--- manual/s_getstarted/text/getting_started.tex	2001/08/08 16:15:31	1.1
+++ manual/s_getstarted/text/getting_started.tex	2004/10/14 14:54:24	1.28
@@ -1,405 +1,596 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.1 2001/08/08 16:15:31 adcroft 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}
 
-\begin{center}
-{\Large \textbf{Using the model}}
+In this section, we describe how to use the model. In the first
+section, we provide enough information to help you get started with
+the model. We believe the best way to familiarize yourself with the
+model is to run the case study examples provided with the base
+version. Information on how to obtain, compile, and run the code is
+found there as well as a brief description of the model structure
+directory and the case study examples.  The latter and the code
+structure are described more fully in chapters
+\ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
+this section, we provide information on how to customize the code when
+you are ready to try implementing the configuration you have in mind.
+
+\section{Where to find information}
+\label{sect:whereToFindInfo}
+
+A web site is maintained for release 2 (``Pelican'') of MITgcm:
+\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
+\begin{verbatim}
+http://mitgcm.org/pelican
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+Here you will find an on-line version of this document, a
+``browsable'' copy of the code and a searchable database of the model
+and site, as well as links for downloading the model and
+documentation, to data-sources, and other related sites.
+
+There is also a web-archived support mailing list for the model that
+you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
+\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
+\begin{verbatim}
+http://mitgcm.org/mailman/listinfo/mitgcm-support/
+http://mitgcm.org/pipermail/mitgcm-support/
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+Essentially all of the MITgcm web pages can be searched using a
+popular web crawler such as Google or through our own search facility:
+\begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
+\begin{verbatim}
+http://mitgcm.org/htdig/
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+%%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
+
+
+
+\section{Obtaining the code}
+\label{sect:obtainingCode}
+
+MITgcm can be downloaded from our system by following
+the instructions below. As a courtesy we ask that you send e-mail to us at
+\begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+to enable us to keep track of who's using the model and in what application.
+You can download the model two ways:
+
+\begin{enumerate}
+\item Using CVS software. CVS is a freely available source code management
+tool. To use CVS you need to have the software installed. Many systems
+come with CVS pre-installed, otherwise good places to look for
+the software for a particular platform are
+\begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
+cvshome.org
+\begin{rawhtml} </A> \end{rawhtml}
+and
+\begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
+wincvs.org
+\begin{rawhtml} </A> \end{rawhtml}
+.
+
+\item Using a tar file. This method is simple and does not
+require any special software. However, this method does not
+provide easy support for maintenance updates.
 
-\vspace*{4mm}
+\end{enumerate}
 
-\vspace*{3mm} {\large July 2001}
-\end{center}
+\subsection{Method 1 - Checkout from CVS}
+\label{sect:cvs_checkout}
 
-In this part, we describe how to use the model. In the first section, we
-provide enough information to help you get started with the model. We
-believe the best way to familiarize yourself with the model is to run the
-case study examples provided with the base version. Information on how to
-obtain, compile, and run the code is found there as well as a brief
-description of the model structure directory and the case study examples.
-The latter and the code structure are described more fully in sections 2 and
-3, respectively. In section 4, we provide information on how to customize
-the code when you are ready to try implementing the configuration you have
-in mind.
-
-\section{Getting started}
-
-\subsection{Obtaining the code}
+If CVS is available on your system, we strongly encourage you to use it. CVS
+provides an efficient and elegant way of organizing your code and keeping
+track of your changes. If CVS is not available on your machine, you can also
+download a tar file.
 
-The reference web site for the model is:
+Before you can use CVS, the following environment variable(s) should
+be set within your shell.  For a csh or tcsh shell, put the following 
 \begin{verbatim}
-http://mitgcm.org
+% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
 \end{verbatim}
-
-On this site, you can download the model as well as find useful information,
-some of which might overlap with what is written here. There is also a
-support news group for the model located at (send your message to \texttt{%
-support@mitgcm.org}):
+in your .cshrc or .tcshrc file.  For bash or sh shells, put:
 \begin{verbatim}
-news://mitgcm.org/mitgcm.support
+% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
 \end{verbatim}
+in your \texttt{.profile} or \texttt{.bashrc} file.
 
-If CVS is available on your system, we strongly encourage you to use it. CVS
-provides an efficient and elegant way of organizing your code and keeping
-track of your changes. If CVS is not available on your machine, you can also
-download a tar file.
-
-\subsubsection{using CVS}
 
-Before you can use CVS, the following environment variable has to be set in
-your .cshrc or .tcshrc:
+To get MITgcm through CVS, first register with the MITgcm CVS server
+using command:
 \begin{verbatim}
-% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
 % cvs login ( CVS password: cvsanon )
 \end{verbatim}
+You only need to do a ``cvs login'' once.
 
-You only need to do ``cvs login'' once. To obtain the latest source:
+To obtain the latest sources type:
 \begin{verbatim}
-% cvs co -d directory models/MITgcmUV
+% cvs co MITgcm
 \end{verbatim}
-
-This creates a directory called \textit{directory}. If \textit{directory}
-exists this command updates your code based on the repository. Each
-directory in the source tree contains a directory \textit{CVS}. This
-information is required by CVS to keep track of your file versions with
-respect to the repository. Don't edit the files in \textit{CVS}! To obtain a
-specific \textit{version} that is not the latest source:
+or to get a specific release type:
 \begin{verbatim}
-% cvs co -d directory -r version models/MITgcmUV
-\end{verbatim}
-
-\subsubsection{other methods}
-
-You can download the model as a tar file from the reference web site at:
+% cvs co -P -r checkpoint52i_post  MITgcm
+\end{verbatim}
+The MITgcm web site contains further directions concerning the source
+code and CVS.  It also contains a web interface to our CVS archive so
+that one may easily view the state of files, revisions, and other
+development milestones:
+\begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
+\begin{verbatim}
+http://mitgcm.org/source_code.html
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+
+As a convenience, the MITgcm CVS server contains aliases which are
+named subsets of the codebase.  These aliases can be especially
+helpful when used over slow internet connections or on machines with
+restricted storage space.  Table \ref{tab:cvsModules} contains a list
+of CVS aliases
+\begin{table}[htb]
+  \centering
+  \begin{tabular}[htb]{|lp{3.25in}|}\hline
+    \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
+    \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
+    \texttt{MITgcm\_verif\_basic}
+    &  Source code plus a small set of the verification examples 
+    (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, 
+    \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
+    \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
+    \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
+    \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
+    verification examples. \\\hline
+  \end{tabular}
+  \caption{MITgcm CVS Modules}
+  \label{tab:cvsModules}
+\end{table}
+
+The checkout process creates a directory called \textit{MITgcm}. If
+the directory \textit{MITgcm} exists this command updates your code
+based on the repository. Each directory in the source tree contains a
+directory \textit{CVS}. This information is required by CVS to keep
+track of your file versions with respect to the repository. Don't edit
+the files in \textit{CVS}!  You can also use CVS to download code
+updates.  More extensive information on using CVS for maintaining
+MITgcm code can be found
+\begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}
+here
+\begin{rawhtml} </A> \end{rawhtml} 
+.
+It is important to note that the CVS aliases in Table
+\ref{tab:cvsModules} cannot be used in conjunction with the CVS
+\texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
+they create can be changed to a different name following the check-out:
+\begin{verbatim}
+   %  cvs co MITgcm_verif_basic
+   %  mv MITgcm MITgcm_verif_basic
+\end{verbatim}
+
+
+\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
+tar file from the web site at:
+\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/download/
 \end{verbatim}
-
-\subsection{Model and directory structure}
-
-The ``numerical'' model is contained within a execution environment support
-wrapper. This wrapper is designed to provide a general framework for
-grid-point models. MITgcmUV is a specific numerical model that uses the
-framework. Under this structure the model is split into execution
-environment support code and conventional numerical model code. The
-execution environment support code is held under the \textit{eesupp}
-directory. The grid point model code is held under the \textit{model}
-directory. Code execution actually starts in the \textit{eesupp} routines
-and not in the \textit{model} routines. For this reason the top-level 
-\textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
-end-users should not need to worry about this level. The top-level routine
-for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
-}. Here is a brief description of the directory structure of the model under
-the root tree (a detailed description is given in section 3: Code structure).
-
-\begin{itemize}
-\item \textit{bin}: this directory is initially empty. It is the default
-directory in which to compile the code.
-
+\begin{rawhtml} </A> \end{rawhtml}
+The tar file still contains CVS information which we urge you not to
+delete; even if you do not use CVS yourself the information can help
+us if you should need to send us your copy of the code.  If a recent
+tar file does not exist, then please contact the developers through
+the 
+\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+mailing list.
+
+\subsubsection{Upgrading from an earlier version}
+
+If you already have an earlier version of the code you can ``upgrade''
+your copy instead of downloading the entire repository again. First,
+``cd'' (change directory) to the top of your working copy:
+\begin{verbatim}
+% cd MITgcm
+\end{verbatim}
+and then issue the cvs update command such as:
+\begin{verbatim}
+% cvs -q update -r checkpoint52i_post -d -P
+\end{verbatim}
+This will update the ``tag'' to ``checkpoint52i\_post'', add any new
+directories (-d) and remove any empty directories (-P). The -q option
+means be quiet which will reduce the number of messages you'll see in
+the terminal. If you have modified the code prior to upgrading, CVS
+will try to merge your changes with the upgrades. If there is a
+conflict between your modifications and the upgrade, it will report
+that file with a ``C'' in front, e.g.:
+\begin{verbatim}
+C model/src/ini_parms.F
+\end{verbatim}
+If the list of conflicts scrolled off the screen, you can re-issue the
+cvs update command and it will report the conflicts. Conflicts are
+indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
+``$>>>>>>>$''. For example,
+{\small
+\begin{verbatim}
+<<<<<<< ini_parms.F
+     & bottomDragLinear,myOwnBottomDragCoefficient,
+=======
+     & bottomDragLinear,bottomDragQuadratic,
+>>>>>>> 1.18
+\end{verbatim}
+}
+means that you added ``myOwnBottomDragCoefficient'' to a namelist at
+the same time and place that we added ``bottomDragQuadratic''. You
+need to resolve this conflict and in this case the line should be
+changed to:
+{\small
+\begin{verbatim}
+     & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
+\end{verbatim}
+}
+and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
+Unless you are making modifications which exactly parallel
+developments we make, these types of conflicts should be rare.
+
+\paragraph*{Upgrading to the current pre-release version}
+
+We don't make a ``release'' for every little patch and bug fix in
+order to keep the frequency of upgrades to a minimum. However, if you
+have run into a problem for which ``we have already fixed in the
+latest code'' and we haven't made a ``tag'' or ``release'' since that
+patch then you'll need to get the latest code:
+\begin{verbatim}
+% cvs -q update -A -d -P
+\end{verbatim}
+Unlike, the ``check-out'' and ``update'' procedures above, there is no
+``tag'' or release name. The -A tells CVS to upgrade to the
+very latest version. As a rule, we don't recommend this since you
+might upgrade while we are in the processes of checking in the code so
+that you may only have part of a patch. Using this method of updating
+also means we can't tell what version of the code you are working
+with. So please be sure you understand what you're doing.
+
+\section{Model and directory structure}
+
+The ``numerical'' model is contained within a execution environment
+support wrapper. This wrapper is designed to provide a general
+framework for grid-point models. MITgcmUV is a specific numerical
+model that uses the framework. Under this structure the model is split
+into execution environment support code and conventional numerical
+model code. The execution environment support code is held under the
+\textit{eesupp} directory. The grid point model code is held under the
+\textit{model} directory. Code execution actually starts in the
+\textit{eesupp} routines and not in the \textit{model} routines. For
+this reason the top-level \textit{MAIN.F} is in the
+\textit{eesupp/src} directory. In general, end-users should not need
+to worry about this level. The top-level routine for the numerical
+part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
+a brief description of the directory structure of the model under the
+root tree (a detailed description is given in section 3: Code
+structure).
+
+\begin{itemize}
+
+\item \textit{bin}: this directory is initially empty. It is the
+  default directory in which to compile the code.
+  
 \item \textit{diags}: contains the code relative to time-averaged
-diagnostics. It is subdivided into two subdirectories \textit{inc} and 
-\textit{src} that contain include files (*.\textit{h} files) and fortran
-subroutines (*.\textit{F} files), respectively.
+  diagnostics. It is subdivided into two subdirectories \textit{inc}
+  and \textit{src} that contain include files (*.\textit{h} files) and
+  Fortran subroutines (*.\textit{F} files), respectively.
 
 \item \textit{doc}: contains brief documentation notes.
-
-\item \textit{eesupp}: contains the execution environment source code. Also
-subdivided into two subdirectories \textit{inc} and \textit{src}.
-
-\item \textit{exe}: this directory is initially empty. It is the default
-directory in which to execute the code.
-
-\item \textit{model}: this directory contains the main source code. Also
-subdivided into two subdirectories \textit{inc} and \textit{src}.
-
-\item \textit{pkg}: contains the source code for the packages. Each package
-corresponds to a subdirectory. For example, \textit{gmredi} contains the
-code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code
-relative to the atmospheric intermediate physics. The packages are described
-in detail in section 3.
-
-\item \textit{tools}: this directory contains various useful tools. For
-example, \textit{genmake} is a script written in csh (C-shell) that should
-be used to generate your makefile. The directory \textit{adjoint} contains
-the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
-generates the adjoint code. The latter is described in details in part V.
-
+  
+\item \textit{eesupp}: contains the execution environment source code.
+  Also subdivided into two subdirectories \textit{inc} and
+  \textit{src}.
+  
+\item \textit{exe}: this directory is initially empty. It is the
+  default directory in which to execute the code.
+  
+\item \textit{model}: this directory contains the main source code.
+  Also subdivided into two subdirectories \textit{inc} and
+  \textit{src}.
+  
+\item \textit{pkg}: contains the source code for the packages. Each
+  package corresponds to a subdirectory. For example, \textit{gmredi}
+  contains the code related to the Gent-McWilliams/Redi scheme,
+  \textit{aim} the code relative to the atmospheric intermediate
+  physics. The packages are described in detail in section 3.
+  
+\item \textit{tools}: this directory contains various useful tools.
+  For example, \textit{genmake2} is a script written in csh (C-shell)
+  that should be used to generate your makefile. The directory
+  \textit{adjoint} contains the makefile specific to the Tangent
+  linear and Adjoint Compiler (TAMC) that generates the adjoint code.
+  The latter is described in details in part V.
+  
 \item \textit{utils}: this directory contains various utilities. The
-subdirectory \textit{knudsen2} contains code and a makefile that compute
-coefficients of the polynomial approximation to the knudsen formula for an
-ocean nonlinear equation of state. The \textit{matlab} subdirectory contains
-matlab scripts for reading model output directly into matlab. \textit{scripts%
-} contains C-shell post-processing scripts for joining processor-based and
-tiled-based model output.
+  subdirectory \textit{knudsen2} contains code and a makefile that
+  compute coefficients of the polynomial approximation to the knudsen
+  formula for an ocean nonlinear equation of state. The
+  \textit{matlab} subdirectory contains matlab scripts for reading
+  model output directly into matlab. \textit{scripts} contains C-shell
+  post-processing scripts for joining processor-based and tiled-based
+  model output.
+  
+\item \textit{verification}: this directory contains the model
+  examples. See section \ref{sect:modelExamples}.
 
-\item \textit{verification}: this directory contains the model examples. See
-below.
 \end{itemize}
 
-\subsection{Model examples}
-
-Now that you have successfully downloaded the model code we recommend that
-you first try to run the examples provided with the base version. You will
-probably want to run the example that is the closest to the configuration
-you will use eventually. The examples are located in subdirectories under
-the directory \textit{verification} and are briefly described below (a full
-description is given in section 2):
+\section[MITgcm Example Experiments]{Example experiments}
+\label{sect:modelExamples}
+
+%% a set of twenty-four pre-configured numerical experiments
+
+The MITgcm distribution comes with more than a dozen pre-configured
+numerical experiments. Some of these example experiments are tests of
+individual parts of the model code, but many are fully fledged
+numerical simulations. A few of the examples are used for tutorial
+documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
+The other examples follow the same general structure as the tutorial
+examples. However, they only include brief instructions in a text file
+called {\it README}.  The examples are located in subdirectories under
+the directory \textit{verification}. Each example is briefly described
+below.
 
-\subsubsection{List of model examples}
+\subsection{Full list of model examples}
 
-\begin{itemize}
+\begin{enumerate}
+  
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with
-free-surface).
-
-\item \textit{exp1} - 4 layers, ocean double gyre.
+  free-surface). This experiment is described in detail in section
+  \ref{sect:eg-baro}.
 
+\item \textit{exp1} - Four layer, ocean double gyre. This experiment
+  is described in detail in section \ref{sect:eg-baroc}.
+  
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady
-climatological forcing.
-
-\item \textit{exp4} - flow over a Gaussian bump in open-water or channel
-with open boundaries.
+  climatological forcing. This experiment is described in detail in
+  section \ref{sect:eg-global}.
+  
+\item \textit{exp4} - Flow over a Gaussian bump in open-water or
+  channel with open boundaries.
+  
+\item \textit{exp5} - Inhomogenously forced ocean convection in a
+  doubly periodic box.
 
-\item \textit{exp5} - inhomogenously forced ocean convection in a doubly
-periodic box.
-
-\item \textit{front\_relax} - relaxation of an ocean thermal front (test for
+\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
 Gent/McWilliams scheme). 2D (Y-Z).
 
-\item \textit{internal wave} - ocean internal wave forced by open boundary
-conditions.
-
-\item \textit{natl\_box} - eastern subtropical North Atlantic with KPP
-scheme; 1 month integration
-
-\item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez
-'94 forcing.
-
-\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
-'94 forcing.
-
+\item \textit{internal wave} - Ocean internal wave forced by open
+  boundary conditions.
+  
+\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
+  scheme; 1 month integration
+  
+\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
+  Suarez '94 forcing.
+  
+\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+  Suarez '94 forcing.
+  
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-Suarez '94 forcing on the cubed sphere.
-
-\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.
-
-\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. Equatorial Slice configuration.
-2D (X-Z).
-
+  Suarez '94 forcing on the cubed sphere.
+  
+\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
+  Global Zonal Mean configuration, 1x64x5 resolution.
+  
+\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
+  Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
+  
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. 3D Equatorial Channel
-configuration (not completely tested).
-
-\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global configuration, 128x64x5 resolution.
+  physics. 3D Equatorial Channel configuration.
+  
+\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+  Global configuration, on latitude longitude grid with 128x64x5 grid
+  points ($2.8^\circ{\rm degree}$ resolution).
+  
+\item \textit{adjustment.128x64x1} Barotropic adjustment problem on
+  latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
+    degree}$ resolution).
+  
+\item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
+  cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
+    degree}$ resolution).
+  
+\item \textit{advect\_cs} Two-dimensional passive advection test on
+  cube sphere grid.
+  
+\item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
+  advection test on Cartesian grid.
+  
+\item \textit{advect\_yz} Two-dimensional (vertical plane) passive
+  advection test on Cartesian grid.
+  
+\item \textit{carbon} Simple passive tracer experiment. Includes
+  derivative calculation. Described in detail in section
+  \ref{sect:eg-carbon-ad}.
+
+\item \textit{flt\_example} Example of using float package.
+  
+\item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
+  boundary conditions and poles.
+
+\item \textit{global\_ocean\_pressure} Global circulation in pressure
+  coordinate (non-Boussinesq ocean model). Described in detail in
+  section \ref{sect:eg-globalpressure}.
+  
+\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
+  sphere grid.
 
-\item \textit{adjustment.128x64x1}
-
-\item \textit{adjustment.cs-32x32x1}
-\end{itemize}
+\end{enumerate}
 
-\subsubsection{Directory structure of model examples}
+\subsection{Directory structure of model examples}
 
 Each example directory has the following subdirectories:
 
 \begin{itemize}
 \item \textit{code}: contains the code particular to the example. At a
-minimum, this directory includes the following files:
-
-\begin{itemize}
-\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the
-``execution environment'' part of the code. The default version is located
-in \textit{eesupp/inc}.
-
-\item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
-``numerical model'' part of the code. The default version is located in 
-\textit{model/inc}.
-
-\item \textit{code/SIZE.h}: declares size of underlying computational grid.
-The default version is located in \textit{model/inc}.
-\end{itemize}
-
-In addition, other include files and subroutines might be present in \textit{%
-code} depending on the particular experiment. See section 2 for more details.
-
-\item \textit{input}: contains the input data files required to run the
-example. At a mimimum, the \textit{input} directory contains the following
-files:
-
-\begin{itemize}
-\item \textit{input/data}: this file, written as a namelist, specifies the
-main parameters for the experiment.
-
-\item \textit{input/data.pkg}: contains parameters relative to the packages
-used in the experiment.
-
-\item \textit{input/eedata}: this file contains ``execution environment''
-data. At present, this consists of a specification of the number of threads
-to use in $X$ and $Y$ under multithreaded execution.
-\end{itemize}
-
-In addition, you will also find in this directory the forcing and topography
-files as well as the files describing the initial state of the experiment.
-This varies from experiment to experiment. See section 2 for more details.
-
-\item \textit{results}: this directory contains the output file \textit{%
-output.txt} produced by the simulation example. This file is useful for
-comparison with your own output when you run the experiment.
-\end{itemize}
-
-Once you have chosen the example you want to run, you are ready to compile
-the code.
+  minimum, this directory includes the following files:
 
-\subsection{Compiling the code}
-
-\subsubsection{The script \textit{genmake}}
-
-To compile the code, use the script \textit{genmake} located in the \textit{%
-tools} directory. \textit{genmake} is a script that generates the makefile.
-It has been written so that the code can be compiled on a wide diversity of
-machines and systems. However, if it doesn't work the first time on your
-platform, you might need to edit certain lines of \textit{genmake} in the
-section containing the setups for the different machines. The file is
-structured like this:
-\begin{verbatim}
-        .
-        .
-        .
-general instructions (machine independent)
-        .
-        .
-        .
-    - setup machine 1
-    - setup machine 2
-    - setup machine 3
-    - setup machine 4
-       etc
-        .
-        .
-        .
-\end{verbatim}
-
-For example, the setup corresponding to a DEC alpha machine is reproduced
-here:
-\begin{verbatim}
-  case OSF1+mpi:
-    echo "Configuring for DEC Alpha"
-    set CPP        = ( '/usr/bin/cpp -P' )
-    set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
-    set KPP        = ( 'kapf' )
-    set KPPFILES   = ( 'main.F' )
-    set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
-    set FC         = ( 'f77' )
-    set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
-    set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
-    set NOOPTFLAGS = ( '-O0' )
-    set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
-    set RMFILES    = ( '*.p.out' )
-    breaksw
-\end{verbatim}
-
-Typically, these are the lines that you might need to edit to make \textit{%
-genmake} work on your platform if it doesn't work the first time. \textit{%
-genmake} understands several options that are described here:
-
-\begin{itemize}
-\item -rootdir=dir
-
-indicates where the model root directory is relative to the directory where
-you are compiling. This option is not needed if you compile in the \textit{%
-bin} directory (which is the default compilation directory) or within the 
-\textit{verification} tree.
-
-\item -mods=dir1,dir2,...
-
-indicates the relative or absolute paths directories where the sources
-should take precedence over the default versions (located in \textit{model}, 
-\textit{eesupp},...). Typically, this option is used when running the
-examples, see below.
-
-\item -enable=pkg1,pkg2,...
-
-enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
-the makefile.
-
-\item -disable=pkg1,pkg2,...
-
-disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
-the makefile.
-
-\item -platform=machine
-
-specifies the platform for which you want the makefile. In general, you
-won't need this option. \textit{genmake} will select the right machine for
-you (the one you're working on!). However, this option is useful if you have
-a choice of several compilers on one machine and you want to use the one
-that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under
-Linux).
-
-\item -mpi
-
-this is used when you want to run the model in parallel processing mode
-under mpi (see section on parallel computation for more details).
+  \begin{itemize}
+  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+    the ``execution environment'' part of the code. The default
+    version is located in \textit{eesupp/inc}.
+  
+  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
+    the ``numerical model'' part of the code. The default version is
+    located in \textit{model/inc}.
+  
+  \item \textit{code/SIZE.h}: declares size of underlying
+    computational grid.  The default version is located in
+    \textit{model/inc}.
+  \end{itemize}
+  
+  In addition, other include files and subroutines might be present in
+  \textit{code} depending on the particular experiment. See Section 2
+  for more details.
+  
+\item \textit{input}: contains the input data files required to run
+  the example. At a minimum, the \textit{input} directory contains the
+  following files:
+
+  \begin{itemize}
+  \item \textit{input/data}: this file, written as a namelist,
+    specifies the main parameters for the experiment.
+  
+  \item \textit{input/data.pkg}: contains parameters relative to the
+    packages used in the experiment.
+  
+  \item \textit{input/eedata}: this file contains ``execution
+    environment'' data. At present, this consists of a specification
+    of the number of threads to use in $X$ and $Y$ under multithreaded
+    execution.
+  \end{itemize}
+  
+  In addition, you will also find in this directory the forcing and
+  topography files as well as the files describing the initial state
+  of the experiment.  This varies from experiment to experiment. See
+  section 2 for more details.
+
+\item \textit{results}: this directory contains the output file
+  \textit{output.txt} produced by the simulation example. This file is
+  useful for comparison with your own output when you run the
+  experiment.
+\end{itemize}
+
+Once you have chosen the example you want to run, you are ready to
+compile 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
+({\em Makefile}) that allows us to pre-process source files, specify
+compiler and optimization options and also figures out any file
+dependencies. We supply a script ({\em genmake2}), described in
+section \ref{sect:genmake}, that automatically creates the {\em
+  Makefile} for you. You then need to build the dependencies and
+compile the code.
+
+As an example, let's assume that you want to build and run experiment
+\textit{verification/exp2}. The are multiple ways and places to
+actually do this but here let's build the code in
+\textit{verification/exp2/input}:
+\begin{verbatim}
+% cd verification/exp2/input
+\end{verbatim}
+First, build the {\em Makefile}:
+\begin{verbatim}
+% ../../../tools/genmake2 -mods=../code
+\end{verbatim}
+The command line option tells {\em genmake} to override model source
+code with any files in the directory {\em ./code/}.
 
-\item -jam
+On many systems, the {\em genmake2} program will be able to
+automatically recognize the hardware, find compilers and other tools
+within the user's path (``echo \$PATH''), and then choose an
+appropriate set of options from the files contained in the {\em
+  tools/build\_options} directory.  Under some circumstances, a user
+may have to create a new ``optfile'' in order to specify the exact
+combination of compiler, compiler flags, libraries, and other options
+necessary to build a particular configuration of MITgcm.  In such
+cases, it is generally helpful to read the existing ``optfiles'' and
+mimic their syntax.
+
+Through the MITgcm-support list, the MITgcm developers are willing to
+provide help writing or modifing ``optfiles''.  And we encourage users
+to post new ``optfiles'' (particularly ones for new machines or
+architectures) to the 
+\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+list.
 
-this is used when you want to run the model in parallel processing mode
-under jam (see section on parallel computation for more details).
-\end{itemize}
+To specify an optfile to {\em genmake2}, the syntax is:
+\begin{verbatim}
+% ../../../tools/genmake2 -mods=../code -of /path/to/optfile
+\end{verbatim}
 
-For some of the examples, there is a file called \textit{.genmakerc} in the 
-\textit{input} directory that has the relevant \textit{genmake} options for
-that particular example. In this way you don't need to type the options when
-invoking \textit{genmake}.
-
-\subsubsection{Compiling}
-
-Let's assume that you want to run, say, example \textit{exp2} in the \textit{%
-input} directory. To compile the code, type the following commands from the
-model root tree:
+Once a {\em Makefile} has been generated, we create the dependencies:
 \begin{verbatim}
-% cd verification/exp2/input
-% ../../../tools/genmake
 % make depend
-% make
 \end{verbatim}
+This modifies the {\em Makefile} by attaching a [long] list of files
+upon which other files depend. The purpose of this is to reduce
+re-compilation if and when you start to modify the code. The {\tt make
+  depend} command also creates links from the model source to this
+directory.
 
-If there is no \textit{.genmakerc} in the \textit{input} directory, you have
-to use the following options when invoking \textit{genmake}:
+Next compile the code:
 \begin{verbatim}
-% ../../../tools/genmake  -mods=../code
+% make
 \end{verbatim}
+The {\tt make} command creates an executable called \textit{mitgcmuv}.
+Additional make ``targets'' are defined within the makefile to aid in
+the production of adjoint and other versions of MITgcm.
 
-In addition, you will probably want to disable some of the packages. Taking
-again the case of \textit{exp2}, the full \textit{genmake} command will
-probably look like this:
+Now you are ready to run the model. General instructions for doing so are
+given in section \ref{sect:runModel}. Here, we can run the model with:
 \begin{verbatim}
-% ../../../tools/genmake  -mods=../code  -disable=kpp,gmredi,aim,...
+./mitgcmuv > output.txt
 \end{verbatim}
+where we are re-directing the stream of text output to the file {\em
+output.txt}.
+
 
-The make command creates an executable called \textit{mitgcmuv}.
+\section[Running MITgcm]{Running the model in prognostic mode}
+\label{sect:runModel}
 
-Note that you can compile and run the code in another directory than \textit{%
-input}. You just need to make sure that you copy the input data files into
-the directory where you want to run the model. For example to compile from 
-\textit{code}:
+If compilation finished succesfuully (section \ref{sect:buildingCode})
+then an executable called \texttt{mitgcmuv} will now exist in the
+local directory.
+
+To run the model as a single process (ie. not in parallel) simply
+type:
 \begin{verbatim}
-% cd verification/exp2/code
-% ../../../tools/genmake
-% make depend
-% make
+% ./mitgcmuv
+\end{verbatim}
+The ``./'' is a safe-guard to make sure you use the local executable
+in case you have others that exist in your path (surely odd if you
+do!). The above command will spew out many lines of text output to
+your screen.  This output contains details such as parameter values as
+well as diagnostics such as mean Kinetic energy, largest CFL number,
+etc. It is worth keeping this text output with the binary output so we
+normally re-direct the {\em stdout} stream as follows:
+\begin{verbatim}
+% ./mitgcmuv > output.txt
 \end{verbatim}
 
-\subsection{Running the model}
+For the example experiments in {\em verification}, an example of the
+output is kept in {\em results/output.txt} for comparison. You can compare
+your {\em output.txt} with this one to check that the set-up works.
 
-The first thing to do is to run the code by typing \textit{mitgcmuv} and see
-what happens. You can compare what you get with what is in the \textit{%
-results} directory. Unless noted otherwise, most examples are set up to run
-for a few time steps only so that you can quickly figure out whether the
-model is working or not.
 
-\subsubsection{Output files}
+
+\subsection{Output files}
 
 The model produces various output files. At a minimum, the instantaneous
 ``state'' of the model is written out, which is made of the following files:
@@ -450,7 +641,7 @@
 used to restart the model but are overwritten every other time they are
 output to save disk space during long integrations.
 
-\subsubsection{Looking at the output}
+\subsection{Looking at the output}
 
 All the model data are written according to a ``meta/data'' file format.
 Each variable is associated with two files with suffix names \textit{.data}
@@ -464,385 +655,18 @@
 \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads
 the data. Look at the comments inside the script to see how to use it.
 
-\section{Code structure}
-
-\section{Doing it yourself: customizing the code}
-
-\subsection{\protect\bigskip Configuration and setup}
-
-When you are ready to run the model in the configuration you want, the
-easiest thing is to use and adapt the setup of the case studies experiment
-(described previously) that is the closest to your configuration. Then, the
-amount of setup will be minimized. In this section, we focus on the setup
-relative to the ''numerical model'' part of the code (the setup relative to
-the ''execution environment'' part is covered in the parallel implementation
-section) and on the variables and parameters that you are likely to change.
-
-The CPP keys relative to the ''numerical model'' part of the code are all
-defined and set in the file \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.
-
-\subsubsection{Computational domain, geometry and time-discretization}
-
-\begin{itemize}
-\item dimensions
-\end{itemize}
-
-The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
-represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
-and \textbf{Nr}\textit{\ }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 section on parallel
-implementation.)
-
-\begin{itemize}
-\item grid
-\end{itemize}
-
-Three different grids are available: cartesian, spherical polar, and
-curvilinear (including the cubed sphere). The grid is set through the
-logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
-usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
-usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
-grids, the southern boundary is defined through the variable \textbf{phiMin}%
-\textit{\ }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}\textit{\ }and \textbf{dely}\textit{\ }(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}\textit{\ }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 put 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}\textit{\ }and \textbf{beta}\textit{\ }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 }\textit{\ }%
-is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
-southern edge of the domain.
-
-\begin{itemize}
-\item topography - full and partial cells
-\end{itemize}
-
-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}\textit{. }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}\textit{\ }%
-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}\textit{\ }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}\textit{\ }or\textit{\ }\textbf{delp}%
-\textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
-\textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
-\ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
-
-(Note: the atmospheric case is a bit more complicated than what is written
-here I think. To come soon...)
-
-\begin{itemize}
-\item time-discretization
-\end{itemize}
-
-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}.'.
-
-\subsubsection{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}\textit{\ }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}\textit{\ }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}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%
-buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and
-needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In
-this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.
-For the ocean, two forms of the equation of state are available: linear (set 
-\textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial
-approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\ 
-}to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the
-thermal and haline expansion coefficients represented by the variables 
-\textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(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). \textit{\ }
-
-\subsubsection{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}\textit{, }and \textit{\ }%
-\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{itemize}
-\item initialization
-\end{itemize}
-
-The velocity components are initialized to 0 unless the simulation is
-starting from a pickup file (see section on simulation control parameters).
-
-\begin{itemize}
-\item forcing
-\end{itemize}
-
-This section only applies to the ocean. You need to generate wind-stress
-data into two files \textbf{zonalWindFile}\textit{\ }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}.\textbf{\ }
-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.
-
-\begin{itemize}
-\item dissipation
-\end{itemize}
-
-The lateral eddy viscosity coefficient is specified through the variable 
-\textbf{viscAh}\textit{\ }(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}\textit{\ }(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}\textit{\ }(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}\textit{\ }%
-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}\textit{\ }in s$%
-^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
-\ }in m$^{-1}$).
-
-The Fourier and Shapiro filters are described elsewhere.
-
-\begin{itemize}
-\item C-D scheme
-\end{itemize}
-
-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.
-
-\begin{itemize} 
-\item calculation of pressure/geopotential
-\end{itemize} 
-
-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}\textit{\ }and \textbf{cg2dTargetResidual }%
-for the 2D case and \textbf{cg3dMaxIters}\textit{\ }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}\textit{\ }(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).
-
-\subsubsection{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}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%
-tempForcing}\textit{,} 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}\textit{, }\textbf{%
-saltAdvection}\textit{\ }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{itemize}
-\item initialization
-\end{itemize}
-
-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.
-
-\begin{itemize} 
-\item forcing
-\end{itemize}
-
-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}\textit{. }%
-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}\textit{. }The corresponding relaxation time scale coefficient
-is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
-same procedure applies for salinity with the variable names \textbf{EmPmRfile%
-}\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
-\textit{\ }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).
-
-\begin{itemize}
-\item dissipation
-\end{itemize}
-
-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).
-
-\begin{itemize}
-\item ocean convection
-\end{itemize}
-
-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.
-
-\subsubsection{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{itemize}
-\item run duration
-\end{itemize}
-
-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\textit{. }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}. 
+Some examples of reading and visualizing some output in {\em Matlab}:
+\begin{verbatim}
+% matlab
+>> H=rdmds('Depth');
+>> contourf(H');colorbar;
+>> title('Depth of fluid as used by model');
+
+>> eta=rdmds('Eta',10);
+>> imagesc(eta');axis ij;colorbar;
+>> title('Surface height at iter=10');
 
-\begin{itemize}
-\item frequency of output
-\end{itemize}
+>> eta=rdmds('Eta',[0:10:100]);
+>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
+\end{verbatim}
 
-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}).
