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--- manual/s_getstarted/text/getting_started.tex 2004/10/13 05:06:25 1.26
+++ manual/s_getstarted/text/getting_started.tex 2004/10/14 14:24:28 1.27
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.26 2004/10/13 05:06:25 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.27 2004/10/14 14:24:28 cnh Exp $
% $Name: $
%\section{Getting started}
@@ -79,7 +79,7 @@
\end{enumerate}
-\subsubsection{Checkout from CVS}
+\subsection{Method 1 - Checkout from CVS}
\label{sect:cvs_checkout}
If CVS is available on your system, we strongly encourage you to use it. CVS
@@ -169,7 +169,7 @@
\end{verbatim}
-\subsubsection{Conventional download method}
+\subsection{Method 2 - Tar file download}
\label{sect:conventionalDownload}
If you do not have CVS on your system, you can download the model as a
@@ -1059,422 +1059,3 @@
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
\end{verbatim}
-\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}
-
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:
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