc/PARAMS.h }and their default values are |  | 
|  | set in the routine \textit{model/src/set\_defaults.F. }The default |  | 
|  | values can be modified in the namelist file \textit{data }which needs |  | 
|  | to be located in the directory where you will run the model. The |  | 
|  | parameters are initialized in the routine |  | 
|  | \textit{model/src/ini\_parms.F}.  Look at this routine to see in what |  | 
|  | part of the namelist the parameters are located. |  | 
|  |  |  | 
|  | In what follows the parameters are grouped into categories related to |  | 
|  | the computational domain, the equations solved in the model, and the |  | 
|  | simulation controls. |  | 
|  |  |  | 
|  | \subsection{Computational domain, geometry and time-discretization} |  | 
|  |  |  | 
|  | \begin{description} |  | 
|  | \item[dimensions] \ |  | 
|  |  |  | 
|  | The number of points in the x, y, and r directions are represented |  | 
|  | by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |  | 
|  | respectively which are declared and set in the file |  | 
|  | \textit{model/inc/SIZE.h}.  (Again, this assumes a mono-processor |  | 
|  | calculation. For multiprocessor calculations see the section on |  | 
|  | parallel implementation.) |  | 
|  |  |  | 
|  | \item[grid] \ |  | 
|  |  |  | 
|  | Three different grids are available: cartesian, spherical polar, and |  | 
|  | curvilinear (which includes the cubed sphere). The grid is set |  | 
|  | through the logical variables \textbf{usingCartesianGrid}, |  | 
|  | \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |  | 
|  | In the case of spherical and curvilinear grids, the southern |  | 
|  | boundary is defined through the variable \textbf{phiMin} which |  | 
|  | corresponds to the latitude of the southern most cell face (in |  | 
|  | degrees). The resolution along the x and y directions is controlled |  | 
|  | by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the |  | 
|  | case of a cartesian grid, in degrees otherwise).  The vertical grid |  | 
|  | spacing is set through the 1D array \textbf{delz} for the ocean (in |  | 
|  | meters) or \textbf{delp} for the atmosphere (in Pa).  The variable |  | 
|  | \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level |  | 
|  | in ``R'' coordinate. This is typically set to 0m for the ocean |  | 
|  | (default value) and 10$^{5}$Pa for the atmosphere. For the |  | 
|  | atmosphere, also set the logical variable \textbf{groundAtK1} to |  | 
|  | \texttt{'.TRUE.'} which puts the first level (k=1) at the lower |  | 
|  | boundary (ground). |  | 
|  |  |  | 
|  | For the cartesian grid case, the Coriolis parameter $f$ is set |  | 
|  | through the variables \textbf{f0} and \textbf{beta} which correspond |  | 
|  | to the reference Coriolis parameter (in s$^{-1}$) and |  | 
|  | $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. |  | 
|  | If \textbf{beta } is set to a nonzero value, \textbf{f0} is the |  | 
|  | value of $f$ at the southern edge of the domain. |  | 
|  |  |  | 
|  | \item[topography - full and partial cells] \ |  | 
|  |  |  | 
|  | The domain bathymetry is read from a file that contains a 2D (x,y) |  | 
|  | map of depths (in m) for the ocean or pressures (in Pa) for the |  | 
|  | atmosphere. The file name is represented by the variable |  | 
|  | \textbf{bathyFile}. The file is assumed to contain binary numbers |  | 
|  | giving the depth (pressure) 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 model code |  | 
|  | applies without modification to enclosed, periodic, and double |  | 
|  | periodic domains. Periodicity is assumed by default and is |  | 
|  | suppressed by setting the depths to 0m for the cells at the limits |  | 
|  | of the computational domain (note: not sure this is the case for the |  | 
|  | atmosphere). The precision with which to read the binary data is |  | 
|  | controlled by the integer variable \textbf{readBinaryPrec} which can |  | 
|  | take the value \texttt{32} (single precision) or \texttt{64} (double |  | 
|  | precision). See the matlab program \textit{gendata.m} in the |  | 
|  | \textit{input} directories under \textit{verification} to see how |  | 
|  | the bathymetry files are generated for the case study experiments. |  | 
|  |  |  | 
|  | To use the partial cell capability, the variable \textbf{hFacMin} |  | 
|  | needs to be set to a value between 0 and 1 (it is set to 1 by |  | 
|  | default) corresponding to the minimum fractional size of the cell. |  | 
|  | For example if the bottom cell is 500m thick and \textbf{hFacMin} is |  | 
|  | set to 0.1, the actual thickness of the cell (i.e. used in the code) |  | 
|  | can cover a range of discrete values 50m apart from 50m to 500m |  | 
|  | depending on the value of the bottom depth (in \textbf{bathyFile}) |  | 
|  | at this point. |  | 
|  |  |  | 
|  | Note that the bottom depths (or pressures) need not coincide with |  | 
|  | the models levels as deduced from \textbf{delz} or \textbf{delp}. |  | 
|  | The model will interpolate the numbers in \textbf{bathyFile} so that |  | 
|  | they match the levels obtained from \textbf{delz} or \textbf{delp} |  | 
|  | and \textbf{hFacMin}. |  | 
|  |  |  | 
|  | (Note: the atmospheric case is a bit more complicated than what is |  | 
|  | written here I think. To come soon...) |  | 
|  |  |  | 
|  | \item[time-discretization] \ |  | 
|  |  |  | 
|  | The time steps are set through the real variables \textbf{deltaTMom} |  | 
|  | and \textbf{deltaTtracer} (in s) which represent the time step for |  | 
|  | the momentum and tracer equations, respectively. For synchronous |  | 
|  | integrations, simply set the two variables to the same value (or you |  | 
|  | can prescribe one time step only through the variable |  | 
|  | \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |  | 
|  | through the variable \textbf{abEps} (dimensionless). The stagger |  | 
|  | baroclinic time stepping can be activated by setting the logical |  | 
|  | variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. |  | 
|  |  |  | 
|  | \end{description} |  | 
|  |  |  | 
|  |  |  | 
|  | \subsection{Equation of state} |  | 
|  |  |  | 
|  | First, because the model equations are written in terms of |  | 
|  | perturbations, a reference thermodynamic state needs to be specified. |  | 
|  | This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}. |  | 
|  | \textbf{tRef} specifies the reference potential temperature profile |  | 
|  | (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting |  | 
|  | from the level k=1. Similarly, \textbf{sRef} specifies the reference |  | 
|  | salinity profile (in ppt) for the ocean or the reference specific |  | 
|  | humidity profile (in g/kg) for the atmosphere. |  | 
|  |  |  | 
|  | The form of the equation of state is controlled by the character |  | 
|  | variables \textbf{buoyancyRelation} and \textbf{eosType}. |  | 
|  | \textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and |  | 
|  | needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. |  | 
|  | In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. |  | 
|  | For the ocean, two forms of the equation of state are available: |  | 
|  | linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial |  | 
|  | approximation to the full nonlinear equation ( set \textbf{eosType} to |  | 
|  | \texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |  | 
|  | thermal and haline expansion coefficients represented by the variables |  | 
|  | \textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For |  | 
|  | the nonlinear case, you need to generate a file of polynomial |  | 
|  | coefficients called \textit{POLY3.COEFFS}. To do this, use the program |  | 
|  | \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |  | 
|  | available in the same directory and you will need to edit the number |  | 
|  | and the values of the vertical levels in \textit{knudsen2.f} so that |  | 
|  | they match those of your configuration). |  | 
|  |  |  | 
|  | There there are also higher polynomials for the equation of state: |  | 
|  | \begin{description} |  | 
|  | \item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of |  | 
|  | Fofonoff and Millard \cite{fofonoff83}. This equation of state |  | 
|  | assumes in-situ temperature, which is not a model variable; {\em its |  | 
|  | use is therefore discouraged, and it is only listed for |  | 
|  | completeness}. |  | 
|  | \item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and |  | 
|  | McDougall \cite{jackett95}, which uses the model variable potential |  | 
|  | temperature as input. The \texttt{'Z'} indicates that this equation |  | 
|  | of state uses a horizontally and temporally constant pressure |  | 
|  | $p_{0}=-g\rho_{0}z$. |  | 
|  | \item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and |  | 
|  | McDougall \cite{jackett95}, which uses the model variable potential |  | 
|  | temperature as input. The \texttt{'P'} indicates that this equation |  | 
|  | of state uses the actual hydrostatic pressure of the last time |  | 
|  | step. Lagging the pressure in this way requires an additional pickup |  | 
|  | file for restarts. |  | 
|  | \item[\texttt{'MDJWF'}:] The new, more accurate and less expensive |  | 
|  | equation of state by McDougall et~al. \cite{mcdougall03}. It also |  | 
|  | requires lagging the pressure and therefore an additional pickup |  | 
|  | file for restarts. |  | 
|  | \end{description} |  | 
|  | For none of these options an reference profile of temperature or |  | 
|  | salinity is required. |  | 
|  |  |  | 
|  | \subsection{Momentum equations} |  | 
|  |  |  | 
|  | In this section, we only focus for now on the parameters that you are |  | 
|  | likely to change, i.e. the ones relative to forcing and dissipation |  | 
|  | for example.  The details relevant to the vector-invariant form of the |  | 
|  | equations and the various advection schemes are not covered for the |  | 
|  | moment. We assume that you use the standard form of the momentum |  | 
|  | equations (i.e. the flux-form) with the default advection scheme. |  | 
|  | Also, there are a few logical variables that allow you to turn on/off |  | 
|  | various terms in the momentum equation. These variables are called |  | 
|  | \textbf{momViscosity, momAdvection, momForcing, useCoriolis, |  | 
|  | momPressureForcing, momStepping} and \textbf{metricTerms }and are |  | 
|  | assumed to be set to \texttt{'.TRUE.'} here.  Look at the file |  | 
|  | \textit{model/inc/PARAMS.h }for a precise definition of these |  | 
|  | variables. |  | 
|  |  |  | 
|  | \begin{description} |  | 
|  | \item[initialization] \ |  | 
|  |  |  | 
|  | The velocity components are initialized to 0 unless the simulation |  | 
|  | is starting from a pickup file (see section on simulation control |  | 
|  | parameters). |  | 
|  |  |  | 
|  | \item[forcing] \ |  | 
|  |  |  | 
|  | This section only applies to the ocean. You need to generate |  | 
|  | wind-stress data into two files \textbf{zonalWindFile} and |  | 
|  | \textbf{meridWindFile} corresponding to the zonal and meridional |  | 
|  | components of the wind stress, respectively (if you want the stress |  | 
|  | to be along the direction of only one of the model horizontal axes, |  | 
|  | you only need to generate one file). The format of the files is |  | 
|  | similar to the bathymetry file. The zonal (meridional) stress data |  | 
|  | are assumed to be in Pa and located at U-points (V-points). As for |  | 
|  | the bathymetry, the precision with which to read the binary data is |  | 
|  | controlled by the variable \textbf{readBinaryPrec}.  See the matlab |  | 
|  | program \textit{gendata.m} in the \textit{input} directories under |  | 
|  | \textit{verification} to see how simple analytical wind forcing data |  | 
|  | are generated for the case study experiments. |  | 
|  |  |  | 
|  | There is also the possibility of prescribing time-dependent periodic |  | 
|  | forcing. To do this, concatenate the successive time records into a |  | 
|  | single file (for each stress component) ordered in a (x,y,t) fashion |  | 
|  | and set the following variables: \textbf{periodicExternalForcing }to |  | 
|  | \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) |  | 
|  | of which the forcing varies (typically 1 month), and |  | 
|  | \textbf{externForcingCycle} to the repeat time (in s) of the forcing |  | 
|  | (typically 1 year -- note: \textbf{ externForcingCycle} must be a |  | 
|  | multiple of \textbf{externForcingPeriod}).  With these variables set |  | 
|  | up, the model will interpolate the forcing linearly at each |  | 
|  | iteration. |  | 
|  |  |  | 
|  | \item[dissipation] \ |  | 
|  |  |  | 
|  | The lateral eddy viscosity coefficient is specified through the |  | 
|  | variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy |  | 
|  | viscosity coefficient is specified through the variable |  | 
|  | \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and |  | 
|  | \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The |  | 
|  | vertical diffusive fluxes can be computed implicitly by setting the |  | 
|  | logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. |  | 
|  | In addition, biharmonic mixing can be added as well through the |  | 
|  | variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar |  | 
|  | grid, you might also need to set the variable \textbf{cosPower} |  | 
|  | which is set to 0 by default and which represents the power of |  | 
|  | cosine of latitude to multiply viscosity. Slip or no-slip conditions |  | 
|  | at lateral and bottom boundaries are specified through the logical |  | 
|  | variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If |  | 
|  | set to \texttt{'.FALSE.'}, free-slip boundary conditions are |  | 
|  | applied. If no-slip boundary conditions are applied at the bottom, a |  | 
|  | bottom drag can be applied as well. Two forms are available: linear |  | 
|  | (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and |  | 
|  | quadratic (set the variable \textbf{bottomDragQuadratic} in |  | 
|  | m$^{-1}$). |  | 
|  |  |  | 
|  | The Fourier and Shapiro filters are described elsewhere. |  | 
|  |  |  | 
|  | \item[C-D scheme] \ |  | 
|  |  |  | 
|  | If you run at a sufficiently coarse resolution, you will need the |  | 
|  | C-D scheme for the computation of the Coriolis terms. The |  | 
|  | variable\textbf{\ tauCD}, which represents the C-D scheme coupling |  | 
|  | timescale (in s) needs to be set. |  | 
|  |  |  | 
|  | \item[calculation of pressure/geopotential] \ |  | 
|  |  |  | 
|  | First, to run a non-hydrostatic ocean simulation, set the logical |  | 
|  | variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure |  | 
|  | field is then inverted through a 3D elliptic equation. (Note: this |  | 
|  | capability is not available for the atmosphere yet.) By default, a |  | 
|  | hydrostatic simulation is assumed and a 2D elliptic equation is used |  | 
|  | to invert the pressure field. The parameters controlling the |  | 
|  | behaviour of the elliptic solvers are the variables |  | 
|  | \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for |  | 
|  | the 2D case and \textbf{cg3dMaxIters} and |  | 
|  | \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to |  | 
|  | alter the default values (are we sure of this?). |  | 
|  |  |  | 
|  | For the calculation of the surface pressure (for the ocean) or |  | 
|  | surface geopotential (for the atmosphere) you need to set the |  | 
|  | logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} |  | 
|  | (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} |  | 
|  | depending on how you want to deal with the ocean upper or atmosphere |  | 
|  | lower boundary). |  | 
|  |  |  | 
|  | \end{description} |  | 
|  |  |  | 
|  | \subsection{Tracer equations} |  | 
|  |  |  | 
|  | This section covers the tracer equations i.e. the potential |  | 
|  | temperature equation and the salinity (for the ocean) or specific |  | 
|  | humidity (for the atmosphere) equation. As for the momentum equations, |  | 
|  | we only describe for now the parameters that you are likely to change. |  | 
|  | The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} |  | 
|  | \textbf{tempForcing}, and \textbf{tempStepping} allow you to turn |  | 
|  | on/off terms in the temperature equation (same thing for salinity or |  | 
|  | specific humidity with variables \textbf{saltDiffusion}, |  | 
|  | \textbf{saltAdvection} etc.). These variables are all assumed here to |  | 
|  | be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} |  | 
|  | for a precise definition. |  | 
|  |  |  | 
|  | \begin{description} |  | 
|  | \item[initialization] \ |  | 
|  |  |  | 
|  | The initial tracer data can be contained in the binary files |  | 
|  | \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files |  | 
|  | should contain 3D data ordered in an (x,y,r) fashion with k=1 as the |  | 
|  | first vertical level.  If no file names are provided, the tracers |  | 
|  | are then initialized with the values of \textbf{tRef} and |  | 
|  | \textbf{sRef} mentioned above (in the equation of state section). In |  | 
|  | this case, the initial tracer data are uniform in x and y for each |  | 
|  | depth level. |  | 
|  |  |  | 
|  | \item[forcing] \ |  | 
|  |  |  | 
|  | This part is more relevant for the ocean, the procedure for the |  | 
|  | atmosphere not being completely stabilized at the moment. |  | 
|  |  |  | 
|  | A combination of fluxes data and relaxation terms can be used for |  | 
|  | driving the tracer equations.  For potential temperature, heat flux |  | 
|  | data (in W/m$ ^{2}$) can be stored in the 2D binary file |  | 
|  | \textbf{surfQfile}.  Alternatively or in addition, the forcing can |  | 
|  | be specified through a relaxation term. The SST data to which the |  | 
|  | model surface temperatures are restored to are supposed to be stored |  | 
|  | in the 2D binary file \textbf{thetaClimFile}. The corresponding |  | 
|  | relaxation time scale coefficient is set through the variable |  | 
|  | \textbf{tauThetaClimRelax} (in s). The same procedure applies for |  | 
|  | salinity with the variable names \textbf{EmPmRfile}, |  | 
|  | \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |  | 
|  | flux (in m/s) and surface salinity (in ppt) data files and |  | 
|  | relaxation time scale coefficient (in s), respectively. Also for |  | 
|  | salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |  | 
|  | natural boundary conditions are applied i.e. when computing the |  | 
|  | surface salinity tendency, the freshwater flux is multiplied by the |  | 
|  | model surface salinity instead of a constant salinity value. |  | 
|  |  |  | 
|  | As for the other input files, the precision with which to read the |  | 
|  | data is controlled by the variable \textbf{readBinaryPrec}. |  | 
|  | Time-dependent, periodic forcing can be applied as well following |  | 
|  | the same procedure used for the wind forcing data (see above). |  | 
|  |  |  | 
|  | \item[dissipation] \ |  | 
|  |  |  | 
|  | Lateral eddy diffusivities for temperature and salinity/specific |  | 
|  | humidity are specified through the variables \textbf{diffKhT} and |  | 
|  | \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are |  | 
|  | specified through the variables \textbf{diffKzT} and |  | 
|  | \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT |  | 
|  | }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The |  | 
|  | vertical diffusive fluxes can be computed implicitly by setting the |  | 
|  | logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. |  | 
|  | In addition, biharmonic diffusivities can be specified as well |  | 
|  | through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in |  | 
|  | m$^{4}$/s). Note that the cosine power scaling (specified through |  | 
|  | \textbf{cosPower}---see the momentum equations section) is applied to |  | 
|  | the tracer diffusivities (Laplacian and biharmonic) as well. The |  | 
|  | Gent and McWilliams parameterization for oceanic tracers is |  | 
|  | described in the package section. Finally, note that tracers can be |  | 
|  | also subject to Fourier and Shapiro filtering (see the corresponding |  | 
|  | section on these filters). |  | 
|  |  |  | 
|  | \item[ocean convection] \ |  | 
|  |  |  | 
|  | Two options are available to parameterize ocean convection: one is |  | 
|  | to use the convective adjustment scheme. In this case, you need to |  | 
|  | set the variable \textbf{cadjFreq}, which represents the frequency |  | 
|  | (in s) with which the adjustment algorithm is called, to a non-zero |  | 
|  | value (if set to a negative value by the user, the model will set it |  | 
|  | to the tracer time step). The other option is to parameterize |  | 
|  | convection with implicit vertical diffusion. To do this, set the |  | 
|  | logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |  | 
|  | and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |  | 
|  | you wish the tracer vertical diffusivities to have when mixing |  | 
|  | tracers vertically due to static instabilities. Note that |  | 
|  | \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |  | 
|  | value. |  | 
|  |  |  | 
|  | \end{description} |  | 
|  |  |  | 
|  | \subsection{Simulation controls} |  | 
|  |  |  | 
|  | The model ''clock'' is defined by the variable \textbf{deltaTClock} |  | 
|  | (in s) which determines the IO frequencies and is used in tagging |  | 
|  | output.  Typically, you will set it to the tracer time step for |  | 
|  | accelerated runs (otherwise it is simply set to the default time step |  | 
|  | \textbf{deltaT}).  Frequency of checkpointing and dumping of the model |  | 
|  | state are referenced to this clock (see below). |  | 
|  |  |  | 
|  | \begin{description} |  | 
|  | \item[run duration] \ |  | 
|  |  |  | 
|  | The beginning of a simulation is set by specifying a start time (in |  | 
|  | s) through the real variable \textbf{startTime} or by specifying an |  | 
|  | initial iteration number through the integer variable |  | 
|  | \textbf{nIter0}. If these variables are set to nonzero values, the |  | 
|  | model will look for a ''pickup'' file \textit{pickup.0000nIter0} to |  | 
|  | restart the integration. The end of a simulation is set through the |  | 
|  | real variable \textbf{endTime} (in s).  Alternatively, you can |  | 
|  | specify instead the number of time steps to execute through the |  | 
|  | integer variable \textbf{nTimeSteps}. |  | 
|  |  |  | 
|  | \item[frequency of output] \ |  | 
|  |  |  | 
|  | Real variables defining frequencies (in s) with which output files |  | 
|  | are written on disk need to be set up. \textbf{dumpFreq} controls |  | 
|  | the frequency with which the instantaneous state of the model is |  | 
|  | saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output |  | 
|  | frequency of rolling and permanent checkpoint files, respectively. |  | 
|  | See section 1.5.1 Output files for the definition of model state and |  | 
|  | checkpoint files. In addition, time-averaged fields can be written |  | 
|  | out by setting the variable \textbf{taveFreq} (in s).  The precision |  | 
|  | with which to write the binary data is controlled by the integer |  | 
|  | variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or |  | 
|  | \texttt{64}). |  | 
|  |  |  | 
|  | \end{description} |  | 
|  |  |  | 
|  |  |  | 
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