--- manual/s_getstarted/text/getting_started.tex	2001/10/21 04:19:40	1.7
+++ manual/s_getstarted/text/getting_started.tex	2004/04/08 02:24:23	1.23
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.7 2001/10/21 04:19:40 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.23 2004/04/08 02:24:23 edhill Exp $
 % $Name:  $
 
 %\section{Getting started}
@@ -18,37 +18,49 @@
 \section{Where to find information}
 \label{sect:whereToFindInfo}
 
-A web site is maintained for release 1 (Sealion) of MITgcm:
+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/sealion
+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.
+documentation, to data-sources, and other related sites.
 
-There is also a support news group for the model that you can email at
-\texttt{support@mitgcm.org} or browse at:
+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}
-news://mitgcm.org/mitgcm.support
+http://mitgcm.org/htdig/
 \end{verbatim}
-A mail to the email list will reach all the developers and be archived
-on the newsgroup. A users email list will be established at some time
-in the future.
+\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:support@mitgcm.org> \end{rawhtml}
-support@mitgcm.org
+\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 managment
+\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
@@ -67,46 +79,101 @@
 
 \end{enumerate}
 
+\subsubsection{Checkout from CVS}
+\label{sect:cvs_checkout}
+
 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.
 
-Before you can use CVS, the following environment variable has to be set in
-your .cshrc or .tcshrc:
+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}
-% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
 \end{verbatim}
+in your .cshrc or .tcshrc file.  For bash or sh shells, put:
+\begin{verbatim}
+% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
+\end{verbatim}
+in your \texttt{.profile} or \texttt{.bashrc} file.
 
-To start using CVS, register with the MITgcm CVS server using command:
+
+To get MITgcm through CVS, first register with the MITgcm CVS server
+using command:
 \begin{verbatim}
 % cvs login ( CVS password: cvsanon )
 \end{verbatim}
-You only need to do ``cvs login'' once.
+You only need to do a ``cvs login'' once.
 
-To obtain the sources for release1 type:
+To obtain the latest sources type:
+\begin{verbatim}
+% cvs co MITgcm
+\end{verbatim}
+or to get a specific release type:
+\begin{verbatim}
+% 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}
-% cvs co -d directory -P -r release1 MITgcmUV
+http://mitgcm.org/source_code.html
 \end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
 
-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}!
-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}
+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}
 
 
-\paragraph*{Conventional download method}
+\subsubsection{Conventional download method}
 \label{sect:conventionalDownload}
 
 If you do not have CVS on your system, you can download the model as a
-tar file from the reference web site at:
+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/
@@ -114,132 +181,251 @@
 \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.
+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).
+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{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
-section \ref{sect:modelExamples}.
 \end{itemize}
 
 \section{Example experiments}
 \label{sect:modelExamples}
 
-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):
+%% a set of twenty-four pre-configured numerical experiments
 
-\subsection{List of model examples}
+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.
 
-\begin{itemize}
-\item \textit{exp0} - single layer, ocean double gyre (barotropic with
-free-surface).
+\subsection{Full list of model examples}
 
-\item \textit{exp1} - 4 layers, ocean double gyre.
+\begin{enumerate}
+  
+\item \textit{exp0} - single layer, ocean double gyre (barotropic with
+  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.
-
-\item \textit{exp5} - inhomogenously forced ocean convection in a doubly
-periodic box.
+  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{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}
 
 \subsection{Directory structure of model examples}
 
@@ -247,51 +433,56 @@
 
 \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.
+  minimum, this directory includes the following files:
 
-\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.
+  \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}
 
-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.
+Once you have chosen the example you want to run, you are ready to
+compile the code.
 
 \section{Building the code}
 \label{sect:buildingCode}
@@ -299,44 +490,67 @@
 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
-dependancies. We supply a script ({\em genmake}), described in section
-\ref{sect:genmake}, that automatically creates the {\em Makefile} for
-you. You then need to build the dependancies and compile the code.
+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}. 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/genmake -mods=../code
+% ../../../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/}.
 
-If there is no \textit{.genmakerc} in the \textit{input} directory, you have
-to use the following options when invoking \textit{genmake}:
+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.
+
+To specify an optfile to {\em genmake2}, the syntax is:
 \begin{verbatim}
-% ../../../tools/genmake  -mods=../code
+% ../../../tools/genmake2 -mods=../code -of /path/to/optfile
 \end{verbatim}
 
-Next, create the dependancies:
+Once a {\em Makefile} has been generated, we create the dependencies:
 \begin{verbatim}
 % make depend
 \end{verbatim}
-This modifies {\em Makefile} by attaching a [long] list of files on
-which other files depend. The purpose of this is to reduce
-re-compilation if and when you start to modify the code. {\tt make
-depend} also created links from the model source to this directory.
+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.
 
-Now compile the code:
+Next compile the code:
 \begin{verbatim}
 % 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.
 
 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:
@@ -354,17 +568,18 @@
 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
-genmake} in your path or you know the absolute path to {\tt genmake}.
+  genmake2} in your path or you know the absolute path to {\tt
+  genmake2}.
 
-The following sections outline some possible methods of organizing you
-source and data.
+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/genmake
+% ../../../tools/genmake2
 % make depend
 % make
 \end{verbatim}
@@ -375,7 +590,7 @@
 % cp ../code/mitgcmuv ./
 % ./mitgcmuv > output.txt
 \end{verbatim}
-or if you will be making muliple runs with the same executable:
+or if you will be making multiple runs with the same executable:
 \begin{verbatim}
 % cd ../
 % cp -r input run1
@@ -387,13 +602,13 @@
 \subsubsection{Building from a new directory}
 
 Since the {\em input} directory contains input files it is often more
-useful to keep {\em input} prestine and build in a new directory
+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/genmake -mods=../code
+% ../../../tools/genmake2 -mods=../code
 % make depend
 % make
 \end{verbatim}
@@ -415,7 +630,7 @@
 % ./mitgcmuv > output.txt
 \end{verbatim}
 
-\subsubsection{Building from on a scratch disk}
+\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
@@ -423,7 +638,8 @@
 following commands will build the model in {\em /scratch/exp2-run1}:
 \begin{verbatim}
 % cd /scratch/exp2-run1
-% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+  -mods=~/MITgcm/verification/exp2/code
 % make depend
 % make
 \end{verbatim}
@@ -439,7 +655,8 @@
 % cd /scratch/exp2
 % mkdir build
 % cd build
-% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+  -mods=~/MITgcm/verification/exp2/code
 % make depend
 % make
 % cd ../
@@ -449,116 +666,270 @@
 \end{verbatim}
 
 
-
-\subsection{\textit{genmake}}
+\subsection{Using \textit{genmake2}}
 \label{sect: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
+To compile the code, first use the program \texttt{genmake2} (located
+in the \textit{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 {\em
+  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.
 
-this is used when you want to run the model in parallel processing mode
-under mpi (see section on parallel computation for more details).
+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.
 
-\item -jam
+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.
 
-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}
+\end{enumerate}
 
-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}.
 
 
 \section{Running the model}
 \label{sect:runModel}
 
-If compilation finished succesfuully (section \ref{sect:buildModel})
-then an executable called {\em mitgcmuv} will now exist in the local
-directory.
+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:
@@ -576,7 +947,7 @@
 % ./mitgcmuv > output.txt
 \end{verbatim}
 
-For the example experiments in {\em vericication}, an example of the
+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.
 
@@ -665,380 +1036,419 @@
 \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.
+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.
+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{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{. }
+\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.'}.
 
-(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}
+\end{description}
 
-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}.'.
 
 \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}\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{\ }
+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}\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}
+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).
 
-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).
+\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}\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.
+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.
 
-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.
+\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{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}. 
-
-\begin{itemize}
-\item frequency of output
-\end{itemize}
-
-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}).
+The model ''clock'' is defined by the variable \textbf{deltaTClock}
+(in s) which determines the IO frequencies and is used in tagging
+output.  Typically, you will set it to the tracer time step for
+accelerated runs (otherwise it is simply set to the default time step
+\textbf{deltaT}).  Frequency of checkpointing and dumping of the model
+state are referenced to this clock (see below).
+
+\begin{description}
+\item[run duration] \ 
+  
+  The beginning of a simulation is set by specifying a start time (in
+  s) through the real variable \textbf{startTime} or by specifying an
+  initial iteration number through the integer variable
+  \textbf{nIter0}. If these variables are set to nonzero values, the
+  model will look for a ''pickup'' file \textit{pickup.0000nIter0} to
+  restart the integration. The end of a simulation is set through the
+  real variable \textbf{endTime} (in s).  Alternatively, you can
+  specify instead the number of time steps to execute through the
+  integer variable \textbf{nTimeSteps}.
+
+\item[frequency of output] \
+  
+  Real variables defining frequencies (in s) with which output files
+  are written on disk need to be set up. \textbf{dumpFreq} controls
+  the frequency with which the instantaneous state of the model is
+  saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output
+  frequency of rolling and permanent checkpoint files, respectively.
+  See section 1.5.1 Output files for the definition of model state and
+  checkpoint files. In addition, time-averaged fields can be written
+  out by setting the variable \textbf{taveFreq} (in s).  The precision
+  with which to write the binary data is controlled by the integer
+  variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or
+  \texttt{64}).
+
+\end{description}
+
+
+%%% Local Variables: 
+%%% mode: latex
+%%% TeX-master: t
+%%% End: