--- manual/s_getstarted/text/getting_started.tex	2004/04/09 15:06:18	1.24
+++ manual/s_getstarted/text/getting_started.tex	2004/10/14 14:54:24	1.28
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.24 2004/04/09 15:06:18 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.28 2004/10/14 14:54:24 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
@@ -324,7 +324,7 @@
 
 \end{itemize}
 
-\section{Example experiments}
+\section[MITgcm Example Experiments]{Example experiments}
 \label{sect:modelExamples}
 
 %% a set of twenty-four pre-configured numerical experiments
@@ -484,7 +484,7 @@
 Once you have chosen the example you want to run, you are ready to
 compile the code.
 
-\section{Building the code}
+\section[Building MITgcm]{Building the code}
 \label{sect:buildingCode}
 
 To compile the code, we use the {\em make} program. This uses a file
@@ -561,380 +561,7 @@
 output.txt}.
 
 
-\subsection{Building/compiling the code elsewhere}
-
-In the example above (section \ref{sect:buildingCode}) we built the
-executable in the {\em input} directory of the experiment for
-convenience. You can also configure and compile the code in other
-locations, for example on a scratch disk with out having to copy the
-entire source tree. The only requirement to do so is you have {\tt
-  genmake2} in your path or you know the absolute path to {\tt
-  genmake2}.
-
-The following sections outline some possible methods of organizing
-your source and data.
-
-\subsubsection{Building from the {\em ../code directory}}
-
-This is just as simple as building in the {\em input/} directory:
-\begin{verbatim}
-% cd verification/exp2/code
-% ../../../tools/genmake2
-% make depend
-% make
-\end{verbatim}
-However, to run the model the executable ({\em mitgcmuv}) and input
-files must be in the same place. If you only have one calculation to make:
-\begin{verbatim}
-% cd ../input
-% cp ../code/mitgcmuv ./
-% ./mitgcmuv > output.txt
-\end{verbatim}
-or if you will be making multiple runs with the same executable:
-\begin{verbatim}
-% cd ../
-% cp -r input run1
-% cp code/mitgcmuv run1
-% cd run1
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-\subsubsection{Building from a new directory}
-
-Since the {\em input} directory contains input files it is often more
-useful to keep {\em input} pristine and build in a new directory
-within {\em verification/exp2/}:
-\begin{verbatim}
-% cd verification/exp2
-% mkdir build
-% cd build
-% ../../../tools/genmake2 -mods=../code
-% make depend
-% make
-\end{verbatim}
-This builds the code exactly as before but this time you need to copy
-either the executable or the input files or both in order to run the
-model. For example,
-\begin{verbatim}
-% cp ../input/* ./
-% ./mitgcmuv > output.txt
-\end{verbatim}
-or if you tend to make multiple runs with the same executable then
-running in a new directory each time might be more appropriate:
-\begin{verbatim}
-% cd ../
-% mkdir run1
-% cp build/mitgcmuv run1/
-% cp input/* run1/
-% cd run1
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-\subsubsection{Building on a scratch disk}
-
-Model object files and output data can use up large amounts of disk
-space so it is often the case that you will be operating on a large
-scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
-following commands will build the model in {\em /scratch/exp2-run1}:
-\begin{verbatim}
-% cd /scratch/exp2-run1
-% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
-  -mods=~/MITgcm/verification/exp2/code
-% make depend
-% make
-\end{verbatim}
-To run the model here, you'll need the input files:
-\begin{verbatim}
-% cp ~/MITgcm/verification/exp2/input/* ./
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-As before, you could build in one directory and make multiple runs of
-the one experiment:
-\begin{verbatim}
-% cd /scratch/exp2
-% mkdir build
-% cd build
-% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
-  -mods=~/MITgcm/verification/exp2/code
-% make depend
-% make
-% cd ../
-% cp -r ~/MITgcm/verification/exp2/input run2
-% cd run2
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-
-\subsection{Using \texttt{genmake2}}
-\label{sect:genmake}
-
-To compile the code, first use the program \texttt{genmake2} (located
-in the \texttt{tools} directory) to generate a Makefile.
-\texttt{genmake2} is a shell script written to work with all
-``sh''--compatible shells including bash v1, bash v2, and Bourne.
-Internally, \texttt{genmake2} determines the locations of needed
-files, the compiler, compiler options, libraries, and Unix tools.  It
-relies upon a number of ``optfiles'' located in the
-\texttt{tools/build\_options} directory.
-
-The purpose of the optfiles is to provide all the compilation options
-for particular ``platforms'' (where ``platform'' roughly means the
-combination of the hardware and the compiler) and code configurations.
-Given the combinations of possible compilers and library dependencies
-({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
-for a single machine.  The naming scheme for the majority of the
-optfiles shipped with the code is
-\begin{center}
-  {\bf OS\_HARDWARE\_COMPILER }
-\end{center}
-where
-\begin{description}
-\item[OS] is the name of the operating system (generally the
-  lower-case output of the {\tt 'uname'} command)
-\item[HARDWARE] is a string that describes the CPU type and
-  corresponds to output from the  {\tt 'uname -m'} command:
-  \begin{description}
-  \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
-    and athlon
-  \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
-  \item[amd64] is AMD x86\_64 systems
-  \item[ppc] is for Mac PowerPC systems
-  \end{description}
-\item[COMPILER] is the compiler name (generally, the name of the
-  FORTRAN executable)
-\end{description}
-
-In many cases, the default optfiles are sufficient and will result in
-usable Makefiles.  However, for some machines or code configurations,
-new ``optfiles'' must be written. To create a new optfile, it is
-generally best to start with one of the defaults and modify it to suit
-your needs.  Like \texttt{genmake2}, the optfiles are all written
-using a simple ``sh''--compatible syntax.  While nearly all variables
-used within \texttt{genmake2} may be specified in the optfiles, the
-critical ones that should be defined are:
-
-\begin{description}
-\item[FC] the FORTRAN compiler (executable) to use
-\item[DEFINES] the command-line DEFINE options passed to the compiler
-\item[CPP] the C pre-processor to use
-\item[NOOPTFLAGS] options flags for special files that should not be
-  optimized
-\end{description}
-
-For example, the optfile for a typical Red Hat Linux machine (``ia32''
-architecture) using the GCC (g77) compiler is
-\begin{verbatim}
-FC=g77
-DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
-CPP='cpp  -traditional -P'
-NOOPTFLAGS='-O0'
-#  For IEEE, use the "-ffloat-store" option
-if test "x$IEEE" = x ; then
-    FFLAGS='-Wimplicit -Wunused -Wuninitialized'
-    FOPTIM='-O3 -malign-double -funroll-loops'
-else
-    FFLAGS='-Wimplicit -Wunused -ffloat-store'
-    FOPTIM='-O0 -malign-double'
-fi
-\end{verbatim}
-
-If you write an optfile for an unrepresented machine or compiler, you
-are strongly encouraged to submit the optfile to the MITgcm project
-for inclusion.  Please send the file to the
-\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
-\begin{center}
-  MITgcm-support@mitgcm.org
-\end{center}
-\begin{rawhtml} </A> \end{rawhtml}
-mailing list.
-
-In addition to the optfiles, \texttt{genmake2} supports a number of
-helpful command-line options.  A complete list of these options can be
-obtained from:
-\begin{verbatim}
-% genmake2 -h
-\end{verbatim}
-
-The most important command-line options are:
-\begin{description}
-  
-\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
-  should be used for a particular build.
-  
-  If no "optfile" is specified (either through the command line or the
-  MITGCM\_OPTFILE environment variable), genmake2 will try to make a
-  reasonable guess from the list provided in {\em
-    tools/build\_options}.  The method used for making this guess is
-  to first determine the combination of operating system and hardware
-  (eg. "linux\_ia32") and then find a working FORTRAN compiler within
-  the user's path.  When these three items have been identified,
-  genmake2 will try to find an optfile that has a matching name.
-  
-\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-  set of packages to be used.  The normal order of precedence for
-  packages is as follows:
-  \begin{enumerate}
-  \item If available, the command line (\texttt{--pdefault}) settings
-    over-rule any others.
-
-  \item Next, \texttt{genmake2} will look for a file named
-    ``\texttt{packages.conf}'' in the local directory or in any of the
-    directories specified with the \texttt{--mods} option.
-    
-  \item Finally, if neither of the above are available,
-    \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
-  \end{enumerate}
-  
-\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
-  used for packages.
-  
-  If not specified, the default dependency file {\em pkg/pkg\_depend}
-  is used.  The syntax for this file is parsed on a line-by-line basis
-  where each line containes either a comment ("\#") or a simple
-  "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
-  specifies a "must be used with" or a "must not be used with"
-  relationship, respectively.  If no rule is specified, then it is
-  assumed that the two packages are compatible and will function
-  either with or without each other.
-  
-\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
-  automatic differentiation options file to be used.  The file is
-  analogous to the ``optfile'' defined above but it specifies
-  information for the AD build process.
-  
-  The default file is located in {\em
-    tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
-  and "TAMC" compilers.  An alternate version is also available at
-  {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
-  "STAF" compiler.  As with any compilers, it is helpful to have their
-  directories listed in your {\tt \$PATH} environment variable.
-  
-\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
-  directories containing ``modifications''.  These directories contain
-  files with names that may (or may not) exist in the main MITgcm
-  source tree but will be overridden by any identically-named sources
-  within the ``MODS'' directories.
-  
-  The order of precedence for this "name-hiding" is as follows:
-  \begin{itemize}
-  \item ``MODS'' directories (in the order given)
-  \item Packages either explicitly specified or provided by default
-    (in the order given)
-  \item Packages included due to package dependencies (in the order
-    that that package dependencies are parsed)
-  \item The "standard dirs" (which may have been specified by the
-    ``-standarddirs'' option)
-  \end{itemize}
-  
-\item[\texttt{--mpi}] This option enables certain MPI features (using
-  CPP \texttt{\#define}s) within the code and is necessary for MPI
-  builds (see Section \ref{sect:mpi-build}).
-  
-\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
-  soft-links and other bugs common with the \texttt{make} versions
-  provided by commercial Unix vendors, GNU \texttt{make} (sometimes
-  called \texttt{gmake}) should be preferred.  This option provides a
-  means for specifying the make executable to be used.
-  
-\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
-  machines, the ``bash'' shell is unavailable.  To run on these
-  systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
-  a Bourne, POSIX, or compatible) shell.  The syntax in these
-  circumstances is:
-  \begin{center}
-    \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
-  \end{center}
-  where \texttt{/bin/sh} can be replaced with the full path and name
-  of the desired shell.
-
-\end{description}
-
-
-\subsection{Building with MPI}
-\label{sect:mpi-build}
-
-Building MITgcm to use MPI libraries can be complicated due to the
-variety of different MPI implementations available, their dependencies
-or interactions with different compilers, and their often ad-hoc
-locations within file systems.  For these reasons, its generally a
-good idea to start by finding and reading the documentation for your
-machine(s) and, if necessary, seeking help from your local systems
-administrator.
-
-The steps for building MITgcm with MPI support are:
-\begin{enumerate}
-  
-\item Determine the locations of your MPI-enabled compiler and/or MPI
-  libraries and put them into an options file as described in Section
-  \ref{sect:genmake}.  One can start with one of the examples in:
-  \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
-  \end{rawhtml}
-  \begin{center}
-    \texttt{MITgcm/tools/build\_options/}
-  \end{center}
-  \begin{rawhtml} </A> \end{rawhtml}
-  such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
-  \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
-  hand.  You may need help from your user guide or local systems
-  administrator to determine the exact location of the MPI libraries.
-  If libraries are not installed, MPI implementations and related
-  tools are available including:
-  \begin{itemize}
-  \item \begin{rawhtml} <A
-      href="http://www-unix.mcs.anl.gov/mpi/mpich/">
-    \end{rawhtml}
-    MPICH
-    \begin{rawhtml} </A> \end{rawhtml}
-
-  \item \begin{rawhtml} <A
-      href="http://www.lam-mpi.org/">
-    \end{rawhtml}
-    LAM/MPI
-    \begin{rawhtml} </A> \end{rawhtml}
-
-  \item \begin{rawhtml} <A
-      href="http://www.osc.edu/~pw/mpiexec/">
-    \end{rawhtml}
-    MPIexec
-    \begin{rawhtml} </A> \end{rawhtml}
-  \end{itemize}
-  
-\item Build the code with the \texttt{genmake2} \texttt{-mpi} option
-  (see Section \ref{sect:genmake}) using commands such as:
-{\footnotesize \begin{verbatim}
-  %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
-  %  make depend
-  %  make
-\end{verbatim} }
-  
-\item Run the code with the appropriate MPI ``run'' or ``exec''
-  program provided with your particular implementation of MPI.
-  Typical MPI packages such as MPICH will use something like:
-\begin{verbatim}
-  %  mpirun -np 4 -machinefile mf ./mitgcmuv
-\end{verbatim}
-  Sightly more complicated scripts may be needed for many machines
-  since execution of the code may be controlled by both the MPI
-  library and a job scheduling and queueing system such as PBS,
-  LoadLeveller, Condor, or any of a number of similar tools.  A few
-  example scripts (those used for our \begin{rawhtml} <A
-    href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
-  verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
-  at:
-  \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
-  \end{rawhtml}
-  {\footnotesize \tt
-    http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
-  \begin{rawhtml} </A> \end{rawhtml}
-
-\end{enumerate}
-
-
-
-\section{Running the model}
+\section[Running MITgcm]{Running the model in prognostic mode}
 \label{sect:runModel}
 
 If compilation finished succesfuully (section \ref{sect:buildingCode})
@@ -1043,422 +670,3 @@
 >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
 \end{verbatim}
 
-\section{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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