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

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-revision 1.11 by adcroft,
Tue Dec  4 18:08:34 2001 UTC
+revision 1.18 by edhill,
Thu Jan 29 19:22:35 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}
+ http://mitgcm.org/mailman/listinfo/mitgcm-support/
+ http://mitgcm.org/pipermail/mitgcm-support/
+ \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
+ Essentially all of the MITgcm web pages can be searched using a
+ popular web crawler such as Google or through our own search facility:
+ \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- news://mitgcm.org/mitgcm.support
+ http://mitgcm.org/htdig/
  \end{verbatim}
- A mail to the email list will reach all the developers and be archived
+ \begin{rawhtml} </A> \end{rawhtml}
- on the newsgroup. A users email list will be established at some time
+ %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
- in the future.
  \section{Obtaining the code}
  \label{sect:obtainingCode}
  MITgcm can be downloaded from our system by following
  the instructions below. As a courtesy we ask that you send e-mail to us at
- \begin{rawhtml} <A href=mailto:support@mitgcm.org> \end{rawhtml}
+ \begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
- support@mitgcm.org
+ 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:
-Line 72 
 provides an efficient and elegant way of
+Line 84 
 provides an efficient and elegant way of
  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/gcmpack
+ \end{verbatim}
+ in your .cshrc or .tcshrc file.  For bash or sh shells, put:
  \begin{verbatim}
- % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+ % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
  \end{verbatim}
+ in your .profile or .bashrc file.
- To start using CVS, register with the MITgcm CVS server using command:
+ To get MITgcm through CVS, first register with the MITgcm CVS server
+ using command:
  \begin{verbatim}
  % cvs login ( CVS password: cvsanon )
  \end{verbatim}
- You only need to do ``cvs login'' once.
+ You only need to do a ``cvs login'' once.
- To obtain the sources for release1 type:
+ To obtain the latest sources type:
+ \begin{verbatim}
+ % cvs co MITgcm
+ \end{verbatim}
+ or to get a specific release type:
  \begin{verbatim}
- % cvs co -d directory -P -r release1_beta1 MITgcm
+ % cvs co -P -r checkpoint52i_post  MITgcm
  \end{verbatim}
+ The MITgcm web site contains further directions concerning the source
+ code and CVS.  It also contains a web interface to our CVS archive so
+ that one may easily view the state of files, revisions, and other
+ development milestones:
+ \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
+ \begin{verbatim}
+ http://mitgcm.org/source_code.html
+ \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
- This creates a directory called \textit{directory}. If \textit{directory}
+ The checkout process creates a directory called \textit{MITgcm}. If
- exists this command updates your code based on the repository. Each
+ the directory \textit{MITgcm} exists this command updates your code
- directory in the source tree contains a directory \textit{CVS}. This
+ based on the repository. Each directory in the source tree contains a
- information is required by CVS to keep track of your file versions with
+ directory \textit{CVS}. This information is required by CVS to keep
- respect to the repository. Don't edit the files in \textit{CVS}!
+ track of your file versions with respect to the repository. Don't edit
- You can also use CVS to download code updates.  More extensive
+ the files in \textit{CVS}!  You can also use CVS to download code
- information on using CVS for maintaining MITgcm code can be found
+ updates.  More extensive information on using CVS for maintaining
- \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
+ MITgcm code can be found
+ \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}
  here
  \begin{rawhtml} </A> \end{rawhtml}
  .
-Line 106 
 here
+Line 140 
 here
  \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/
-Line 114 
 http://mitgcm.org/download/
+Line 148 
 http://mitgcm.org/download/
  \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}
- The MITgcm distribution comes with a set of twenty-four pre-configured
+ %% a set of twenty-four pre-configured numerical experiments
- numerical experiments. Some of these examples experiments are tests of
- individual parts of the model code, but many are fully fledged numerical
+ The MITgcm distribution comes with more than a dozen pre-configured
- simulations. A few of the examples are used for tutorial documentation
+ numerical experiments. Some of these example experiments are tests of
- in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. The other examples
+ individual parts of the model code, but many are fully fledged
- follow the same general structure as the tutorial examples. However,
+ numerical simulations. A few of the examples are used for tutorial
- they only include brief instructions in a text file called {\it README}.
+ documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
- The examples are located in subdirectories under
+ The other examples follow the same general structure as the tutorial
- the directory \textit{verification}. Each
+ examples. However, they only include brief instructions in a text file
- example is briefly described below.
+ called {\it README}.  The examples are located in subdirectories under
+ the directory \textit{verification}. Each example is briefly described
+ below.
  \subsection{Full list of model examples}
  \begin{enumerate}
  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
- free-surface). This experiment is described in detail in section
+   free-surface). This experiment is described in detail in section
- \ref{sect:eg-baro}.
+   \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{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. This experiment is described in detail in section
+   climatological forcing. This experiment is described in detail in
- \ref{sect:eg-global}.
+   section \ref{sect:eg-global}.
- \item \textit{exp4} - Flow over a Gaussian bump in open-water or channel
+ \item \textit{exp4} - Flow over a Gaussian bump in open-water or
- with open boundaries.
+   channel with open boundaries.
- \item \textit{exp5} - Inhomogenously forced ocean convection in a doubly
+ \item \textit{exp5} - Inhomogenously forced ocean convection in a
- periodic box.
+   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
- 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. Global
+ \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
- 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, equatorial Slice configuration.
+   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
-D (X-Z).
  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
- physics. 3D Equatorial Channel configuration.
+   physics. 3D Equatorial Channel configuration.
  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
- Global configuration, on latitude longitude grid with 128x64x5 grid points
+   Global configuration, on latitude longitude grid with 128x64x5 grid
- ($2.8^\circ{\rm degree}$ resolution).
+   points ($2.8^\circ{\rm degree}$ resolution).
- \item \textit{adjustment.128x64x1} Barotropic adjustment
+ \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
- problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution).
+   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
+     degree}$ resolution).
- \item \textit{adjustment.cs-32x32x1}
- Barotropic adjustment
+ \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
- problem on cube sphere grid with 32x32 points per face ( roughly
+   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
- $2.8^\circ{\rm degree}$ resolution).
+     degree}$ resolution).
  \item \textit{advect\_cs} Two-dimensional passive advection test on
- cube sphere grid.
+   cube sphere grid.
- \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection
+ \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
- test on Cartesian grid.
+   advection test on Cartesian grid.
- \item \textit{advect\_yz} Two-dimensional (vertical 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{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
+ \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
- GM, flux boundary conditions and poles.
+   boundary conditions and poles.
- \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere
+ \item \textit{global\_ocean\_pressure} Global circulation in pressure
- grid.
+   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.
  \end{enumerate}
-Line 278 
 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}
+   \begin{itemize}
- \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the
+   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
- ``execution environment'' part of the code. The default version is located
+     the ``execution environment'' part of the code. The default
- in \textit{eesupp/inc}.
+     version is located in \textit{eesupp/inc}.
- \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
+   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
- ``numerical model'' part of the code. The default version is located in
+     the ``numerical model'' part of the code. The default version is
- \textit{model/inc}.
+     located in \textit{model/inc}.
- \item \textit{code/SIZE.h}: declares size of underlying computational grid.
+   \item \textit{code/SIZE.h}: declares size of underlying
- The default version is located in \textit{model/inc}.
+     computational grid.  The default version is located in
+     \textit{model/inc}.
+   \end{itemize}
+   In addition, other include files and subroutines might be present in
+   \textit{code} depending on the particular experiment. See Section 2
+   for more details.
+ \item \textit{input}: contains the input data files required to run
+   the example. At a minimum, the \textit{input} directory contains the
+   following files:
+   \begin{itemize}
+   \item \textit{input/data}: this file, written as a namelist,
+     specifies the main parameters for the experiment.
+   \item \textit{input/data.pkg}: contains parameters relative to the
+     packages used in the experiment.
+   \item \textit{input/eedata}: this file contains ``execution
+     environment'' data. At present, this consists of a specification
+     of the number of threads to use in $X$ and $Y$ under multithreaded
+     execution.
+   \end{itemize}
+   In addition, you will also find in this directory the forcing and
+   topography files as well as the files describing the initial state
+   of the experiment.  This varies from experiment to experiment. See
+   section 2 for more details.
+ \item \textit{results}: this directory contains the output file
+   \textit{output.txt} produced by the simulation example. This file is
+   useful for comparison with your own output when you run the
+   experiment.
  \end{itemize}
- In addition, other include files and subroutines might be present in \textit{%
+ Once you have chosen the example you want to run, you are ready to
- code} depending on the particular experiment. See section 2 for more details.
+ compile the code.
- \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}
-Line 330 
 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
- dependencies. 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 dependencies 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 dependencies:
+ 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 385 
 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 424 
 within {\em verification/exp2/}:
+Line 575 
 within {\em verification/exp2/}:
  % cd verification/exp2
  % mkdir build
  % cd build
- % ../../../tools/genmake -mods=../code
+ % ../../../tools/genmake2 -mods=../code
  % make depend
  % make
  \end{verbatim}
-Line 446 
 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 454 
 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 470 
 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 481 
 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}
- \item -platform=machine
+ \begin{center}
+   MITgcm-support@mitgcm.org
- specifies the platform for which you want the makefile. In general, you
+ \end{center}
- won't need this option. \textit{genmake} will select the right machine for
+ \begin{rawhtml} </A> \end{rawhtml}
- you (the one you're working on!). However, this option is useful if you have
+ mailing list.
- 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
+ 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.
- this is used when you want to run the model in parallel processing mode
+ \end{description}
- 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 607 
 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 696 
 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{Configuration and setup}
- The CPP keys relative to the ''numerical model'' part of the code are all
+ The CPP keys relative to the ``numerical model'' part of the code are
- defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
+ all defined and set in the file \textit{CPP\_OPTIONS.h }in the
- model/inc }or in one of the \textit{code }directories of the case study
+ directory \textit{ model/inc }or in one of the \textit{code
- experiments under \textit{verification.} The model parameters are defined
+ }directories of the case study experiments under
- and declared in the file \textit{model/inc/PARAMS.h }and their default
+ \textit{verification.} The model parameters are defined and declared
- values are set in the routine \textit{model/src/set\_defaults.F. }The
+ in the file \textit{model/inc/PARAMS.h }and their default values are
- default values can be modified in the namelist file \textit{data }which
+ set in the routine \textit{model/src/set\_defaults.F. }The default
- needs to be located in the directory where you will run the model. The
+ values can be modified in the namelist file \textit{data }which needs
- parameters are initialized in the routine \textit{model/src/ini\_parms.F}.
+ to be located in the directory where you will run the model. The
- Look at this routine to see in what part of the namelist the parameters are
+ parameters are initialized in the routine
- located.
+ \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
+ part of the namelist the parameters are located.
- In what follows the parameters are grouped into categories related to the
- computational domain, the equations solved in the model, and the simulation
+ In what follows the parameters are grouped into categories related to
- controls.
+ 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, and r directions are represented
- The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
+   by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr}
- represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
+   respectively which are declared and set in the file
- and \textbf{Nr}\textit{\ }respectively which are declared and set in the
+   \textit{model/inc/SIZE.h}.  (Again, this assumes a mono-processor
- file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor
+   calculation. For multiprocessor calculations see the section on
- calculation. For multiprocessor calculations see section on parallel
+   parallel implementation.)
- implementation.)
+ \item[grid] \
- \begin{itemize}
- \item grid
+   Three different grids are available: cartesian, spherical polar, and
- \end{itemize}
+   curvilinear (which includes the cubed sphere). The grid is set
+   through the logical variables \textbf{usingCartesianGrid},
- Three different grids are available: cartesian, spherical polar, and
+   \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
- curvilinear (including the cubed sphere). The grid is set through the
+   In the case of spherical and curvilinear grids, the southern
- logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
+   boundary is defined through the variable \textbf{phiMin} which
- usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
+   corresponds to the latitude of the southern most cell face (in
- usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
+   degrees). The resolution along the x and y directions is controlled
- grids, the southern boundary is defined through the variable \textbf{phiMin}%
+   by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the
- \textit{\ }which corresponds to the latitude of the southern most cell face
+   case of a cartesian grid, in degrees otherwise).  The vertical grid
- (in degrees). The resolution along the x and y directions is controlled by
+   spacing is set through the 1D array \textbf{delz} for the ocean (in
- the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters
+   meters) or \textbf{delp} for the atmosphere (in Pa).  The variable
- in the case of a cartesian grid, in degrees otherwise). The vertical grid
+   \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level
- spacing is set through the 1D array \textbf{delz }for the ocean (in meters)
+   in ``R'' coordinate. This is typically set to 0m for the ocean
- or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%
+   (default value) and 10$^{5}$Pa for the atmosphere. For the
- Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''
+   atmosphere, also set the logical variable \textbf{groundAtK1} to
- coordinate. This is typically set to 0m for the ocean (default value) and 10$%
+   \texttt{'.TRUE.'} which puts the first level (k=1) at the lower
- ^{5}$Pa for the atmosphere. For the atmosphere, also set the logical
+   boundary (ground).
- variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level
- (k=1) at the lower boundary (ground).
+   For the cartesian grid case, the Coriolis parameter $f$ is set
+   through the variables \textbf{f0} and \textbf{beta} which correspond
- For the cartesian grid case, the Coriolis parameter $f$ is set through the
+   to the reference Coriolis parameter (in s$^{-1}$) and
- variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond
+   $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively.
- to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%
+   If \textbf{beta } is set to a nonzero value, \textbf{f0} is the
- \partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%
+   value of $f$ at the southern edge of the domain.
- is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
- southern edge of the domain.
+ \item[topography - full and partial cells] \
- \begin{itemize}
+   The domain bathymetry is read from a file that contains a 2D (x,y)
- \item topography - full and partial cells
+   map of depths (in m) for the ocean or pressures (in Pa) for the
- \end{itemize}
+   atmosphere. The file name is represented by the variable
+   \textbf{bathyFile}. The file is assumed to contain binary numbers
- The domain bathymetry is read from a file that contains a 2D (x,y) map of
+   giving the depth (pressure) of the model at each grid cell, ordered
- depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The
+   with the x coordinate varying fastest. The points are ordered from
- file name is represented by the variable \textbf{bathyFile}\textit{. }The
+   low coordinate to high coordinate for both axes. The model code
- file is assumed to contain binary numbers giving the depth (pressure) of the
+   applies without modification to enclosed, periodic, and double
- model at each grid cell, ordered with the x coordinate varying fastest. The
+   periodic domains. Periodicity is assumed by default and is
- points are ordered from low coordinate to high coordinate for both axes. The
+   suppressed by setting the depths to 0m for the cells at the limits
- model code applies without modification to enclosed, periodic, and double
+   of the computational domain (note: not sure this is the case for the
- periodic domains. Periodicity is assumed by default and is suppressed by
+   atmosphere). The precision with which to read the binary data is
- setting the depths to 0m for the cells at the limits of the computational
+   controlled by the integer variable \textbf{readBinaryPrec} which can
- domain (note: not sure this is the case for the atmosphere). The precision
+   take the value \texttt{32} (single precision) or \texttt{64} (double
- with which to read the binary data is controlled by the integer variable
+   precision). See the matlab program \textit{gendata.m} in the
- \textbf{readBinaryPrec }which can take the value \texttt{32} (single
+   \textit{input} directories under \textit{verification} to see how
- precision) or \texttt{64} (double precision). See the matlab program \textit{%
+   the bathymetry files are generated for the case study experiments.
- gendata.m }in the \textit{input }directories under \textit{verification }to
- see how the bathymetry files are generated for the case study experiments.
+   To use the partial cell capability, the variable \textbf{hFacMin}
+   needs to be set to a value between 0 and 1 (it is set to 1 by
- To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%
+   default) corresponding to the minimum fractional size of the cell.
- needs to be set to a value between 0 and 1 (it is set to 1 by default)
+   For example if the bottom cell is 500m thick and \textbf{hFacMin} is
- corresponding to the minimum fractional size of the cell. For example if the
+   set to 0.1, the actual thickness of the cell (i.e. used in the code)
- bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the
+   can cover a range of discrete values 50m apart from 50m to 500m
- actual thickness of the cell (i.e. used in the code) can cover a range of
+   depending on the value of the bottom depth (in \textbf{bathyFile})
- discrete values 50m apart from 50m to 500m depending on the value of the
+   at this point.
- bottom depth (in \textbf{bathyFile}) at this point.
+   Note that the bottom depths (or pressures) need not coincide with
- Note that the bottom depths (or pressures) need not coincide with the models
+   the models levels as deduced from \textbf{delz} or \textbf{delp}.
- levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%
+   The model will interpolate the numbers in \textbf{bathyFile} so that
- \textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
+   they match the levels obtained from \textbf{delz} or \textbf{delp}
- \textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
+   and \textbf{hFacMin}.
- \ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
+   (Note: the atmospheric case is a bit more complicated than what is
- (Note: the atmospheric case is a bit more complicated than what is written
+   written here I think. To come soon...)
- 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.'}.
- \begin{itemize}
+ \end{description}
- \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 \textbf{eosType} to
- }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the
+ \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$%
+ \textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For
- ^{-1}$). For the nonlinear case, you need to generate a file of polynomial
+ the nonlinear case, you need to generate a file of polynomial
- coefficients called \textit{POLY3.COEFFS. }To do this, use the program
+ coefficients called \textit{POLY3.COEFFS}. To do this, use the program
- \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is
+ \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
+ available in the same directory and you will need to edit the number
- values of the vertical levels in \textit{knudsen2.f }so that they match
+ and the values of the vertical levels in \textit{knudsen2.f} so that
- those of your configuration). \textit{\ }
+ they match those of your configuration).
+ There there are also higher polynomials for the equation of state:
+ \begin{description}
+ \item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of
+   Fofonoff and Millard \cite{fofonoff83}. This equation of state
+   assumes in-situ temperature, which is not a model variable; {\em its
+     use is therefore discouraged, and it is only listed for
+     completeness}.
+ \item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and
+   McDougall \cite{jackett95}, which uses the model variable potential
+   temperature as input. The \texttt{'Z'} indicates that this equation
+   of state uses a horizontally and temporally constant pressure
+   $p_{0}=-g\rho_{0}z$.
+ \item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and
+   McDougall \cite{jackett95}, which uses the model variable potential
+   temperature as input. The \texttt{'P'} indicates that this equation
+   of state uses the actual hydrostatic pressure of the last time
+   step. Lagging the pressure in this way requires an additional pickup
+   file for restarts.
+ \item[\texttt{'MDJWF'}:] The new, more accurate and less expensive
+   equation of state by McDougall et~al. \cite{mcdougall03}. It also
+   requires lagging the pressure and therefore an additional pickup
+   file for restarts.
+ \end{description}
+ For none of these options an reference profile of temperature or
+ salinity is required.
  \subsection{Momentum equations}
- In this section, we only focus for now on the parameters that you are likely
+ In this section, we only focus for now on the parameters that you are
- to change, i.e. the ones relative to forcing and dissipation for example.
+ likely to change, i.e. the ones relative to forcing and dissipation
- The details relevant to the vector-invariant form of the equations and the
+ for example.  The details relevant to the vector-invariant form of the
- various advection schemes are not covered for the moment. We assume that you
+ equations and the various advection schemes are not covered for the
- use the standard form of the momentum equations (i.e. the flux-form) with
+ moment. We assume that you use the standard form of the momentum
- the default advection scheme. Also, there are a few logical variables that
+ equations (i.e. the flux-form) with the default advection scheme.
- allow you to turn on/off various terms in the momentum equation. These
+ Also, there are a few logical variables that allow you to turn on/off
- variables are called \textbf{momViscosity, momAdvection, momForcing,
+ various terms in the momentum equation. These variables are called
- useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }%
+ \textbf{momViscosity, momAdvection, momForcing, useCoriolis,
- \textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here.
+   momPressureForcing, momStepping} and \textbf{metricTerms }and are
- Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
+ assumed to be set to \texttt{'.TRUE.'} here.  Look at the file
- these variables.
+ \textit{model/inc/PARAMS.h }for a precise definition of these
+ variables.
+ \begin{description}
+ \item[initialization] \
+   The velocity components are initialized to 0 unless the simulation
+   is starting from a pickup file (see section on simulation control
+   parameters).
+ \item[forcing] \
+   This section only applies to the ocean. You need to generate
+   wind-stress data into two files \textbf{zonalWindFile} and
+   \textbf{meridWindFile} corresponding to the zonal and meridional
+   components of the wind stress, respectively (if you want the stress
+   to be along the direction of only one of the model horizontal axes,
+   you only need to generate one file). The format of the files is
+   similar to the bathymetry file. The zonal (meridional) stress data
+   are assumed to be in Pa and located at U-points (V-points). As for
+   the bathymetry, the precision with which to read the binary data is
+   controlled by the variable \textbf{readBinaryPrec}.  See the matlab
+   program \textit{gendata.m} in the \textit{input} directories under
+   \textit{verification} to see how simple analytical wind forcing data
+   are generated for the case study experiments.
+   There is also the possibility of prescribing time-dependent periodic
+   forcing. To do this, concatenate the successive time records into a
+   single file (for each stress component) ordered in a (x,y,t) fashion
+   and set the following variables: \textbf{periodicExternalForcing }to
+   \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)
+   of which the forcing varies (typically 1 month), and
+   \textbf{externForcingCycle} to the repeat time (in s) of the forcing
+   (typically 1 year -- note: \textbf{ externForcingCycle} must be a
+   multiple of \textbf{externForcingPeriod}).  With these variables set
+   up, the model will interpolate the forcing linearly at each
+   iteration.
+ \item[dissipation] \
+   The lateral eddy viscosity coefficient is specified through the
+   variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy
+   viscosity coefficient is specified through the variable
+   \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and
+   \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The
+   vertical diffusive fluxes can be computed implicitly by setting the
+   logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.
+   In addition, biharmonic mixing can be added as well through the
+   variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar
+   grid, you might also need to set the variable \textbf{cosPower}
+   which is set to 0 by default and which represents the power of
+   cosine of latitude to multiply viscosity. Slip or no-slip conditions
+   at lateral and bottom boundaries are specified through the logical
+   variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If
+   set to \texttt{'.FALSE.'}, free-slip boundary conditions are
+   applied. If no-slip boundary conditions are applied at the bottom, a
+   bottom drag can be applied as well. Two forms are available: linear
+   (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
+   quadratic (set the variable \textbf{bottomDragQuadratic} in
+   m$^{-1}$).
+   The Fourier and Shapiro filters are described elsewhere.
+ \item[C-D scheme] \
+   If you run at a sufficiently coarse resolution, you will need the
+   C-D scheme for the computation of the Coriolis terms. The
+   variable\textbf{\ tauCD}, which represents the C-D scheme coupling
+   timescale (in s) needs to be set.
+ \item[calculation of pressure/geopotential] \
+   First, to run a non-hydrostatic ocean simulation, set the logical
+   variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure
+   field is then inverted through a 3D elliptic equation. (Note: this
+   capability is not available for the atmosphere yet.) By default, a
+   hydrostatic simulation is assumed and a 2D elliptic equation is used
+   to invert the pressure field. The parameters controlling the
+   behaviour of the elliptic solvers are the variables
+   \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for
+   the 2D case and \textbf{cg3dMaxIters} and
+   \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to
+   alter the default values (are we sure of this?).
+   For the calculation of the surface pressure (for the ocean) or
+   surface geopotential (for the atmosphere) you need to set the
+   logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}
+   (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}
+   depending on how you want to deal with the ocean upper or atmosphere
+   lower boundary).
- \begin{itemize}
+ \end{description}
- \item initialization
- \end{itemize}
- The velocity components are initialized to 0 unless the simulation is
- starting from a pickup file (see section on simulation control parameters).
- \begin{itemize}
- \item forcing
- \end{itemize}
- This section only applies to the ocean. You need to generate wind-stress
- data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
- meridWindFile }corresponding to the zonal and meridional components of the
- wind stress, respectively (if you want the stress to be along the direction
- of only one of the model horizontal axes, you only need to generate one
- file). The format of the files is similar to the bathymetry file. The zonal
- (meridional) stress data are assumed to be in Pa and located at U-points
- (V-points). As for the bathymetry, the precision with which to read the
- binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
- See the matlab program \textit{gendata.m }in the \textit{input }directories
- under \textit{verification }to see how simple analytical wind forcing data
- are generated for the case study experiments.
- There is also the possibility of prescribing time-dependent periodic
- forcing. To do this, concatenate the successive time records into a single
- file (for each stress component) ordered in a (x, y, t) fashion and set the
- following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
- \textbf{externForcingPeriod }to the period (in s) of which the forcing
- varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
- time (in s) of the forcing (typically 1 year -- note: \textbf{%
- externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
- With these variables set up, the model will interpolate the forcing linearly
- at each iteration.
- \begin{itemize}
- \item dissipation
- \end{itemize}
- The lateral eddy viscosity coefficient is specified through the variable
- \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
- coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
- ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
- for the atmosphere. The vertical diffusive fluxes can be computed implicitly
- by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
- .'. In addition, biharmonic mixing can be added as well through the variable
- \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
- you might also need to set the variable \textbf{cosPower} which is set to 0
- by default and which represents the power of cosine of latitude to multiply
- viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
- specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
- and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
- boundary conditions are applied. If no-slip boundary conditions are applied
- at the bottom, a bottom drag can be applied as well. Two forms are
- available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
- ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
- \ }in m$^{-1}$).
- The Fourier and Shapiro filters are described elsewhere.
- \begin{itemize}
- \item C-D scheme
- \end{itemize}
- If you run at a sufficiently coarse resolution, you will need the C-D scheme
- for the computation of the Coriolis terms. The variable\textbf{\ tauCD},
- which represents the C-D scheme coupling timescale (in s) needs to be set.
- \begin{itemize}
- \item calculation of pressure/geopotential
- \end{itemize}
- First, to run a non-hydrostatic ocean simulation, set the logical variable
- \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then
- inverted through a 3D elliptic equation. (Note: this capability is not
- available for the atmosphere yet.) By default, a hydrostatic simulation is
- assumed and a 2D elliptic equation is used to invert the pressure field. The
- parameters controlling the behaviour of the elliptic solvers are the
- variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }%
- for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{%
- cg3dTargetResidual }for the 3D case. You probably won't need to alter the
- default values (are we sure of this?).
- For the calculation of the surface pressure (for the ocean) or surface
- geopotential (for the atmosphere) you need to set the logical variables
- \textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.%
- \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
- want to deal with the ocean upper or atmosphere lower boundary).
  \subsection{Tracer equations}
- This section covers the tracer equations i.e. the potential temperature
+ This section covers the tracer equations i.e. the potential
- equation and the salinity (for the ocean) or specific humidity (for the
+ temperature equation and the salinity (for the ocean) or specific
- atmosphere) equation. As for the momentum equations, we only describe for
+ humidity (for the atmosphere) equation. As for the momentum equations,
- now the parameters that you are likely to change. The logical variables
+ we only describe for now the parameters that you are likely to change.
- \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%
+ The logical variables \textbf{tempDiffusion} \textbf{tempAdvection}
- tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off
+ \textbf{tempForcing}, and \textbf{tempStepping} allow you to turn
- terms in the temperature equation (same thing for salinity or specific
+ on/off terms in the temperature equation (same thing for salinity or
- humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{%
+ specific humidity with variables \textbf{saltDiffusion},
- saltAdvection}\textit{\ }etc). These variables are all assumed here to be
+ \textbf{saltAdvection} etc.). These variables are all assumed here to
- set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a
+ be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h}
- precise definition.
+ for a precise definition.
+ \begin{description}
+ \item[initialization] \
+   The initial tracer data can be contained in the binary files
+   \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files
+   should contain 3D data ordered in an (x,y,r) fashion with k=1 as the
+   first vertical level.  If no file names are provided, the tracers
+   are then initialized with the values of \textbf{tRef} and
+   \textbf{sRef} mentioned above (in the equation of state section). In
+   this case, the initial tracer data are uniform in x and y for each
+   depth level.
+ \item[forcing] \
+   This part is more relevant for the ocean, the procedure for the
+   atmosphere not being completely stabilized at the moment.
+   A combination of fluxes data and relaxation terms can be used for
+   driving the tracer equations.  For potential temperature, heat flux
+   data (in W/m$ ^{2}$) can be stored in the 2D binary file
+   \textbf{surfQfile}.  Alternatively or in addition, the forcing can
+   be specified through a relaxation term. The SST data to which the
+   model surface temperatures are restored to are supposed to be stored
+   in the 2D binary file \textbf{thetaClimFile}. The corresponding
+   relaxation time scale coefficient is set through the variable
+   \textbf{tauThetaClimRelax} (in s). The same procedure applies for
+   salinity with the variable names \textbf{EmPmRfile},
+   \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater
+   flux (in m/s) and surface salinity (in ppt) data files and
+   relaxation time scale coefficient (in s), respectively. Also for
+   salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on,
+   natural boundary conditions are applied i.e. when computing the
+   surface salinity tendency, the freshwater flux is multiplied by the
+   model surface salinity instead of a constant salinity value.
+   As for the other input files, the precision with which to read the
+   data is controlled by the variable \textbf{readBinaryPrec}.
+   Time-dependent, periodic forcing can be applied as well following
+   the same procedure used for the wind forcing data (see above).
+ \item[dissipation] \
+   Lateral eddy diffusivities for temperature and salinity/specific
+   humidity are specified through the variables \textbf{diffKhT} and
+   \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are
+   specified through the variables \textbf{diffKzT} and
+   \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT
+   }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The
+   vertical diffusive fluxes can be computed implicitly by setting the
+   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}.
+   In addition, biharmonic diffusivities can be specified as well
+   through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in
+   m$^{4}$/s). Note that the cosine power scaling (specified through
+   \textbf{cosPower}---see the momentum equations section) is applied to
+   the tracer diffusivities (Laplacian and biharmonic) as well. The
+   Gent and McWilliams parameterization for oceanic tracers is
+   described in the package section. Finally, note that tracers can be
+   also subject to Fourier and Shapiro filtering (see the corresponding
+   section on these filters).
+ \item[ocean convection] \
+   Two options are available to parameterize ocean convection: one is
+   to use the convective adjustment scheme. In this case, you need to
+   set the variable \textbf{cadjFreq}, which represents the frequency
+   (in s) with which the adjustment algorithm is called, to a non-zero
+   value (if set to a negative value by the user, the model will set it
+   to the tracer time step). The other option is to parameterize
+   convection with implicit vertical diffusion. To do this, set the
+   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}
+   and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero
+   value.
- \begin{itemize}
+ \end{description}
- \item initialization
- \end{itemize}
- The initial tracer data can be contained in the binary files \textbf{%
- hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D
- data ordered in an (x, y, r) fashion with k=1 as the first vertical level.
- If no file names are provided, the tracers are then initialized with the
- values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation
- of state section). In this case, the initial tracer data are uniform in x
- and y for each depth level.
- \begin{itemize}
- \item forcing
- \end{itemize}
- This part is more relevant for the ocean, the procedure for the atmosphere
- not being completely stabilized at the moment.
- A combination of fluxes data and relaxation terms can be used for driving
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
- ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
- Alternatively or in addition, the forcing can be specified through a
- relaxation term. The SST data to which the model surface temperatures are
- restored to are supposed to be stored in the 2D binary file \textbf{%
- thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
- is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
- same procedure applies for salinity with the variable names \textbf{EmPmRfile%
- }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
- \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
- files and relaxation time scale coefficient (in s), respectively. Also for
- salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
- boundary conditions are applied i.e. when computing the surface salinity
- tendency, the freshwater flux is multiplied by the model surface salinity
- instead of a constant salinity value.
- As for the other input files, the precision with which to read the data is
- controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
- forcing can be applied as well following the same procedure used for the
- wind forcing data (see above).
- \begin{itemize}
- \item dissipation
- \end{itemize}
- Lateral eddy diffusivities for temperature and salinity/specific humidity
- are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
- (in m$^{2}$/s). Vertical eddy diffusivities are specified through the
- variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean
- and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the
- atmosphere. The vertical diffusive fluxes can be computed implicitly by
- setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .'. In addition, biharmonic diffusivities can be specified as well through
- the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note
- that the cosine power scaling (specified through \textbf{cosPower }- see the
- momentum equations section) is applied to the tracer diffusivities
- (Laplacian and biharmonic) as well. The Gent and McWilliams parameterization
- for oceanic tracers is described in the package section. Finally, note that
- tracers can be also subject to Fourier and Shapiro filtering (see the
- corresponding section on these filters).
- \begin{itemize}
- \item ocean convection
- \end{itemize}
- Two options are available to parameterize ocean convection: one is to use
- the convective adjustment scheme. In this case, you need to set the variable
- \textbf{cadjFreq}, which represents the frequency (in s) with which the
- adjustment algorithm is called, to a non-zero value (if set to a negative
- value by the user, the model will set it to the tracer time step). The other
- option is to parameterize convection with implicit vertical diffusion. To do
- this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) you
- wish the tracer vertical diffusivities to have when mixing tracers
- vertically due to static instabilities. Note that \textbf{cadjFreq }and
- \textbf{ivdc\_kappa }can not both have non-zero value.
  \subsection{Simulation controls}
- The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)
+ The model ''clock'' is defined by the variable \textbf{deltaTClock}
- which determines the IO frequencies and is used in tagging output.
+ (in s) which determines the IO frequencies and is used in tagging
- Typically, you will set it to the tracer time step for accelerated runs
+ output.  Typically, you will set it to the tracer time step for
- (otherwise it is simply set to the default time step \textbf{deltaT}).
+ accelerated runs (otherwise it is simply set to the default time step
- Frequency of checkpointing and dumping of the model state are referenced to
+ \textbf{deltaT}).  Frequency of checkpointing and dumping of the model
- this clock (see below).
+ 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. The end of a simulation is set through the
- of a simulation is set through the real variable \textbf{endTime }(in s).
+   real variable \textbf{endTime} (in s).  Alternatively, you can
- Alternatively, you can specify instead the number of time steps to execute
+   specify instead the number of time steps to execute through the
- through the integer variable \textbf{nTimeSteps}.
+   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 output
- with which the instantaneous state of the model is saved. \textbf{chkPtFreq }%
+   frequency of rolling and permanent checkpoint files, respectively.
- and \textbf{pchkPtFreq }control the output frequency of rolling and
+   See section 1.5.1 Output files for the definition of model state and
- permanent checkpoint files, respectively. See section 1.5.1 Output files for the
+   checkpoint files. In addition, time-averaged fields can be written
- definition of model state and checkpoint files. In addition, time-averaged
+   out by setting the variable \textbf{taveFreq} (in s).  The precision
- fields can be written out by setting the variable \textbf{taveFreq} (in s).
+   with which to write the binary data is controlled by the integer
- The precision with which to write the binary data is controlled by the
+   variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or
- integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
+   \texttt{64}).
-}).
+ \end{description}
+ %%% Local Variables:
+ %%% mode: latex
+ %%% TeX-master: t
+ %%% End:

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