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

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-revision 1.16 by edhill,
Thu Jan 29 03:02:33 2004 UTC
+revision 1.19 by edhill,
Mon Feb 16 02:27:33 2004 UTC
 Line 79 
 provide easy support for maintenance upd
  \end{enumerate}
+ \subsubsection{Checkout from CVS}
+ \label{sect:cvs_checkout}
  If CVS is available on your system, we strongly encourage you to use it. CVS
  provides an efficient and elegant way of organizing your code and keeping
  track of your changes. If CVS is not available on your machine, you can also
-Line 115 
 The MITgcm web site contains further dir
+Line 118 
 The MITgcm web site contains further dir
  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{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- http://mitgcm.org/source\_code.html
+ http://mitgcm.org/source_code.html
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
+ As a convenience, the MITgcm CVS server contains aliases which are
+ named subsets of the codebase.  These aliases can be especially
+ helpful when used over slow internet connections or on machines with
+ restricted storage space.  Table \ref{tab:cvsModules} contains a list
+ of CVS aliases
+ \begin{table}[htb]
+   \centering
+   \begin{tabular}[htb]{|lp{3.25in}|}\hline
+     \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
+     \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
+     \texttt{MITgcm\_verif\_basic}
+     &  Source code plus a small set of the verification examples
+     (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
+     \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
+     \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
+     \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
+     \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
+     verification examples. \\\hline
+   \end{tabular}
+   \caption{MITgcm CVS Modules}
+   \label{tab:cvsModules}
+ \end{table}
  The checkout process creates a directory called \textit{MITgcm}. If
  the directory \textit{MITgcm} exists this command updates your code
-Line 130 
 track of your file versions with respect
+Line 155 
 track of your file versions with respect
  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}
+ \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}
  here
  \begin{rawhtml} </A> \end{rawhtml}
  .
+ It is important to note that the CVS aliases in Table
+ \ref{tab:cvsModules} cannot be used in conjunction with the CVS
+ \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
+ they create can be changed to a different name following the check-out:
+ \begin{verbatim}
+    %  cvs co MITgcm_verif_basic
+    %  mv MITgcm MITgcm_verif_basic
+ \end{verbatim}
- \paragraph*{Conventional download method}
+ \subsubsection{Conventional download method}
  \label{sect:conventionalDownload}
  If you do not have CVS on your system, you can download the model as a
-Line 150 
 The tar file still contains CVS informat
+Line 183 
 The tar file still contains CVS informat
  delete; even if you do not use CVS yourself the information can help
  us if you should need to send us your copy of the code.  If a recent
  tar file does not exist, then please contact the developers through
- the MITgcm-support list.
+ 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}
+ \subsubsection{Upgrading from an earlier version}
  If you already have an earlier version of the code you can ``upgrade''
  your copy instead of downloading the entire repository again. First,
-Line 178 
 If the list of conflicts scrolled off th
+Line 215 
 If the list of conflicts scrolled off th
  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,
-Line 185 
 indicated in the code by the delimites `
+Line 223 
 indicated in the code by the delimites `
       & 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.
-Line 225 
 model code. The execution environment su
+Line 266 
 model code. The execution environment su
  \textit{eesupp} directory. The grid point model code is held under the
  \textit{model} directory. Code execution actually starts in the
  \textit{eesupp} routines and not in the \textit{model} routines. For
- this reason the top-level
+ this reason the top-level \textit{MAIN.F} is in the
- \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
+ \textit{eesupp/src} directory. In general, end-users should not need
- end-users should not need to worry about this level. The top-level routine
+ to worry about this level. The top-level routine for the numerical
- for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
+ part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
- }. Here is a brief description of the directory structure of the model under
+ a brief description of the directory structure of the model under the
- the root tree (a detailed description is given in section 3: Code structure).
+ 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{genmake2} 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}
-Line 295 
 below.
+Line 343 
 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
    \ref{sect:eg-baro}.
-Line 420 
 Each example directory has the following
+Line 469 
 Each example directory has the following
      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
+   In addition, you will also find in this directory the forcing and
- topography files as well as the files describing the initial state of
+   topography files as well as the files describing the initial state
- the experiment.  This varies from experiment to experiment. See
+   of the experiment.  This varies from experiment to experiment. See
- section 2 for more details.
+   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
-Line 432 
 section 2 for more details.
+Line 481 
 section 2 for more details.
    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 474 
 mimic their syntax.
+Line 523 
 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 MITgcm-support list.
+ 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}
-Line 707 
 obtained from:
+Line 760 
 obtained from:
  The most important command-line options are:
  \begin{description}
- \item[--optfile=/PATH/FILENAME] specifies the optfile that should be
+ \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
-   used for a particular build.
+   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
-Line 719 
 The most important command-line options
+Line 772 
 The most important command-line options
    the user's path.  When these three items have been identified,
    genmake2 will try to find an optfile that has a matching name.
- \item[--pdepend=/PATH/FILENAME] specifies the dependency file used for
+ \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
-   packages.
+   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
-Line 731 
 The most important command-line options
+Line 784 
 The most important command-line options
    assumed that the two packages are compatible and will function
    either with or without each other.
- \item[--pdefault='PKG1 PKG2 PKG3 ...'] specifies the default set of
+ \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-   packages to be used.
+   set of packages to be used.
    If not set, the default package list will be read from {\em
      pkg/pkg\_default}
- \item[--adof=/path/to/file] specifies the "adjoint" or automatic
+ \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
-   differentiation options file to be used.  The file is analogous to
+   automatic differentiation options file to be used.  The file is
-   the ``optfile'' defined above but it specifies information for the
+   analogous to the ``optfile'' defined above but it specifies
-   AD build process.
+   information for the AD build process.
    The default file is located in {\em
      tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
-Line 749 
 The most important command-line options
+Line 802 
 The most important command-line options
    "STAF" compiler.  As with any compilers, it is helpful to have their
    directories listed in your {\tt \$PATH} environment variable.
- \item[--mods='DIR1 DIR2 DIR3 ...'] specifies a list of directories
+ \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
-   containing ``modifications''.  These directories contain files with
+   directories containing ``modifications''.  These directories contain
-   names that may (or may not) exist in the main MITgcm source tree but
+   files with names that may (or may not) exist in the main MITgcm
-   will be overridden by any identically-named sources within the
+   source tree but will be overridden by any identically-named sources
-   ``MODS'' directories.
+   within the ``MODS'' directories.
    The order of precedence for this "name-hiding" is as follows:
    \begin{itemize}
-Line 766 
 The most important command-line options
+Line 819 
 The most important command-line options
      ``-standarddirs'' option)
    \end{itemize}
- \item[--make=/path/to/gmake] Due to the poor handling of soft-links and
+ \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
-   other bugs common with the \texttt{make} versions provided by
+   soft-links and other bugs common with the \texttt{make} versions
-   commercial Unix vendors, GNU \texttt{make} (sometimes called
+   provided by commercial Unix vendors, GNU \texttt{make} (sometimes
-   \texttt{gmake}) should be preferred.  This option provides a means
+   called \texttt{gmake}) should be preferred.  This option provides a
-   for specifying the make executable to be used.
+   means for specifying the make executable to be used.
  \end{description}
-Line 799 
 normally re-direct the {\em stdout} stre
+Line 852 
 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 888 
 Some examples of reading and visualizing
+Line 941 
 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}
-Line 1019 
 humidity profile (in g/kg) for the atmos
+Line 1074 
 humidity profile (in g/kg) for the atmos
  The form of the equation of state is controlled by the character
  variables \textbf{buoyancyRelation} and \textbf{eosType}.
- \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
+ \textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and
- needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
+ needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations.
- In this case, \textbf{eosType} 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 \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
+ linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial
- approximation to the full nonlinear equation ( set
+ approximation to the full nonlinear equation ( set \textbf{eosType} to
- \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
+ \texttt{'POLYNOMIAL'}). In the linear case, you need to specify the
- case, you need to specify the thermal and haline expansion
+ thermal and haline expansion coefficients represented by the variables
- coefficients represented by the variables \textbf{tAlpha}\textit{\
+ \textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For
-   }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
+ the nonlinear case, you need to generate a file of polynomial
- case, you need to generate a file of polynomial coefficients called
+ coefficients called \textit{POLY3.COEFFS}. To do this, use the program
- \textit{POLY3.COEFFS}. To do this, use the program
  \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
  available in the same directory and you will need to edit the number
  and the values of the vertical levels in \textit{knudsen2.f} so that
-Line 1038 
 they match those of your configuration).
+Line 1092 
 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
+ \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
+   assumes in-situ temperature, which is not a model variable; {\em its
-   is therefore discouraged, and it is only listed for completeness}.
+     use is therefore discouraged, and it is only listed for
- \item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
+     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
+   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
+ \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
+   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
+ \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.
-Line 1063 
 salinity is required.
+Line 1118 
 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{itemize}
- \item initialization
- \end{itemize}
- The velocity components are initialized to 0 unless the simulation is
+ \begin{description}
- starting from a pickup file (see section on simulation control parameters).
+ \item[initialization] \
- \begin{itemize}
+   The velocity components are initialized to 0 unless the simulation
- \item forcing
+   is starting from a pickup file (see section on simulation control
- \end{itemize}
+   parameters).
- This section only applies to the ocean. You need to generate wind-stress
+ \item[forcing] \
- data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
- meridWindFile }corresponding to the zonal and meridional components of the
+   This section only applies to the ocean. You need to generate
- wind stress, respectively (if you want the stress to be along the direction
+   wind-stress data into two files \textbf{zonalWindFile} and
- of only one of the model horizontal axes, you only need to generate one
+   \textbf{meridWindFile} corresponding to the zonal and meridional
- file). The format of the files is similar to the bathymetry file. The zonal
+   components of the wind stress, respectively (if you want the stress
- (meridional) stress data are assumed to be in Pa and located at U-points
+   to be along the direction of only one of the model horizontal axes,
- (V-points). As for the bathymetry, the precision with which to read the
+   you only need to generate one file). The format of the files is
- binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
+   similar to the bathymetry file. The zonal (meridional) stress data
- See the matlab program \textit{gendata.m }in the \textit{input }directories
+   are assumed to be in Pa and located at U-points (V-points). As for
- under \textit{verification }to see how simple analytical wind forcing data
+   the bathymetry, the precision with which to read the binary data is
- are generated for the case study experiments.
+   controlled by the variable \textbf{readBinaryPrec}.  See the matlab
+   program \textit{gendata.m} in the \textit{input} directories under
- There is also the possibility of prescribing time-dependent periodic
+   \textit{verification} to see how simple analytical wind forcing data
- forcing. To do this, concatenate the successive time records into a single
+   are generated for the case study experiments.
- file (for each stress component) ordered in a (x, y, t) fashion and set the
- following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+   There is also the possibility of prescribing time-dependent periodic
- \textbf{externForcingPeriod }to the period (in s) of which the forcing
+   forcing. To do this, concatenate the successive time records into a
- varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
+   single file (for each stress component) ordered in a (x,y,t) fashion
- time (in s) of the forcing (typically 1 year -- note: \textbf{%
+   and set the following variables: \textbf{periodicExternalForcing }to
- externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
+   \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)
- With these variables set up, the model will interpolate the forcing linearly
+   of which the forcing varies (typically 1 month), and
- at each iteration.
+   \textbf{externForcingCycle} to the repeat time (in s) of the forcing
+   (typically 1 year -- note: \textbf{ externForcingCycle} must be a
- \begin{itemize}
+   multiple of \textbf{externForcingPeriod}).  With these variables set
- \item dissipation
+   up, the model will interpolate the forcing linearly at each
- \end{itemize}
+   iteration.
- The lateral eddy viscosity coefficient is specified through the variable
+ \item[dissipation] \
- \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
- coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
+   The lateral eddy viscosity coefficient is specified through the
- ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
+   variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy
- for the atmosphere. The vertical diffusive fluxes can be computed implicitly
+   viscosity coefficient is specified through the variable
- by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
+   \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and
- .'. In addition, biharmonic mixing can be added as well through the variable
+   \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The
- \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
+   vertical diffusive fluxes can be computed implicitly by setting the
- you might also need to set the variable \textbf{cosPower} which is set to 0
+   logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.
- by default and which represents the power of cosine of latitude to multiply
+   In addition, biharmonic mixing can be added as well through the
- viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
+   variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar
- specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
+   grid, you might also need to set the variable \textbf{cosPower}
- and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
+   which is set to 0 by default and which represents the power of
- boundary conditions are applied. If no-slip boundary conditions are applied
+   cosine of latitude to multiply viscosity. Slip or no-slip conditions
- at the bottom, a bottom drag can be applied as well. Two forms are
+   at lateral and bottom boundaries are specified through the logical
- available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
+   variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If
- ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
+   set to \texttt{'.FALSE.'}, free-slip boundary conditions are
- \ }in m$^{-1}$).
+   applied. If no-slip boundary conditions are applied at the bottom, a
+   bottom drag can be applied as well. Two forms are available: linear
- The Fourier and Shapiro filters are described elsewhere.
+   (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
+   quadratic (set the variable \textbf{bottomDragQuadratic} in
- \begin{itemize}
+   m$^{-1}$).
- \item C-D scheme
- \end{itemize}
+   The Fourier and Shapiro filters are described elsewhere.
+ \item[C-D scheme] \
+   If you run at a sufficiently coarse resolution, you will need the
+   C-D scheme for the computation of the Coriolis terms. The
+   variable\textbf{\ tauCD}, which represents the C-D scheme coupling
+   timescale (in s) needs to be set.
+ \item[calculation of pressure/geopotential] \
+   First, to run a non-hydrostatic ocean simulation, set the logical
+   variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure
+   field is then inverted through a 3D elliptic equation. (Note: this
+   capability is not available for the atmosphere yet.) By default, a
+   hydrostatic simulation is assumed and a 2D elliptic equation is used
+   to invert the pressure field. The parameters controlling the
+   behaviour of the elliptic solvers are the variables
+   \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for
+   the 2D case and \textbf{cg3dMaxIters} and
+   \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to
+   alter the default values (are we sure of this?).
+   For the calculation of the surface pressure (for the ocean) or
+   surface geopotential (for the atmosphere) you need to set the
+   logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}
+   (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}
+   depending on how you want to deal with the ocean upper or atmosphere
+   lower boundary).
- If you run at a sufficiently coarse resolution, you will need the C-D scheme
+ \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}
- 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{itemize}
- \item initialization
- \end{itemize}
- The initial tracer data can be contained in the binary files \textbf{%
- hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D
- data ordered in an (x, y, r) fashion with k=1 as the first vertical level.
- If no file names are provided, the tracers are then initialized with the
- values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation
- of state section). In this case, the initial tracer data are uniform in x
- and y for each depth level.
- \begin{itemize}
- \item forcing
- \end{itemize}
- This part is more relevant for the ocean, the procedure for the atmosphere
+ \begin{description}
- not being completely stabilized at the moment.
+ \item[initialization] \
- A combination of fluxes data and relaxation terms can be used for driving
+   The initial tracer data can be contained in the binary files
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
+   \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files
- ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
+   should contain 3D data ordered in an (x,y,r) fashion with k=1 as the
- Alternatively or in addition, the forcing can be specified through a
+   first vertical level.  If no file names are provided, the tracers
- relaxation term. The SST data to which the model surface temperatures are
+   are then initialized with the values of \textbf{tRef} and
- restored to are supposed to be stored in the 2D binary file \textbf{%
+   \textbf{sRef} mentioned above (in the equation of state section). In
- thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
+   this case, the initial tracer data are uniform in x and y for each
- is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
+   depth level.
- same procedure applies for salinity with the variable names \textbf{EmPmRfile%
- }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
+ \item[forcing] \
- \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
- files and relaxation time scale coefficient (in s), respectively. Also for
+   This part is more relevant for the ocean, the procedure for the
- salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
+   atmosphere not being completely stabilized at the moment.
- boundary conditions are applied i.e. when computing the surface salinity
- tendency, the freshwater flux is multiplied by the model surface salinity
+   A combination of fluxes data and relaxation terms can be used for
- instead of a constant salinity value.
+   driving the tracer equations.  For potential temperature, heat flux
+   data (in W/m$ ^{2}$) can be stored in the 2D binary file
- As for the other input files, the precision with which to read the data is
+   \textbf{surfQfile}.  Alternatively or in addition, the forcing can
- controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
+   be specified through a relaxation term. The SST data to which the
- forcing can be applied as well following the same procedure used for the
+   model surface temperatures are restored to are supposed to be stored
- wind forcing data (see above).
+   in the 2D binary file \textbf{thetaClimFile}. The corresponding
+   relaxation time scale coefficient is set through the variable
- \begin{itemize}
+   \textbf{tauThetaClimRelax} (in s). The same procedure applies for
- \item dissipation
+   salinity with the variable names \textbf{EmPmRfile},
- \end{itemize}
+   \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater
+   flux (in m/s) and surface salinity (in ppt) data files and
- Lateral eddy diffusivities for temperature and salinity/specific humidity
+   relaxation time scale coefficient (in s), respectively. Also for
- are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
+   salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on,
- (in m$^{2}$/s). Vertical eddy diffusivities are specified through the
+   natural boundary conditions are applied i.e. when computing the
- variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean
+   surface salinity tendency, the freshwater flux is multiplied by the
- and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the
+   model surface salinity instead of a constant salinity value.
- atmosphere. The vertical diffusive fluxes can be computed implicitly by
- setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
+   As for the other input files, the precision with which to read the
- .'. In addition, biharmonic diffusivities can be specified as well through
+   data is controlled by the variable \textbf{readBinaryPrec}.
- the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note
+   Time-dependent, periodic forcing can be applied as well following
- that the cosine power scaling (specified through \textbf{cosPower }- see the
+   the same procedure used for the wind forcing data (see above).
- momentum equations section) is applied to the tracer diffusivities
- (Laplacian and biharmonic) as well. The Gent and McWilliams parameterization
+ \item[dissipation] \
- for oceanic tracers is described in the package section. Finally, note that
- tracers can be also subject to Fourier and Shapiro filtering (see the
+   Lateral eddy diffusivities for temperature and salinity/specific
- corresponding section on these filters).
+   humidity are specified through the variables \textbf{diffKhT} and
+   \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are
- \begin{itemize}
+   specified through the variables \textbf{diffKzT} and
- \item ocean convection
+   \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT
- \end{itemize}
+   }and \textbf{diffKpS} (in Pa$^{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}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero
+   value.
- Two options are available to parameterize ocean convection: one is to use
+ \end{description}
- the convective adjustment scheme. In this case, you need to set the variable
- \textbf{cadjFreq}, which represents the frequency (in s) with which the
- adjustment algorithm is called, to a non-zero value (if set to a negative
- value by the user, the model will set it to the tracer time step). The other
- option is to parameterize convection with implicit vertical diffusion. To do
- this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{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}.
+ \item[frequency of output] \
+   Real variables defining frequencies (in s) with which output files
+   are written on disk need to be set up. \textbf{dumpFreq} controls
+   the frequency with which the instantaneous state of the model is
+   saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output
+   frequency of rolling and permanent checkpoint files, respectively.
+   See section 1.5.1 Output files for the definition of model state and
+   checkpoint files. In addition, time-averaged fields can be written
+   out by setting the variable \textbf{taveFreq} (in s).  The precision
+   with which to write the binary data is controlled by the integer
+   variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or
+   \texttt{64}).
- \begin{itemize}
+ \end{description}
- \item frequency of output
- \end{itemize}
- Real variables defining frequencies (in s) with which output files are
- written on disk need to be set up. \textbf{dumpFreq }controls the frequency
- with which the instantaneous state of the model is saved. \textbf{chkPtFreq }%
- and \textbf{pchkPtFreq }control the output frequency of rolling and
- permanent checkpoint files, respectively. See section 1.5.1 Output files for the
- definition of model state and checkpoint files. In addition, time-averaged
- fields can be written out by setting the variable \textbf{taveFreq} (in s).
- The precision with which to write the binary data is controlled by the
- integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
-}).
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