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\section[Customizing MITgcm]{Doing it yourself: customizing the code} |
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When you are ready to run the model in the configuration you want, the |
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easiest thing is to use and adapt the setup of the case studies |
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experiment (described previously) that is the closest to your |
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configuration. Then, the amount of setup will be minimized. In this |
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section, we focus on the setup relative to the ``numerical model'' |
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part of the code (the setup relative to the ``execution environment'' |
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part is covered in the parallel implementation section) and on the |
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variables and parameters that you are likely to change. |
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\subsection{Configuration and setup} |
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The CPP keys relative to the ``numerical model'' part of the code are |
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all defined and set in the file \textit{CPP\_OPTIONS.h }in the |
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directory \textit{ model/inc }or in one of the \textit{code |
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}directories of the case study experiments under |
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\textit{verification.} The model parameters are defined and declared |
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in the file \textit{model/inc/PARAMS.h }and their default values are |
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set in the routine \textit{model/src/set\_defaults.F. }The default |
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values can be modified in the namelist file \textit{data }which needs |
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to be located in the directory where you will run the model. The |
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parameters are initialized in the routine |
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\textit{model/src/ini\_parms.F}. Look at this routine to see in what |
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part of the namelist the parameters are located. |
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In what follows the parameters are grouped into categories related to |
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the computational domain, the equations solved in the model, and the |
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simulation controls. |
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\subsection{Computational domain, geometry and time-discretization} |
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\begin{description} |
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\item[dimensions] \ |
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The number of points in the x, y, and r directions are represented |
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by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |
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respectively which are declared and set in the file |
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\textit{model/inc/SIZE.h}. (Again, this assumes a mono-processor |
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calculation. For multiprocessor calculations see the section on |
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parallel implementation.) |
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\item[grid] \ |
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Three different grids are available: cartesian, spherical polar, and |
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curvilinear (which includes the cubed sphere). The grid is set |
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through the logical variables \textbf{usingCartesianGrid}, |
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\textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |
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In the case of spherical and curvilinear grids, the southern |
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boundary is defined through the variable \textbf{phiMin} which |
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corresponds to the latitude of the southern most cell face (in |
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degrees). The resolution along the x and y directions is controlled |
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by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the |
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case of a cartesian grid, in degrees otherwise). The vertical grid |
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spacing is set through the 1D array \textbf{delz} for the ocean (in |
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meters) or \textbf{delp} for the atmosphere (in Pa). The variable |
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\textbf{Ro\_SeaLevel} represents the standard position of Sea-Level |
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in ``R'' coordinate. This is typically set to 0m for the ocean |
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(default value) and 10$^{5}$Pa for the atmosphere. For the |
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atmosphere, also set the logical variable \textbf{groundAtK1} to |
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\texttt{'.TRUE.'} which puts the first level (k=1) at the lower |
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boundary (ground). |
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For the cartesian grid case, the Coriolis parameter $f$ is set |
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through the variables \textbf{f0} and \textbf{beta} which correspond |
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to the reference Coriolis parameter (in s$^{-1}$) and |
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$\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. |
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If \textbf{beta } is set to a nonzero value, \textbf{f0} is the |
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value of $f$ at the southern edge of the domain. |
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\item[topography - full and partial cells] \ |
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The domain bathymetry is read from a file that contains a 2D (x,y) |
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map of depths (in m) for the ocean or pressures (in Pa) for the |
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atmosphere. The file name is represented by the variable |
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\textbf{bathyFile}. The file is assumed to contain binary numbers |
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giving the depth (pressure) of the model at each grid cell, ordered |
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with the x coordinate varying fastest. The points are ordered from |
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low coordinate to high coordinate for both axes. The model code |
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applies without modification to enclosed, periodic, and double |
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periodic domains. Periodicity is assumed by default and is |
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suppressed by setting the depths to 0m for the cells at the limits |
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of the computational domain (note: not sure this is the case for the |
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atmosphere). The precision with which to read the binary data is |
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controlled by the integer variable \textbf{readBinaryPrec} which can |
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take the value \texttt{32} (single precision) or \texttt{64} (double |
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precision). See the matlab program \textit{gendata.m} in the |
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\textit{input} directories under \textit{verification} to see how |
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the bathymetry files are generated for the case study experiments. |
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To use the partial cell capability, the variable \textbf{hFacMin} |
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needs to be set to a value between 0 and 1 (it is set to 1 by |
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default) corresponding to the minimum fractional size of the cell. |
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For example if the bottom cell is 500m thick and \textbf{hFacMin} is |
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set to 0.1, the actual thickness of the cell (i.e. used in the code) |
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can cover a range of discrete values 50m apart from 50m to 500m |
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depending on the value of the bottom depth (in \textbf{bathyFile}) |
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at this point. |
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Note that the bottom depths (or pressures) need not coincide with |
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the models levels as deduced from \textbf{delz} or \textbf{delp}. |
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The model will interpolate the numbers in \textbf{bathyFile} so that |
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they match the levels obtained from \textbf{delz} or \textbf{delp} |
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and \textbf{hFacMin}. |
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(Note: the atmospheric case is a bit more complicated than what is |
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written here I think. To come soon...) |
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\item[time-discretization] \ |
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The time steps are set through the real variables \textbf{deltaTMom} |
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and \textbf{deltaTtracer} (in s) which represent the time step for |
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the momentum and tracer equations, respectively. For synchronous |
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integrations, simply set the two variables to the same value (or you |
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can prescribe one time step only through the variable |
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\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |
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through the variable \textbf{abEps} (dimensionless). The stagger |
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baroclinic time stepping can be activated by setting the logical |
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variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. |
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\end{description} |
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\subsection{Equation of state} |
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First, because the model equations are written in terms of |
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perturbations, a reference thermodynamic state needs to be specified. |
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This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}. |
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\textbf{tRef} specifies the reference potential temperature profile |
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(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting |
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from the level k=1. Similarly, \textbf{sRef} specifies the reference |
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salinity profile (in ppt) for the ocean or the reference specific |
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humidity profile (in g/kg) for the atmosphere. |
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The form of the equation of state is controlled by the character |
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variables \textbf{buoyancyRelation} and \textbf{eosType}. |
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\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and |
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needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. |
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In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. |
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For the ocean, two forms of the equation of state are available: |
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linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial |
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approximation to the full nonlinear equation ( set \textbf{eosType} to |
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\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |
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thermal and haline expansion coefficients represented by the variables |
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\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For |
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the nonlinear case, you need to generate a file of polynomial |
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coefficients called \textit{POLY3.COEFFS}. To do this, use the program |
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\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |
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available in the same directory and you will need to edit the number |
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and the values of the vertical levels in \textit{knudsen2.f} so that |
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they match those of your configuration). |
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There there are also higher polynomials for the equation of state: |
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\begin{description} |
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\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of |
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Fofonoff and Millard \cite{fofonoff83}. This equation of state |
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assumes in-situ temperature, which is not a model variable; {\em its |
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use is therefore discouraged, and it is only listed for |
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completeness}. |
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\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and |
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McDougall \cite{jackett95}, which uses the model variable potential |
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temperature as input. The \texttt{'Z'} indicates that this equation |
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of state uses a horizontally and temporally constant pressure |
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$p_{0}=-g\rho_{0}z$. |
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\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and |
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McDougall \cite{jackett95}, which uses the model variable potential |
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temperature as input. The \texttt{'P'} indicates that this equation |
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of state uses the actual hydrostatic pressure of the last time |
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step. Lagging the pressure in this way requires an additional pickup |
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file for restarts. |
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\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive |
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equation of state by McDougall et~al. \cite{mcdougall03}. It also |
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requires lagging the pressure and therefore an additional pickup |
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file for restarts. |
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\end{description} |
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For none of these options an reference profile of temperature or |
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salinity is required. |
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\subsection{Momentum equations} |
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In this section, we only focus for now on the parameters that you are |
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likely to change, i.e. the ones relative to forcing and dissipation |
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for example. The details relevant to the vector-invariant form of the |
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equations and the various advection schemes are not covered for the |
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moment. We assume that you use the standard form of the momentum |
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equations (i.e. the flux-form) with the default advection scheme. |
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Also, there are a few logical variables that allow you to turn on/off |
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various terms in the momentum equation. These variables are called |
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\textbf{momViscosity, momAdvection, momForcing, useCoriolis, |
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momPressureForcing, momStepping} and \textbf{metricTerms }and are |
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assumed to be set to \texttt{'.TRUE.'} here. Look at the file |
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\textit{model/inc/PARAMS.h }for a precise definition of these |
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variables. |
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\begin{description} |
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\item[initialization] \ |
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The velocity components are initialized to 0 unless the simulation |
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is starting from a pickup file (see section on simulation control |
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parameters). |
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\item[forcing] \ |
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This section only applies to the ocean. You need to generate |
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wind-stress data into two files \textbf{zonalWindFile} and |
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\textbf{meridWindFile} corresponding to the zonal and meridional |
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components of the wind stress, respectively (if you want the stress |
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to be along the direction of only one of the model horizontal axes, |
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you only need to generate one file). The format of the files is |
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similar to the bathymetry file. The zonal (meridional) stress data |
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are assumed to be in Pa and located at U-points (V-points). As for |
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the bathymetry, the precision with which to read the binary data is |
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controlled by the variable \textbf{readBinaryPrec}. See the matlab |
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program \textit{gendata.m} in the \textit{input} directories under |
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\textit{verification} to see how simple analytical wind forcing data |
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are generated for the case study experiments. |
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There is also the possibility of prescribing time-dependent periodic |
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forcing. To do this, concatenate the successive time records into a |
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single file (for each stress component) ordered in a (x,y,t) fashion |
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and set the following variables: \textbf{periodicExternalForcing }to |
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\texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) |
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of which the forcing varies (typically 1 month), and |
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\textbf{externForcingCycle} to the repeat time (in s) of the forcing |
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(typically 1 year -- note: \textbf{ externForcingCycle} must be a |
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multiple of \textbf{externForcingPeriod}). With these variables set |
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up, the model will interpolate the forcing linearly at each |
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iteration. |
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\item[dissipation] \ |
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The lateral eddy viscosity coefficient is specified through the |
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variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy |
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viscosity coefficient is specified through the variable |
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\textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and |
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\textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere. The |
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vertical diffusive fluxes can be computed implicitly by setting the |
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logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. |
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In addition, biharmonic mixing can be added as well through the |
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variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar |
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grid, you might also need to set the variable \textbf{cosPower} |
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which is set to 0 by default and which represents the power of |
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cosine of latitude to multiply viscosity. Slip or no-slip conditions |
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at lateral and bottom boundaries are specified through the logical |
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variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If |
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set to \texttt{'.FALSE.'}, free-slip boundary conditions are |
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applied. If no-slip boundary conditions are applied at the bottom, a |
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bottom drag can be applied as well. Two forms are available: linear |
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(set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and |
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quadratic (set the variable \textbf{bottomDragQuadratic} in |
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m$^{-1}$). |
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The Fourier and Shapiro filters are described elsewhere. |
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\item[C-D scheme] \ |
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If you run at a sufficiently coarse resolution, you will need the |
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C-D scheme for the computation of the Coriolis terms. The |
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variable\textbf{\ tauCD}, which represents the C-D scheme coupling |
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timescale (in s) needs to be set. |
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\item[calculation of pressure/geopotential] \ |
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First, to run a non-hydrostatic ocean simulation, set the logical |
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variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure |
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field is then inverted through a 3D elliptic equation. (Note: this |
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capability is not available for the atmosphere yet.) By default, a |
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hydrostatic simulation is assumed and a 2D elliptic equation is used |
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to invert the pressure field. The parameters controlling the |
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behaviour of the elliptic solvers are the variables |
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\textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for |
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the 2D case and \textbf{cg3dMaxIters} and |
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\textbf{cg3dTargetResidual} for the 3D case. You probably won't need to |
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alter the default values (are we sure of this?). |
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For the calculation of the surface pressure (for the ocean) or |
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surface geopotential (for the atmosphere) you need to set the |
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logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} |
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(set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} |
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depending on how you want to deal with the ocean upper or atmosphere |
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lower boundary). |
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\end{description} |
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\subsection{Tracer equations} |
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This section covers the tracer equations i.e. the potential |
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temperature equation and the salinity (for the ocean) or specific |
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humidity (for the atmosphere) equation. As for the momentum equations, |
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we only describe for now the parameters that you are likely to change. |
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The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} |
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\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn |
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on/off terms in the temperature equation (same thing for salinity or |
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specific humidity with variables \textbf{saltDiffusion}, |
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\textbf{saltAdvection} etc.). These variables are all assumed here to |
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be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} |
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for a precise definition. |
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\begin{description} |
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\item[initialization] \ |
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The initial tracer data can be contained in the binary files |
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\textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files |
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should contain 3D data ordered in an (x,y,r) fashion with k=1 as the |
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first vertical level. If no file names are provided, the tracers |
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are then initialized with the values of \textbf{tRef} and |
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\textbf{sRef} mentioned above (in the equation of state section). In |
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this case, the initial tracer data are uniform in x and y for each |
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depth level. |
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\item[forcing] \ |
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This part is more relevant for the ocean, the procedure for the |
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atmosphere not being completely stabilized at the moment. |
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A combination of fluxes data and relaxation terms can be used for |
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driving the tracer equations. For potential temperature, heat flux |
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data (in W/m$ ^{2}$) can be stored in the 2D binary file |
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\textbf{surfQfile}. Alternatively or in addition, the forcing can |
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be specified through a relaxation term. The SST data to which the |
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model surface temperatures are restored to are supposed to be stored |
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in the 2D binary file \textbf{thetaClimFile}. The corresponding |
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relaxation time scale coefficient is set through the variable |
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\textbf{tauThetaClimRelax} (in s). The same procedure applies for |
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salinity with the variable names \textbf{EmPmRfile}, |
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\textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |
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flux (in m/s) and surface salinity (in ppt) data files and |
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relaxation time scale coefficient (in s), respectively. Also for |
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salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |
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natural boundary conditions are applied i.e. when computing the |
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surface salinity tendency, the freshwater flux is multiplied by the |
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model surface salinity instead of a constant salinity value. |
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|
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As for the other input files, the precision with which to read the |
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data is controlled by the variable \textbf{readBinaryPrec}. |
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Time-dependent, periodic forcing can be applied as well following |
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the same procedure used for the wind forcing data (see above). |
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|
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\item[dissipation] \ |
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|
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Lateral eddy diffusivities for temperature and salinity/specific |
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humidity are specified through the variables \textbf{diffKhT} and |
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\textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are |
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specified through the variables \textbf{diffKzT} and |
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\textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT |
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}and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The |
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vertical diffusive fluxes can be computed implicitly by setting the |
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logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. |
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In addition, biharmonic diffusivities can be specified as well |
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through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in |
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m$^{4}$/s). Note that the cosine power scaling (specified through |
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\textbf{cosPower}---see the momentum equations section) is applied to |
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the tracer diffusivities (Laplacian and biharmonic) as well. The |
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Gent and McWilliams parameterization for oceanic tracers is |
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described in the package section. Finally, note that tracers can be |
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also subject to Fourier and Shapiro filtering (see the corresponding |
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section on these filters). |
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|
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\item[ocean convection] \ |
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|
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Two options are available to parameterize ocean convection: one is |
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to use the convective adjustment scheme. In this case, you need to |
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set the variable \textbf{cadjFreq}, which represents the frequency |
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(in s) with which the adjustment algorithm is called, to a non-zero |
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|
value (if set to a negative value by the user, the model will set it |
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|
to the tracer time step). The other option is to parameterize |
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|
convection with implicit vertical diffusion. To do this, set the |
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logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |
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and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |
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|
|
you wish the tracer vertical diffusivities to have when mixing |
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|
tracers vertically due to static instabilities. Note that |
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\textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |
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|
value. |
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|
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\end{description} |
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|
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\subsection{Simulation controls} |
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|
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The model ''clock'' is defined by the variable \textbf{deltaTClock} |
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|
(in s) which determines the IO frequencies and is used in tagging |
381 |
|
|
output. Typically, you will set it to the tracer time step for |
382 |
|
|
accelerated runs (otherwise it is simply set to the default time step |
383 |
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|
\textbf{deltaT}). Frequency of checkpointing and dumping of the model |
384 |
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|
state are referenced to this clock (see below). |
385 |
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|
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\begin{description} |
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\item[run duration] \ |
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|
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The beginning of a simulation is set by specifying a start time (in |
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|
|
s) through the real variable \textbf{startTime} or by specifying an |
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|
initial iteration number through the integer variable |
392 |
|
|
\textbf{nIter0}. If these variables are set to nonzero values, the |
393 |
|
|
model will look for a ''pickup'' file \textit{pickup.0000nIter0} to |
394 |
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|
restart the integration. The end of a simulation is set through the |
395 |
|
|
real variable \textbf{endTime} (in s). Alternatively, you can |
396 |
|
|
specify instead the number of time steps to execute through the |
397 |
|
|
integer variable \textbf{nTimeSteps}. |
398 |
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|
|
399 |
|
|
\item[frequency of output] \ |
400 |
|
|
|
401 |
|
|
Real variables defining frequencies (in s) with which output files |
402 |
|
|
are written on disk need to be set up. \textbf{dumpFreq} controls |
403 |
|
|
the frequency with which the instantaneous state of the model is |
404 |
|
|
saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output |
405 |
|
|
frequency of rolling and permanent checkpoint files, respectively. |
406 |
|
|
See section 1.5.1 Output files for the definition of model state and |
407 |
|
|
checkpoint files. In addition, time-averaged fields can be written |
408 |
|
|
out by setting the variable \textbf{taveFreq} (in s). The precision |
409 |
|
|
with which to write the binary data is controlled by the integer |
410 |
|
|
variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or |
411 |
|
|
\texttt{64}). |
412 |
|
|
|
413 |
|
|
\end{description} |
414 |
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|
415 |
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|
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%%% Local Variables: |
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