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

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+revision 1.17 by edhill,
Thu Jan 29 15:11:39 2004 UTC
 Line 18 
 you are ready to try implementing the co
  \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
+ There is also a web-archived support mailing list for the model that
- \texttt{support@mitgcm.org} or browse at:
+ 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}
- news://mitgcm.org/mitgcm.support
+ http://mitgcm.org/mailman/listinfo/mitgcm-support/
+ http://mitgcm.org/pipermail/mitgcm-support/
  \end{verbatim}
- A mail to the email list will reach all the developers and be archived
+ \begin{rawhtml} </A> \end{rawhtml}
- on the newsgroup. A users email list will be established at some time
+ Essentially all of the MITgcm web pages can be searched using a
- in the future.
+ popular web crawler such as Google or through our own search facility:
+ \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
+ \begin{verbatim}
+ http://mitgcm.org/htdig/
+ \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
+ %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
  \section{Obtaining the code}
  \label{sect:obtainingCode}
+ MITgcm can be downloaded from our system by following
+ the instructions below. As a courtesy we ask that you send e-mail to us at
+ \begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
+ MITgcm-support@mitgcm.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ to enable us to keep track of who's using the model and in what application.
+ You can download the model two ways:
+ \begin{enumerate}
+ \item Using CVS software. CVS is a freely available source code management
+ tool. To use CVS you need to have the software installed. Many systems
+ come with CVS pre-installed, otherwise good places to look for
+ the software for a particular platform are
+ \begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
+ cvshome.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ and
+ \begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
+ wincvs.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ .
+ \item Using a tar file. This method is simple and does not
+ require any special software. However, this method does not
+ provide easy support for maintenance updates.
+ \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.
- Before you can use CVS, the following environment variable has to be set in
+ Before you can use CVS, the following environment variable(s) should
- your .cshrc or .tcshrc:
+ 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
- % cvs login ( CVS password: cvsanon )
+ \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.
- You only need to do ``cvs login'' once. To obtain the source for the release:
+ To get MITgcm through CVS, first register with the MITgcm CVS server
+ using command:
  \begin{verbatim}
- % cvs co -d directory -P -r release1 MITgcmUV
+ % cvs login ( CVS password: cvsanon )
  \end{verbatim}
+ You only need to do a ``cvs login'' once.
- This creates a directory called \textit{directory}. If \textit{directory}
+ To obtain the latest sources type:
- exists this command updates your code based on the repository. Each
+ \begin{verbatim}
- directory in the source tree contains a directory \textit{CVS}. This
+ % cvs co MITgcm
- information is required by CVS to keep track of your file versions with
+ \end{verbatim}
- respect to the repository. Don't edit the files in \textit{CVS}! To obtain a
+ or to get a specific release type:
- 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}
+ 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 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/
  \end{verbatim}
+ \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.
+ \paragraph*{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
+ The ``numerical'' model is contained within a execution environment
- wrapper. This wrapper is designed to provide a general framework for
+ support wrapper. This wrapper is designed to provide a general
- grid-point models. MITgcmUV is a specific numerical model that uses the
+ framework for grid-point models. MITgcmUV is a specific numerical
- framework. Under this structure the model is split into execution
+ model that uses the framework. Under this structure the model is split
- environment support code and conventional numerical model code. The
+ into execution environment support code and conventional numerical
- execution environment support code is held under the \textit{eesupp}
+ model code. The execution environment support code is held under the
- directory. The grid point model code is held under the \textit{model}
+ \textit{eesupp} directory. The grid point model code is held under the
- directory. Code execution actually starts in the \textit{eesupp} routines
+ \textit{model} directory. Code execution actually starts in the
- and not in the \textit{model} routines. For this reason the top-level
+ \textit{eesupp} routines and not in the \textit{model} routines. For
- \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
+ this reason the top-level \textit{MAIN.F} is in the
- end-users should not need to worry about this level. The top-level routine
+ \textit{eesupp/src} directory. In general, end-users should not need
- for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
+ to worry about this level. The top-level routine for the numerical
- }. Here is a brief description of the directory structure of the model under
+ part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
- the root tree (a detailed description is given in section 3: Code structure).
+ 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
+   subdirectory \textit{knudsen2} contains code and a makefile that
- compute coefficients of the polynomial approximation to the knudsen
+   compute coefficients of the polynomial approximation to the knudsen
- formula for an ocean nonlinear equation of state. The \textit{matlab}
+   formula for an ocean nonlinear equation of state. The
- subdirectory contains matlab scripts for reading model output directly
+   \textit{matlab} subdirectory contains matlab scripts for reading
- into matlab. \textit{scripts} contains C-shell post-processing
+   model output directly into matlab. \textit{scripts} contains C-shell
- scripts for joining processor-based and 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
- section \ref{sect:modelExamples}.
  \end{itemize}
  \section{Example experiments}
  \label{sect:modelExamples}
- Now that you have successfully downloaded the model code we recommend that
+ %% a set of twenty-four pre-configured numerical experiments
- 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):
- \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}
+ \subsection{Full list of model examples}
- \item \textit{exp0} - single layer, ocean double gyre (barotropic with
- free-surface).
- \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.
+   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{exp4} - Flow over a Gaussian bump in open-water or
+   channel with open boundaries.
+ \item \textit{exp5} - Inhomogenously forced ocean convection in a
+   doubly periodic box.
- \item \textit{exp5} - inhomogenously forced ocean convection in a doubly
+ \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
- 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}
- \end{itemize}
  \subsection{Directory structure of model examples}
-Line 214 
 Each example directory has the following
+Line 400 
 Each example directory has the following
  \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{%
- code} depending on the particular experiment. See section 2 for more details.
- \item \textit{input}: contains the input data files required to run the
- example. At a mimimum, the \textit{input} directory contains the following
- files:
- \begin{itemize}
- \item \textit{input/data}: this file, written as a namelist, specifies the
- main parameters for the experiment.
- \item \textit{input/data.pkg}: contains parameters relative to the packages
+   \begin{itemize}
- used in the experiment.
+   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+     the ``execution environment'' part of the code. The default
- \item \textit{input/eedata}: this file contains ``execution environment''
+     version is located in \textit{eesupp/inc}.
- data. At present, this consists of a specification of the number of threads
- to use in $X$ and $Y$ under multithreaded execution.
+   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
- \end{itemize}
+     the ``numerical model'' part of the code. The default version is
+     located in \textit{model/inc}.
- 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.
+   \item \textit{code/SIZE.h}: declares size of underlying
- This varies from experiment to experiment. See section 2 for more details.
+     computational grid.  The default version is located in
+     \textit{model/inc}.
- \item \textit{results}: this directory contains the output file \textit{%
+   \end{itemize}
- output.txt} produced by the simulation example. This file is useful for
- comparison with your own output when you run the experiment.
+   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
+ Once you have chosen the example you want to run, you are ready to
- the code.
+ compile the code.
  \section{Building the code}
  \label{sect:buildingCode}
-Line 266 
 the code.
+Line 457 
 the code.
  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
+ dependencies. We supply a script ({\em genmake2}), described in
- \ref{sect:genmake}, that automatically creates the {\em Makefile} for
+ section \ref{sect:genmake}, that automatically creates the {\em
- you. You then need to build the dependancies and compile the code.
+   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
+ \textit{verification/exp2}. The are multiple ways and places to
- do this but here let's build the code in
+ 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
+ On many systems, the {\em genmake2} program will be able to
- to use the following options when invoking \textit{genmake}:
+ 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
+ This modifies the {\em Makefile} by attaching a [long] list of files
- which other files depend. The purpose of this is to reduce
+ upon which other files depend. The purpose of this is to reduce
- re-compilation if and when you start to modify the code. {\tt make
+ re-compilation if and when you start to modify the code. The {\tt make
- depend} also created links from the model source to this directory.
+   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:
-Line 321 
 executable in the {\em input} directory
+Line 535 
 executable in the {\em input} directory
  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
+ The following sections outline some possible methods of organizing
- source and data.
+ 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}
-Line 342 
 files must be in the same place. If you
+Line 557 
 files must be in the same place. If you
  % 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
-Line 354 
 or if you will be making muliple runs wi
+Line 569 
 or if you will be making muliple runs wi
  \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}
-Line 382 
 running in a new directory each time mig
+Line 597 
 running in a new directory each time mig
  % ./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
-Line 390 
 scratch disk. Assuming the model source
+Line 605 
 scratch disk. Assuming the model source
  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}
-Line 406 
 the one experiment:
+Line 622 
 the one experiment:
  % 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 ../
-Line 417 
 the one experiment:
+Line 634 
 the one experiment:
- \subsection{\textit{genmake}}
+ \subsection{Using \textit{genmake2}}
  \label{sect:genmake}
- To compile the code, use the script \textit{genmake} located in the \textit{%
+ To compile the code, first use the program \texttt{genmake2} (located
- tools} directory. \textit{genmake} is a script that generates the makefile.
+ in the \textit{tools} directory) to generate a Makefile.
- It has been written so that the code can be compiled on a wide diversity of
+ \texttt{genmake2} is a shell script written to work with all
- machines and systems. However, if it doesn't work the first time on your
+ ``sh''--compatible shells including bash v1, bash v2, and Bourne.
- platform, you might need to edit certain lines of \textit{genmake} in the
+ Internally, \texttt{genmake2} determines the locations of needed
- section containing the setups for the different machines. The file is
+ files, the compiler, compiler options, libraries, and Unix tools.  It
- structured like this:
+ relies upon a number of ``optfiles'' located in the {\em
- \begin{verbatim}
+   tools/build\_options} directory.
-         .
-         .
+ The purpose of the optfiles is to provide all the compilation options
-         .
+ for particular ``platforms'' (where ``platform'' roughly means the
- general instructions (machine independent)
+ 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
-     - setup machine 1
+ optfiles shipped with the code is
-     - setup machine 2
+ \begin{center}
-     - setup machine 3
+   {\bf OS\_HARDWARE\_COMPILER }
-     - setup machine 4
+ \end{center}
-        etc
+ where
-         .
+ \begin{description}
-         .
+ \item[OS] is the name of the operating system (generally the
-         .
+   lower-case output of the {\tt 'uname'} command)
- \end{verbatim}
+ \item[HARDWARE] is a string that describes the CPU type and
+   corresponds to output from the  {\tt 'uname -m'} command:
- For example, the setup corresponding to a DEC alpha machine is reproduced
+   \begin{description}
- here:
+   \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
- \begin{verbatim}
+     and athlon
-   case OSF1+mpi:
+   \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
-     echo "Configuring for DEC Alpha"
+   \item[amd64] is AMD x86\_64 systems
-     set CPP        = ( '/usr/bin/cpp -P' )
+   \item[ppc] is for Mac PowerPC systems
-     set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
+   \end{description}
-     set KPP        = ( 'kapf' )
+ \item[COMPILER] is the compiler name (generally, the name of the
-     set KPPFILES   = ( 'main.F' )
+   FORTRAN executable)
-     set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
+ \end{description}
-     set FC         = ( 'f77' )
-     set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
+ In many cases, the default optfiles are sufficient and will result in
-     set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
+ usable Makefiles.  However, for some machines or code configurations,
-     set NOOPTFLAGS = ( '-O0' )
+ new ``optfiles'' must be written. To create a new optfile, it is
-     set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
+ generally best to start with one of the defaults and modify it to suit
-     set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
+ your needs.  Like \texttt{genmake2}, the optfiles are all written
-     set RMFILES    = ( '*.p.out' )
+ using a simple ``sh''--compatible syntax.  While nearly all variables
-     breaksw
+ used within \texttt{genmake2} may be specified in the optfiles, the
- \end{verbatim}
+ critical ones that should be defined are:
- Typically, these are the lines that you might need to edit to make \textit{%
+ \begin{description}
- genmake} work on your platform if it doesn't work the first time. \textit{%
+ \item[FC] the FORTRAN compiler (executable) to use
- genmake} understands several options that are described here:
+ \item[DEFINES] the command-line DEFINE options passed to the compiler
+ \item[CPP] the C pre-processor to use
- \begin{itemize}
+ \item[NOOPTFLAGS] options flags for special files that should not be
- \item -rootdir=dir
+   optimized
+ \end{description}
- 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{%
+ For example, the optfile for a typical Red Hat Linux machine (``ia32''
- bin} directory (which is the default compilation directory) or within the
+ architecture) using the GCC (g77) compiler is
- \textit{verification} tree.
+ \begin{verbatim}
+ FC=g77
- \item -mods=dir1,dir2,...
+ DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
+ CPP='cpp  -traditional -P'
- indicates the relative or absolute paths directories where the sources
+ NOOPTFLAGS='-O0'
- should take precedence over the default versions (located in \textit{model},
+ #  For IEEE, use the "-ffloat-store" option
- \textit{eesupp},...). Typically, this option is used when running the
+ if test "x$IEEE" = x ; then
- examples, see below.
+     FFLAGS='-Wimplicit -Wunused -Wuninitialized'
+     FOPTIM='-O3 -malign-double -funroll-loops'
- \item -enable=pkg1,pkg2,...
+ else
+     FFLAGS='-Wimplicit -Wunused -ffloat-store'
- enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
+     FOPTIM='-O0 -malign-double'
- the makefile.
+ fi
+ \end{verbatim}
- \item -disable=pkg1,pkg2,...
+ If you write an optfile for an unrepresented machine or compiler, you
- disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
+ are strongly encouraged to submit the optfile to the MITgcm project
- the makefile.
+ for inclusion.  Please send the file to the
+ \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
+ \begin{center}
+   MITgcm-support@mitgcm.org
+ \end{center}
+ \begin{rawhtml} </A> \end{rawhtml}
+ mailing list.
+ In addition to the optfiles, \texttt{genmake2} supports a number of
+ helpful command-line options.  A complete list of these options can be
+ obtained from:
+ \begin{verbatim}
+ % genmake2 -h
+ \end{verbatim}
+ The most important command-line options are:
+ \begin{description}
+ \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
+   should be used for a particular build.
+   If no "optfile" is specified (either through the command line or the
+   MITGCM\_OPTFILE environment variable), genmake2 will try to make a
+   reasonable guess from the list provided in {\em
+     tools/build\_options}.  The method used for making this guess is
+   to first determine the combination of operating system and hardware
+   (eg. "linux\_ia32") and then find a working FORTRAN compiler within
+   the user's path.  When these three items have been identified,
+   genmake2 will try to find an optfile that has a matching name.
+ \item[\texttt{--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.
- \item -platform=machine
+ \end{description}
- specifies the platform for which you want the makefile. In general, you
- won't need this option. \textit{genmake} will select the right machine for
- you (the one you're working on!). However, this option is useful if you have
- a choice of several compilers on one machine and you want to use the one
- that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under
- Linux).
- \item -mpi
- this is used when you want to run the model in parallel processing mode
- under mpi (see section on parallel computation for more details).
- \item -jam
- 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}
- 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}
-Line 543 
 normally re-direct the {\em stdout} stre
+Line 819 
 normally re-direct the {\em stdout} stre
  % ./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.
-Line 632 
 Some examples of reading and visualizing
+Line 908 
 Some examples of reading and visualizing
  \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.
- \subsection{\protect\bigskip Configuration and setup}
+ \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{%
+ The CPP keys relative to the ``numerical model'' part of the code are
- model/inc }or in one of the \textit{code }directories of the case study
+ all defined and set in the file \textit{CPP\_OPTIONS.h }in the
- experiments under \textit{verification.} The model parameters are defined
+ directory \textit{ model/inc }or in one of the \textit{code
- and declared in the file \textit{model/inc/PARAMS.h }and their default
+ }directories of the case study experiments under
- values are set in the routine \textit{model/src/set\_defaults.F. }The
+ \textit{verification.} The model parameters are defined and declared
- default values can be modified in the namelist file \textit{data }which
+ in the file \textit{model/inc/PARAMS.h }and their default values are
- needs to be located in the directory where you will run the model. The
+ set in the routine \textit{model/src/set\_defaults.F. }The default
- parameters are initialized in the routine \textit{model/src/ini\_parms.F}.
+ values can be modified in the namelist file \textit{data }which needs
- Look at this routine to see in what part of the namelist the parameters are
+ to be located in the directory where you will run the model. The
- located.
+ parameters are initialized in the routine
+ \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
- In what follows the parameters are grouped into categories related to the
+ part of the namelist the parameters are located.
- computational domain, the equations solved in the model, and the simulation
- controls.
+ 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}
+ \begin{description}
- \item dimensions
+ \item[dimensions] \
- \end{itemize}
+   The number of points in the x, y,\textit{\ }and r\textit{\
- The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
+   }directions are represented by the variables \textbf{sNx}\textit{,
- represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
+   }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
- and \textbf{Nr}\textit{\ }respectively which are declared and set in the
+   which are declared and set in the file \textit{model/inc/SIZE.h.
- file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor
+   }(Again, this assumes a mono-processor calculation. For
- calculation. For multiprocessor calculations see section on parallel
+   multiprocessor calculations see section on parallel implementation.)
- implementation.)
+ \item[grid] \
- \begin{itemize}
- \item grid
+   Three different grids are available: cartesian, spherical polar, and
- \end{itemize}
+   curvilinear (including the cubed sphere). The grid is set through
+   the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
- Three different grids are available: cartesian, spherical polar, and
+     usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
- curvilinear (including the cubed sphere). The grid is set through the
+     usingCurvilinearGrid}\textit{. }In the case of spherical and
- logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
+   curvilinear grids, the southern boundary is defined through the
- usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
+   variable \textbf{phiMin} \textit{\ }which corresponds to the
- usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
+   latitude of the southern most cell face (in degrees). The resolution
- grids, the southern boundary is defined through the variable \textbf{phiMin}%
+   along the x and y directions is controlled by the 1D arrays
- \textit{\ }which corresponds to the latitude of the southern most cell face
+   \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
- (in degrees). The resolution along the x and y directions is controlled by
+   the case of a cartesian grid, in degrees otherwise). The vertical
- the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters
+   grid spacing is set through the 1D array \textbf{delz }for the ocean
- in the case of a cartesian grid, in degrees otherwise). The vertical grid
+   (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
- spacing is set through the 1D array \textbf{delz }for the ocean (in meters)
+   The variable \textbf{ Ro\_SeaLevel} represents the standard position
- or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%
+   of Sea-Level in ''R'' coordinate. This is typically set to 0m for
- Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''
+   the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
- coordinate. This is typically set to 0m for the ocean (default value) and 10$%
+   the atmosphere, also set the logical variable \textbf{groundAtK1} to
- ^{5}$Pa for the atmosphere. For the atmosphere, also set the logical
+   '.\texttt{TRUE}.'. which put the first level (k=1) at the lower
- variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level
+   boundary (ground).
- (k=1) at the lower boundary (ground).
+   For the cartesian grid case, the Coriolis parameter $f$ is set
- For the cartesian grid case, the Coriolis parameter $f$ is set through the
+   through the variables \textbf{f0}\textit{\ }and
- variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond
+   \textbf{beta}\textit{\ }which correspond to the reference Coriolis
- to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%
+   parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
- \partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%
+   m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
- is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
+   to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
- southern edge of the domain.
+   southern edge of the domain.
- \begin{itemize}
+ \item[topography - full and partial cells] \
- \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
+(it is set to 1 by default) corresponding to the minimum
+   fractional size of the cell. For example if the bottom cell is 500m
+   thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
+   thickness of the cell (i.e. used in the code) can cover a range of
+   discrete values 50m apart from 50m to 500m depending on the value of
+   the bottom depth (in \textbf{bathyFile}) at this point.
+   Note that the bottom depths (or pressures) need not coincide with
+   the models levels as deduced from \textbf{delz}\textit{\
+   }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
+   the numbers in \textbf{bathyFile} \textit{\ }so that they match the
+   levels obtained from \textbf{delz}\textit{ \ }or\textit{\
+   }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
+   (Note: the atmospheric case is a bit more complicated than what is
+   written here I think. To come soon...)
+ \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}.'.
- The domain bathymetry is read from a file that contains a 2D (x,y) map of
+ \end{description}
- depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The
- file name is represented by the variable \textbf{bathyFile}\textit{. }The
- file is assumed to contain binary numbers giving the depth (pressure) of the
- model at each grid cell, ordered with the x coordinate varying fastest. The
- points are ordered from low coordinate to high coordinate for both axes. The
- model code applies without modification to enclosed, periodic, and double
- periodic domains. Periodicity is assumed by default and is suppressed by
- setting the depths to 0m for the cells at the limits of the computational
- domain (note: not sure this is the case for the atmosphere). The precision
- with which to read the binary data is controlled by the integer variable
- \textbf{readBinaryPrec }which can take the value \texttt{32} (single
- precision) or \texttt{64} (double precision). See the matlab program \textit{%
- gendata.m }in the \textit{input }directories under \textit{verification }to
- see how the bathymetry files are generated for the case study experiments.
- To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%
- needs to be set to a value between 0 and 1 (it is set to 1 by default)
- corresponding to the minimum fractional size of the cell. For example if the
- bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the
- actual thickness of the cell (i.e. used in the code) can cover a range of
- discrete values 50m apart from 50m to 500m depending on the value of the
- bottom depth (in \textbf{bathyFile}) at this point.
- Note that the bottom depths (or pressures) need not coincide with the models
- levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%
- \textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
- \textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
- \ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
- (Note: the atmospheric case is a bit more complicated than what is written
- here I think. To come soon...)
- \begin{itemize}
- \item time-discretization
- \end{itemize}
- The time steps are set through the real variables \textbf{deltaTMom }and
- \textbf{deltaTtracer }(in s) which represent the time step for the momentum
- and tracer equations, respectively. For synchronous integrations, simply set
- the two variables to the same value (or you can prescribe one time step only
- through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing
- parameter is set through the variable \textbf{abEps }(dimensionless). The
- stagger baroclinic time stepping can be activated by setting the logical
- variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.
  \subsection{Equation of state}
- First, because the model equations are written in terms of perturbations, a
+ First, because the model equations are written in terms of
- reference thermodynamic state needs to be specified. This is done through
+ perturbations, a reference thermodynamic state needs to be specified.
- the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%
+ This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
- specifies the reference potential temperature profile (in $^{o}$C for
+ \textbf{tRef} specifies the reference potential temperature profile
- the ocean and $^{o}$K for the atmosphere) starting from the level
+ (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
- k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity
+ from the level k=1. Similarly, \textbf{sRef} specifies the reference
- profile (in ppt) for the ocean or the reference specific humidity profile
+ salinity profile (in ppt) for the ocean or the reference specific
- (in g/kg) for the atmosphere.
+ humidity profile (in g/kg) for the atmosphere.
- The form of the equation of state is controlled by the character variables
+ The form of the equation of state is controlled by the character
- \textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%
+ variables \textbf{buoyancyRelation} and \textbf{eosType}.
- buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and
+ \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
- needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In
+ needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
- this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.
+ 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
+ For the ocean, two forms of the equation of state are available:
- \textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial
+ linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
- approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\
+ approximation to the full nonlinear equation ( set
- }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the
+ \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
- thermal and haline expansion coefficients represented by the variables
+ case, you need to specify the thermal and haline expansion
- \textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%
+ coefficients represented by the variables \textbf{tAlpha}\textit{\
- ^{-1}$). For the nonlinear case, you need to generate a file of polynomial
+   }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
- coefficients called \textit{POLY3.COEFFS. }To do this, use the program
+ case, you need to generate a file of polynomial coefficients called
- \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is
+ \textit{POLY3.COEFFS}. To do this, use the program
- available in the same directory and you will need to edit the number and the
+ \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
- values of the vertical levels in \textit{knudsen2.f }so that they match
+ available in the same directory and you will need to edit the number
- those of your configuration). \textit{\ }
+ 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.
  \subsection{Momentum equations}
-Line 793 
 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).
  \subsection{Tracer equations}
-Line 888 
 This section covers the tracer equations
+Line 1198 
 This section covers the tracer equations
  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.
- \begin{itemize}
+ \item[forcing] \
- \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 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
- A combination of fluxes data and relaxation terms can be used for driving
+   data (in W/m$ ^{2}$) can be stored in the 2D binary file
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
+   \textbf{surfQfile}\textit{. }  Alternatively or in addition, the
- ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
+   forcing can be specified through a relaxation term. The SST data to
- Alternatively or in addition, the forcing can be specified through a
+   which the model surface temperatures are restored to are supposed to
- relaxation term. The SST data to which the model surface temperatures are
+   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
- restored to are supposed to be stored in the 2D binary file \textbf{%
+   }The corresponding relaxation time scale coefficient is set through
- thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
+   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
- is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
+   procedure applies for salinity with the variable names
- same procedure applies for salinity with the variable names \textbf{EmPmRfile%
+   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
- }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
+   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
- \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
+   and surface salinity (in ppt) data files and relaxation time scale
- files and relaxation time scale coefficient (in s), respectively. Also for
+   coefficient (in s), respectively. Also for salinity, if the CPP key
- salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
+   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
- boundary conditions are applied i.e. when computing the surface salinity
+   are applied i.e. when computing the surface salinity tendency, the
- tendency, the freshwater flux is multiplied by the model surface salinity
+   freshwater flux is multiplied by the model surface salinity instead
- instead of a constant salinity value.
+   of a constant salinity value.
- As for the other input files, the precision with which to read the data is
+   As for the other input files, the precision with which to read the
- controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
+   data is controlled by the variable \textbf{readBinaryPrec}.
- forcing can be applied as well following the same procedure used for the
+   Time-dependent, periodic forcing can be applied as well following
- wind forcing data (see above).
+   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}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have
+   non-zero value.
- \begin{itemize}
+ \end{description}
- \item dissipation
- \end{itemize}
- Lateral eddy diffusivities for temperature and salinity/specific humidity
- are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
- (in m$^{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.
  \subsection{Simulation controls}
-Line 982 
 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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