/[MITgcm]/manual/s_getstarted/text/getting_started.tex

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-revision 1.3 by adcroft,
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+revision 1.17 by edhill,
Thu Jan 29 15:11:39 2004 UTC
 Line 1
  % $Header$
  % $Name$
- \section{Getting started}
+ %\section{Getting started}
- In this part, we describe how to use the model. In the first section, we
+ In this section, we describe how to use the model. In the first
- provide enough information to help you get started with the model. We
+ section, we provide enough information to help you get started with
- believe the best way to familiarize yourself with the model is to run the
+ the model. We believe the best way to familiarize yourself with the
- case study examples provided with the base version. Information on how to
+ model is to run the case study examples provided with the base
- obtain, compile, and run the code is found there as well as a brief
+ version. Information on how to obtain, compile, and run the code is
- description of the model structure directory and the case study examples.
+ found there as well as a brief description of the model structure
- The latter and the code structure are described more fully in sections 2 and
+ directory and the case study examples.  The latter and the code
-, respectively. In section 4, we provide information on how to customize
+ structure are described more fully in chapters
- the code when you are ready to try implementing the configuration you have
+ \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
- in mind.
+ this section, we provide information on how to customize the code when
+ you are ready to try implementing the configuration you have in mind.
- \subsection{Obtaining the code}
+ \section{Where to find information}
+ \label{sect:whereToFindInfo}
- The reference web site for the model is:
+ 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
+ http://mitgcm.org/pelican
  \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
- On this site, you can download the model as well as find useful information,
+ Here you will find an on-line version of this document, a
- some of which might overlap with what is written here. There is also a
+ ``browsable'' copy of the code and a searchable database of the model
- support news group for the model located at (send your message to \texttt{%
+ and site, as well as links for downloading the model and
- support@mitgcm.org}):
+ 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}
- news://mitgcm.org/mitgcm.support
+ 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.
+ \end{enumerate}
  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(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/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 .profile or .bashrc file.
- Before you can use CVS, the following environment variable has to be set in
+ To get MITgcm through CVS, first register with the MITgcm CVS server
- your .cshrc or .tcshrc:
+ 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 source for the release:
+ To obtain the latest sources type:
  \begin{verbatim}
- % cvs co -d directory -P -r release1 MITgcmUV
+ % cvs co MITgcm
  \end{verbatim}
+ or to get a specific release type:
- 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
- different \textit{version} that is not the latest source:
  \begin{verbatim}
- % cvs co -d directory -P -r version MITgcm
+ % cvs co -P -r checkpoint52i_post  MITgcm
  \end{verbatim}
- or the latest development version:
+ 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 MITgcm
+ http://mitgcm.org/source_code.html
  \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
- \subsubsection{other methods}
- You can download the model as a tar file from the reference web site at:
+ 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}
+ .
+ \paragraph*{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 web site at:
+ \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
  \begin{verbatim}
  http://mitgcm.org/download/
  \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
- \subsection{Model and directory structure}
+ 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
- The ``numerical'' model is contained within a execution environment support
+ us if you should need to send us your copy of the code.  If a recent
- wrapper. This wrapper is designed to provide a general framework for
+ tar file does not exist, then please contact the developers through
- grid-point models. MITgcmUV is a specific numerical model that uses the
+ the
- framework. Under this structure the model is split into execution
+ \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
- environment support code and conventional numerical model code. The
+ MITgcm-support@mitgcm.org
- execution environment support code is held under the \textit{eesupp}
+ \begin{rawhtml} </A> \end{rawhtml}
- directory. The grid point model code is held under the \textit{model}
+ mailing list.
- directory. Code execution actually starts in the \textit{eesupp} routines
- and not in the \textit{model} routines. For this reason the top-level
+ \paragraph*{Upgrading from an earlier version}
- \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
+ If you already have an earlier version of the code you can ``upgrade''
- for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
+ your copy instead of downloading the entire repository again. First,
- }. Here is a brief description of the directory structure of the model under
+ ``cd'' (change directory) to the top of your working copy:
- the root tree (a detailed description is given in section 3: Code structure).
+ \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{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
+   diagnostics. It is subdivided into two subdirectories \textit{inc}
- \textit{src} that contain include files (*.\textit{h} files) and fortran
+   and \textit{src} that contain include files (*.\textit{h} files) and
- subroutines (*.\textit{F} files), respectively.
+   Fortran subroutines (*.\textit{F} files), respectively.
  \item \textit{doc}: contains brief documentation notes.
- \item \textit{eesupp}: contains the execution environment source code. Also
+ \item \textit{eesupp}: contains the execution environment source code.
- subdivided into two subdirectories \textit{inc} and \textit{src}.
+   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{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{model}: this directory contains the main source code.
+   Also subdivided into two subdirectories \textit{inc} and
- \item \textit{pkg}: contains the source code for the packages. Each package
+   \textit{src}.
- corresponds to a subdirectory. For example, \textit{gmredi} contains the
- code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code
+ \item \textit{pkg}: contains the source code for the packages. Each
- relative to the atmospheric intermediate physics. The packages are described
+   package corresponds to a subdirectory. For example, \textit{gmredi}
- in detail in section 3.
+   contains the code related to the Gent-McWilliams/Redi scheme,
+   \textit{aim} the code relative to the atmospheric intermediate
- \item \textit{tools}: this directory contains various useful tools. For
+   physics. The packages are described in detail in section 3.
- example, \textit{genmake} is a script written in csh (C-shell) that should
- be used to generate your makefile. The directory \textit{adjoint} contains
+ \item \textit{tools}: this directory contains various useful tools.
- the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
+   For example, \textit{genmake2} is a script written in csh (C-shell)
- generates the adjoint code. The latter is described in details in part V.
+   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
+   subdirectory \textit{knudsen2} contains code and a makefile that
- coefficients of the polynomial approximation to the knudsen formula for an
+   compute coefficients of the polynomial approximation to the knudsen
- ocean nonlinear equation of state. The \textit{matlab} subdirectory contains
+   formula for an ocean nonlinear equation of state. The
- matlab scripts for reading model output directly into matlab. \textit{scripts%
+   \textit{matlab} subdirectory contains matlab scripts for reading
- } contains C-shell post-processing scripts for joining processor-based and
+   model output directly into matlab. \textit{scripts} contains C-shell
- tiled-based model output.
+   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}
+ \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
+ %% a set of twenty-four pre-configured numerical experiments
- 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 MITgcm distribution comes with more than a dozen pre-configured
- the directory \textit{verification} and are briefly described below (a full
+ numerical experiments. Some of these example experiments are tests of
- description is given in section 2):
+ 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).
+   free-surface). This experiment is described in detail in section
+   \ref{sect:eg-baro}.
- \item \textit{exp1} - 4 layers, ocean double gyre.
+ \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.
+   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{exp4} - flow over a Gaussian bump in open-water or channel
+ \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
- 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
  Gent/McWilliams scheme). 2D (Y-Z).
- \item \textit{internal wave} - ocean internal wave forced by open boundary
+ \item \textit{internal wave} - Ocean internal wave forced by open
- conditions.
+   boundary conditions.
- \item \textit{natl\_box} - eastern subtropical North Atlantic with KPP
+ \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
- scheme; 1 month integration
+   scheme; 1 month integration
- \item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez
+ \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
- '94 forcing.
+   Suarez '94 forcing.
- \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
+ \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
- '94 forcing.
+   Suarez '94 forcing.
  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
- Suarez '94 forcing on the cubed sphere.
+   Suarez '94 forcing on the cubed sphere.
- \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers
+ \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
- Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.
+   Global Zonal Mean configuration, 1x64x5 resolution.
- \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
+ \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
- physics, 5 layers Molteni physics package. Equatorial Slice configuration.
+   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
-D (X-Z).
  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
- physics, 5 layers Molteni physics package. 3D Equatorial Channel
+   physics. 3D Equatorial Channel configuration.
- configuration (not completely tested).
+ \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
- \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
+   Global configuration, on latitude longitude grid with 128x64x5 grid
- Molteni physics package. Global configuration, 128x64x5 resolution.
+   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}
+ \end{enumerate}
- \item \textit{adjustment.cs-32x32x1}
+ \subsection{Directory structure of model examples}
- \end{itemize}
- \subsubsection{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:
+   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{%
+   \begin{itemize}
- code} depending on the particular experiment. See section 2 for more details.
+   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+     the ``execution environment'' part of the code. The default
- \item \textit{input}: contains the input data files required to run the
+     version is located in \textit{eesupp/inc}.
- example. At a mimimum, the \textit{input} directory contains the following
- files:
+   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
+     the ``numerical model'' part of the code. The default version is
- \begin{itemize}
+     located in \textit{model/inc}.
- \item \textit{input/data}: this file, written as a namelist, specifies the
- main parameters for the experiment.
+   \item \textit{code/SIZE.h}: declares size of underlying
+     computational grid.  The default version is located in
- \item \textit{input/data.pkg}: contains parameters relative to the packages
+     \textit{model/inc}.
- used in the experiment.
+   \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 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 \textit{input/eedata}: this file contains ``execution environment''
+ On many systems, the {\em genmake2} program will be able to
- data. At present, this consists of a specification of the number of threads
+ automatically recognize the hardware, find compilers and other tools
- to use in $X$ and $Y$ under multithreaded execution.
+ within the user's path (``echo \$PATH''), and then choose an
- \end{itemize}
+ 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.
- In addition, you will also find in this directory the forcing and topography
+ To specify an optfile to {\em genmake2}, the syntax is:
- files as well as the files describing the initial state of the experiment.
+ \begin{verbatim}
- This varies from experiment to experiment. See section 2 for more details.
+ % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
+ \end{verbatim}
- \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
+ Once a {\em Makefile} has been generated, we create the dependencies:
- the code.
+ \begin{verbatim}
+ % make depend
+ \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.
- \subsection{Compiling 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.
- \subsubsection{The script \textit{genmake}}
+ 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}
+ ./mitgcmuv > output.txt
+ \end{verbatim}
+ where we are re-directing the stream of text output to the file {\em
+ output.txt}.
- 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}
+ \subsection{Building/compiling the code elsewhere}
- \item -rootdir=dir
- indicates where the model root directory is relative to the directory where
+ In the example above (section \ref{sect:buildingCode}) we built the
- you are compiling. This option is not needed if you compile in the \textit{%
+ executable in the {\em input} directory of the experiment for
- bin} directory (which is the default compilation directory) or within the
+ convenience. You can also configure and compile the code in other
- \textit{verification} tree.
+ locations, for example on a scratch disk with out having to copy the
+ entire source tree. The only requirement to do so is you have {\tt
+   genmake2} in your path or you know the absolute path to {\tt
+   genmake2}.
- \item -mods=dir1,dir2,...
+ The following sections outline some possible methods of organizing
+ your source and data.
- indicates the relative or absolute paths directories where the sources
+ \subsubsection{Building from the {\em ../code directory}}
- 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,...
+ This is just as simple as building in the {\em input/} directory:
+ \begin{verbatim}
+ % cd verification/exp2/code
+ % ../../../tools/genmake2
+ % make depend
+ % make
+ \end{verbatim}
+ However, to run the model the executable ({\em mitgcmuv}) and input
+ files must be in the same place. If you only have one calculation to make:
+ \begin{verbatim}
+ % cd ../input
+ % cp ../code/mitgcmuv ./
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ or if you will be making multiple runs with the same executable:
+ \begin{verbatim}
+ % cd ../
+ % cp -r input run1
+ % cp code/mitgcmuv run1
+ % cd run1
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
- enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
+ \subsubsection{Building from a new directory}
- the makefile.
- \item -disable=pkg1,pkg2,...
+ Since the {\em input} directory contains input files it is often more
+ useful to keep {\em input} pristine and build in a new directory
+ within {\em verification/exp2/}:
+ \begin{verbatim}
+ % cd verification/exp2
+ % mkdir build
+ % cd build
+ % ../../../tools/genmake2 -mods=../code
+ % make depend
+ % make
+ \end{verbatim}
+ This builds the code exactly as before but this time you need to copy
+ either the executable or the input files or both in order to run the
+ model. For example,
+ \begin{verbatim}
+ % cp ../input/* ./
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ or if you tend to make multiple runs with the same executable then
+ running in a new directory each time might be more appropriate:
+ \begin{verbatim}
+ % cd ../
+ % mkdir run1
+ % cp build/mitgcmuv run1/
+ % cp input/* run1/
+ % cd run1
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
- disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
+ \subsubsection{Building on a scratch disk}
- the makefile.
- \item -platform=machine
+ Model object files and output data can use up large amounts of disk
+ space so it is often the case that you will be operating on a large
+ scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
+ following commands will build the model in {\em /scratch/exp2-run1}:
+ \begin{verbatim}
+ % cd /scratch/exp2-run1
+ % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+   -mods=~/MITgcm/verification/exp2/code
+ % make depend
+ % make
+ \end{verbatim}
+ To run the model here, you'll need the input files:
+ \begin{verbatim}
+ % cp ~/MITgcm/verification/exp2/input/* ./
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
- specifies the platform for which you want the makefile. In general, you
+ As before, you could build in one directory and make multiple runs of
- won't need this option. \textit{genmake} will select the right machine for
+ the one experiment:
- you (the one you're working on!). However, this option is useful if you have
+ \begin{verbatim}
- a choice of several compilers on one machine and you want to use the one
+ % cd /scratch/exp2
- that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under
+ % mkdir build
- Linux).
+ % cd build
+ % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+   -mods=~/MITgcm/verification/exp2/code
+ % make depend
+ % make
+ % cd ../
+ % cp -r ~/MITgcm/verification/exp2/input run2
+ % cd run2
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
- \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).
- \item -jam
+ \subsection{Using \textit{genmake2}}
+ \label{sect:genmake}
- this is used when you want to run the model in parallel processing mode
+ To compile the code, first use the program \texttt{genmake2} (located
- under jam (see section on parallel computation for more details).
+ in the \textit{tools} directory) to generate a Makefile.
- \end{itemize}
+ \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 some of the examples, there is a file called \textit{.genmakerc} in the
+ For example, the optfile for a typical Red Hat Linux machine (``ia32''
- \textit{input} directory that has the relevant \textit{genmake} options for
+ architecture) using the GCC (g77) compiler is
- 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:
  \begin{verbatim}
- % cd verification/exp2/input
+ FC=g77
- % ../../../tools/genmake
+ DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
- % make depend
+ CPP='cpp  -traditional -P'
- % make
+ 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 there is no \textit{.genmakerc} in the \textit{input} directory, you have
+ If you write an optfile for an unrepresented machine or compiler, you
- to use the following options when invoking \textit{genmake}:
+ are strongly encouraged to submit the optfile to the MITgcm project
+ for inclusion.  Please send the file to the
+ \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
+ \begin{center}
+   MITgcm-support@mitgcm.org
+ \end{center}
+ \begin{rawhtml} </A> \end{rawhtml}
+ mailing list.
+ In addition to the optfiles, \texttt{genmake2} supports a number of
+ helpful command-line options.  A complete list of these options can be
+ obtained from:
  \begin{verbatim}
- % ../../../tools/genmake  -mods=../code
+ % genmake2 -h
  \end{verbatim}
- In addition, you will probably want to disable some of the packages. Taking
+ The most important command-line options are:
- again the case of \textit{exp2}, the full \textit{genmake} command will
+ \begin{description}
- probably look like this:
+ \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{--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{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
+   set of packages to be used.
+   If not set, the default package list will be read from {\em
+     pkg/pkg\_default}
+ \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{--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.
+ \end{description}
+ \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.
+ To run the model as a single process (ie. not in parallel) simply
+ type:
  \begin{verbatim}
- % ../../../tools/genmake  -mods=../code  -disable=kpp,gmredi,aim,...
+ % ./mitgcmuv
  \end{verbatim}
+ The ``./'' is a safe-guard to make sure you use the local executable
- The make command creates an executable called \textit{mitgcmuv}.
+ 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
- Note that you can compile and run the code in another directory than \textit{%
+ your screen.  This output contains details such as parameter values as
- input}. You just need to make sure that you copy the input data files into
+ well as diagnostics such as mean Kinetic energy, largest CFL number,
- the directory where you want to run the model. For example to compile from
+ etc. It is worth keeping this text output with the binary output so we
- \textit{code}:
+ normally re-direct the {\em stdout} stream as follows:
  \begin{verbatim}
- % cd verification/exp2/code
+ % ./mitgcmuv > output.txt
- % ../../../tools/genmake
- % make depend
- % make
  \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:
-Line 445 
 as the pickup files but are named differ
+Line 876 
 as the pickup files but are named differ
  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}
-Line 459 
 written in this format. The matlab scrip
+Line 890 
 written in this format. The matlab scrip
  \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}
+ 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');
- \section{Doing it yourself: customizing the code}
+ >> eta=rdmds('Eta',[0:10:100]);
+ >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
+ \end{verbatim}
- \subsection{\protect\bigskip Configuration and setup}
+ \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
+ easiest thing is to use and adapt the setup of the case studies
- (described previously) that is the closest to your configuration. Then, the
+ experiment (described previously) that is the closest to your
- amount of setup will be minimized. In this section, we focus on the setup
+ configuration. Then, the amount of setup will be minimized. In this
- relative to the ''numerical model'' part of the code (the setup relative to
+ section, we focus on the setup relative to the ``numerical model''
- the ''execution environment'' part is covered in the parallel implementation
+ part of the code (the setup relative to the ``execution environment''
- section) and on the variables and parameters that you are likely to change.
+ 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{%
+ \subsection{Configuration and setup}
- model/inc }or in one of the \textit{code }directories of the case study
- experiments under \textit{verification.} The model parameters are defined
+ The CPP keys relative to the ``numerical model'' part of the code are
- and declared in the file \textit{model/inc/PARAMS.h }and their default
+ all defined and set in the file \textit{CPP\_OPTIONS.h }in the
- values are set in the routine \textit{model/src/set\_defaults.F. }The
+ directory \textit{ model/inc }or in one of the \textit{code
- default values can be modified in the namelist file \textit{data }which
+ }directories of the case study experiments under
- needs to be located in the directory where you will run the model. The
+ \textit{verification.} The model parameters are defined and declared
- parameters are initialized in the routine \textit{model/src/ini\_parms.F}.
+ in the file \textit{model/inc/PARAMS.h }and their default values are
- Look at this routine to see in what part of the namelist the parameters are
+ set in the routine \textit{model/src/set\_defaults.F. }The default
- located.
+ 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
- In what follows the parameters are grouped into categories related to the
+ parameters are initialized in the routine
- computational domain, the equations solved in the model, and the simulation
+ \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
- controls.
+ part of the namelist the parameters are located.
- \subsubsection{Computational domain, geometry and time-discretization}
+ In what follows the parameters are grouped into categories related to
+ the computational domain, the equations solved in the model, and the
- \begin{itemize}
+ simulation controls.
- \item dimensions
- \end{itemize}
+ \subsection{Computational domain, geometry and time-discretization}
- The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
+ \begin{description}
- represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
+ \item[dimensions] \
- and \textbf{Nr}\textit{\ }respectively which are declared and set in the
- file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor
+   The number of points in the x, y,\textit{\ }and r\textit{\
- calculation. For multiprocessor calculations see section on parallel
+   }directions are represented by the variables \textbf{sNx}\textit{,
- implementation.)
+   }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
+   which are declared and set in the file \textit{model/inc/SIZE.h.
- \begin{itemize}
+   }(Again, this assumes a mono-processor calculation. For
- \item grid
+   multiprocessor calculations see section on parallel implementation.)
- \end{itemize}
+ \item[grid] \
- Three different grids are available: cartesian, spherical polar, and
- curvilinear (including the cubed sphere). The grid is set through the
+   Three different grids are available: cartesian, spherical polar, and
- logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
+   curvilinear (including the cubed sphere). The grid is set through
- usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
+   the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
- usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
+     usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
- grids, the southern boundary is defined through the variable \textbf{phiMin}%
+     usingCurvilinearGrid}\textit{. }In the case of spherical and
- \textit{\ }which corresponds to the latitude of the southern most cell face
+   curvilinear grids, the southern boundary is defined through the
- (in degrees). The resolution along the x and y directions is controlled by
+   variable \textbf{phiMin} \textit{\ }which corresponds to the
- the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters
+   latitude of the southern most cell face (in degrees). The resolution
- in the case of a cartesian grid, in degrees otherwise). The vertical grid
+   along the x and y directions is controlled by the 1D arrays
- spacing is set through the 1D array \textbf{delz }for the ocean (in meters)
+   \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
- or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%
+   the case of a cartesian grid, in degrees otherwise). The vertical
- Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''
+   grid spacing is set through the 1D array \textbf{delz }for the ocean
- coordinate. This is typically set to 0m for the ocean (default value) and 10$%
+   (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
- ^{5}$Pa for the atmosphere. For the atmosphere, also set the logical
+   The variable \textbf{ Ro\_SeaLevel} represents the standard position
- variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level
+   of Sea-Level in ''R'' coordinate. This is typically set to 0m for
- (k=1) at the lower boundary (ground).
+   the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
+   the atmosphere, also set the logical variable \textbf{groundAtK1} to
- For the cartesian grid case, the Coriolis parameter $f$ is set through the
+   '.\texttt{TRUE}.'. which put the first level (k=1) at the lower
- variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond
+   boundary (ground).
- to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%
- \partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%
+   For the cartesian grid case, the Coriolis parameter $f$ is set
- is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
+   through the variables \textbf{f0}\textit{\ }and
- southern edge of the domain.
+   \textbf{beta}\textit{\ }which correspond to the reference Coriolis
+   parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
- \begin{itemize}
+   m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
- \item topography - full and partial cells
+   to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
- \end{itemize}
+   southern edge of the domain.
- The domain bathymetry is read from a file that contains a 2D (x,y) map of
+ \item[topography - full and partial cells] \
- 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
+   The domain bathymetry is read from a file that contains a 2D (x,y)
- file is assumed to contain binary numbers giving the depth (pressure) of the
+   map of depths (in m) for the ocean or pressures (in Pa) for the
- model at each grid cell, ordered with the x coordinate varying fastest. The
+   atmosphere. The file name is represented by the variable
- points are ordered from low coordinate to high coordinate for both axes. The
+   \textbf{bathyFile}\textit{. }The file is assumed to contain binary
- model code applies without modification to enclosed, periodic, and double
+   numbers giving the depth (pressure) of the model at each grid cell,
- periodic domains. Periodicity is assumed by default and is suppressed by
+   ordered with the x coordinate varying fastest. The points are
- setting the depths to 0m for the cells at the limits of the computational
+   ordered from low coordinate to high coordinate for both axes. The
- domain (note: not sure this is the case for the atmosphere). The precision
+   model code applies without modification to enclosed, periodic, and
- with which to read the binary data is controlled by the integer variable
+   double periodic domains. Periodicity is assumed by default and is
- \textbf{readBinaryPrec }which can take the value \texttt{32} (single
+   suppressed by setting the depths to 0m for the cells at the limits
- precision) or \texttt{64} (double precision). See the matlab program \textit{%
+   of the computational domain (note: not sure this is the case for the
- gendata.m }in the \textit{input }directories under \textit{verification }to
+   atmosphere). The precision with which to read the binary data is
- see how the bathymetry files are generated for the case study experiments.
+   controlled by the integer variable \textbf{readBinaryPrec }which can
+   take the value \texttt{32} (single precision) or \texttt{64} (double
- To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%
+   precision). See the matlab program \textit{ gendata.m }in the
- needs to be set to a value between 0 and 1 (it is set to 1 by default)
+   \textit{input }directories under \textit{verification }to see how
- corresponding to the minimum fractional size of the cell. For example if the
+   the bathymetry files are generated for the case study experiments.
- 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
+   To use the partial cell capability, the variable
- discrete values 50m apart from 50m to 500m depending on the value of the
+   \textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and
- bottom depth (in \textbf{bathyFile}) at this point.
+(it is set to 1 by default) corresponding to the minimum
+   fractional size of the cell. For example if the bottom cell is 500m
- Note that the bottom depths (or pressures) need not coincide with the models
+   thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
- levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%
+   thickness of the cell (i.e. used in the code) can cover a range of
- \textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
+   discrete values 50m apart from 50m to 500m depending on the value of
- \textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
+   the bottom depth (in \textbf{bathyFile}) at this point.
- \ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
+   Note that the bottom depths (or pressures) need not coincide with
- (Note: the atmospheric case is a bit more complicated than what is written
+   the models levels as deduced from \textbf{delz}\textit{\
- here I think. To come soon...)
+   }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
+   the numbers in \textbf{bathyFile} \textit{\ }so that they match the
- \begin{itemize}
+   levels obtained from \textbf{delz}\textit{ \ }or\textit{\
- \item time-discretization
+   }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
- \end{itemize}
+   (Note: the atmospheric case is a bit more complicated than what is
+   written here I think. To come soon...)
+ \item[time-discretization] \
+   The time steps are set through the real variables \textbf{deltaTMom}
+   and \textbf{deltaTtracer} (in s) which represent the time step for
+   the momentum and tracer equations, respectively. For synchronous
+   integrations, simply set the two variables to the same value (or you
+   can prescribe one time step only through the variable
+   \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
+   through the variable \textbf{abEps} (dimensionless). The stagger
+   baroclinic time stepping can be activated by setting the logical
+   variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
+ \end{description}
+ \subsection{Equation of state}
+ First, because the model equations are written in terms of
+ perturbations, a reference thermodynamic state needs to be specified.
+ This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
+ \textbf{tRef} specifies the reference potential temperature profile
+ (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
+ from the level k=1. Similarly, \textbf{sRef} specifies the reference
+ salinity profile (in ppt) for the ocean or the reference specific
+ humidity profile (in g/kg) for the atmosphere.
+ The form of the equation of state is controlled by the character
+ variables \textbf{buoyancyRelation} and \textbf{eosType}.
+ \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
+ needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
+ In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
+ For the ocean, two forms of the equation of state are available:
+ linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
+ approximation to the full nonlinear equation ( set
+ \textbf{eosType}\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} (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; \emph{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.
- The time steps are set through the real variables \textbf{deltaTMom }and
+ \subsection{Momentum equations}
- \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.
-Line 625 
 useCoriolis, momPressureForcing, momStep
+Line 1101 
 useCoriolis, momPressureForcing, momStep
  Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
  these variables.
- \begin{itemize}
+ \begin{description}
- \item initialization
+ \item[initialization] \
- \end{itemize}
+   The velocity components are initialized to 0 unless the simulation
- The velocity components are initialized to 0 unless the simulation is
+   is starting from a pickup file (see section on simulation control
- starting from a pickup file (see section on simulation control parameters).
+   parameters).
- \begin{itemize}
+ \item[forcing] \
- \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
- This section only applies to the ocean. You need to generate wind-stress
+   \textbf{ meridWindFile }corresponding to the zonal and meridional
- data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
+   components of the wind stress, respectively (if you want the stress
- meridWindFile }corresponding to the zonal and meridional components of the
+   to be along the direction of only one of the model horizontal axes,
- wind stress, respectively (if you want the stress to be along the direction
+   you only need to generate one file). The format of the files is
- of only one of the model horizontal axes, you only need to generate one
+   similar to the bathymetry file. The zonal (meridional) stress data
- file). The format of the files is similar to the bathymetry file. The zonal
+   are assumed to be in Pa and located at U-points (V-points). As for
- (meridional) stress data are assumed to be in Pa and located at U-points
+   the bathymetry, the precision with which to read the binary data is
- (V-points). As for the bathymetry, the precision with which to read the
+   controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See
- binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
+   the matlab program \textit{gendata.m }in the \textit{input
- See the matlab program \textit{gendata.m }in the \textit{input }directories
+   }directories under \textit{verification }to see how simple
- under \textit{verification }to see how simple analytical wind forcing data
+   analytical wind forcing data are generated for the case study
- are generated for the case study experiments.
+   experiments.
- There is also the possibility of prescribing time-dependent periodic
+   There is also the possibility of prescribing time-dependent periodic
- forcing. To do this, concatenate the successive time records into a single
+   forcing. To do this, concatenate the successive time records into a
- file (for each stress component) ordered in a (x, y, t) fashion and set the
+   single file (for each stress component) ordered in a (x, y, t)
- following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+   fashion and set the following variables:
- \textbf{externForcingPeriod }to the period (in s) of which the forcing
+   \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
- varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
+   \textbf{externForcingPeriod }to the period (in s) of which the
- time (in s) of the forcing (typically 1 year -- note: \textbf{%
+   forcing varies (typically 1 month), and \textbf{externForcingCycle
- externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
+   }to the repeat time (in s) of the forcing (typically 1 year -- note:
- With these variables set up, the model will interpolate the forcing linearly
+   \textbf{ externForcingCycle }must be a multiple of
- at each iteration.
+   \textbf{externForcingPeriod}).  With these variables set up, the
+   model will interpolate the forcing linearly at each iteration.
- \begin{itemize}
- \item dissipation
+ \item[dissipation] \
- \end{itemize}
+   The lateral eddy viscosity coefficient is specified through the
- The lateral eddy viscosity coefficient is specified through the variable
+   variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The
- \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
+   vertical eddy viscosity coefficient is specified through the
- coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
+   variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and
- ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
+   \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.
- for the atmosphere. The vertical diffusive fluxes can be computed implicitly
+   The vertical diffusive fluxes can be computed implicitly by setting
- by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
+   the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}
- .'. In addition, biharmonic mixing can be added as well through the variable
+   .'. In addition, biharmonic mixing can be added as well through the
- \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
+   variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a
- you might also need to set the variable \textbf{cosPower} which is set to 0
+   spherical polar grid, you might also need to set the variable
- by default and which represents the power of cosine of latitude to multiply
+   \textbf{cosPower} which is set to 0 by default and which represents
- viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
+   the power of cosine of latitude to multiply viscosity. Slip or
- specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
+   no-slip conditions at lateral and bottom boundaries are specified
- and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
+   through the logical variables \textbf{no\_slip\_sides}\textit{\ }
- boundary conditions are applied. If no-slip boundary conditions are applied
+   and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',
- at the bottom, a bottom drag can be applied as well. Two forms are
+   free-slip boundary conditions are applied. If no-slip boundary
- available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
+   conditions are applied at the bottom, a bottom drag can be applied
- ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
+   as well. Two forms are available: linear (set the variable
- \ }in m$^{-1}$).
+   \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.
+   The Fourier and Shapiro filters are described elsewhere.
- \begin{itemize}
- \item C-D scheme
+ \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.
+ \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}\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).
- If you run at a sufficiently coarse resolution, you will need the C-D scheme
+ \end{description}
- 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}
+ \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{%
+ \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{%
+ 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}
+ \begin{description}
- \item initialization
+ \item[initialization] \
- \end{itemize}
+   The initial tracer data can be contained in the binary files
- The initial tracer data can be contained in the binary files \textbf{%
+   \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files
- hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D
+   should contain 3D data ordered in an (x, y, r) fashion with k=1 as
- data ordered in an (x, y, r) fashion with k=1 as the first vertical level.
+   the first vertical level.  If no file names are provided, the
- If no file names are provided, the tracers are then initialized with the
+   tracers are then initialized with the values of \textbf{tRef }and
- values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation
+   \textbf{sRef }mentioned above (in the equation of state section). In
- of state section). In this case, the initial tracer data are uniform in x
+   this case, the initial tracer data are uniform in x and y for each
- and y for each depth level.
+   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}$) can be stored in the 2D binary file
+   \textbf{surfQfile}\textit{. }  Alternatively or in addition, the
+   forcing can be specified through a relaxation term. The SST data to
+   which the model surface temperatures are restored to are supposed to
+   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
+   }The corresponding relaxation time scale coefficient is set through
+   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
+   procedure applies for salinity with the variable names
+   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
+   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
+   and surface salinity (in ppt) data files and relaxation time scale
+   coefficient (in s), respectively. Also for salinity, if the CPP key
+   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
+   are applied i.e. when computing the surface salinity tendency, the
+   freshwater flux is multiplied by the model surface salinity instead
+   of a constant salinity value.
+   As for the other input files, the precision with which to read the
+   data is controlled by the variable \textbf{readBinaryPrec}.
+   Time-dependent, periodic forcing can be applied as well following
+   the same procedure used for the wind forcing data (see above).
+ \item[dissipation] \
+   Lateral eddy diffusivities for temperature and salinity/specific
+   humidity are specified through the variables \textbf{diffKhT }and
+   \textbf{diffKhS } (in m$^{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}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have
+   non-zero value.
- \begin{itemize}
+ \end{description}
- \item forcing
- \end{itemize}
- This part is more relevant for the ocean, the procedure for the atmosphere
- not being completely stabilized at the moment.
- A combination of fluxes data and relaxation terms can be used for driving
+ \subsection{Simulation controls}
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
- ^{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.
-Line 814 
 Typically, you will set it to the tracer
+Line 1294 
 Typically, you will set it to the tracer
  Frequency of checkpointing and dumping of the model state are referenced to
  this clock (see below).
- \begin{itemize}
+ \begin{description}
- \item run duration
+ \item[run duration] \
- \end{itemize}
+   The beginning of a simulation is set by specifying a start time (in
- The beginning of a simulation is set by specifying a start time (in s)
+   s) through the real variable \textbf{startTime }or by specifying an
- through the real variable \textbf{startTime }or by specifying an initial
+   initial iteration number through the integer variable
- iteration number through the integer variable \textbf{nIter0}. If these
+   \textbf{nIter0}. If these variables are set to nonzero values, the
- variables are set to nonzero values, the model will look for a ''pickup''
+   model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to
- file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end
+   restart the integration\textit{. }The end of a simulation is set
- of a simulation is set through the real variable \textbf{endTime }(in s).
+   through the real variable \textbf{endTime }(in s).  Alternatively,
- Alternatively, you can specify instead the number of time steps to execute
+   you can specify instead the number of time steps to execute through
- through the integer variable \textbf{nTimeSteps}.
+   the integer variable \textbf{nTimeSteps}.
- \begin{itemize}
+ \item[frequency of output] \
- \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
- Real variables defining frequencies (in s) with which output files are
+   the frequency with which the instantaneous state of the model is
- written on disk need to be set up. \textbf{dumpFreq }controls the frequency
+   saved. \textbf{chkPtFreq } and \textbf{pchkPtFreq }control the
- with which the instantaneous state of the model is saved. \textbf{chkPtFreq }%
+   output frequency of rolling and permanent checkpoint files,
- and \textbf{pchkPtFreq }control the output frequency of rolling and
+   respectively. See section 1.5.1 Output files for the definition of
- permanent checkpoint files, respectively. See section 1.5.1 Output files for the
+   model state and checkpoint files. In addition, time-averaged fields
- definition of model state and checkpoint files. In addition, time-averaged
+   can be written out by setting the variable \textbf{taveFreq} (in s).
- 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 precision with which to write the binary data is controlled by the
+   the integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32}
- integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
+   or \texttt{ 64}).
-}).
+ \end{description}
+ %%% Local Variables:
+ %%% mode: latex
+ %%% TeX-master: t
+ %%% End:

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