/[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 1.17 by edhill,
Thu Jan 29 15:11:39 2004 UTC
 Line 115 
 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}
 Line 130 
 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}
  .
 Line 150 
 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}
-Line 178 
 If the list of conflicts scrolled off th
+Line 182 
 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 190 
 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 233 
 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 310 
 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 436 
 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 448 
 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 490 
 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 727 
 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 739 
 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 751 
 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 769 
 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 786 
 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 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 888 
 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,\textit{\ }and r\textit{\
- The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
+   }directions are represented by the variables \textbf{sNx}\textit{,
- represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
+   }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
- and \textbf{Nr}\textit{\ }respectively which are declared and set in the
+   which are declared and set in the file \textit{model/inc/SIZE.h.
- file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor
+   }(Again, this assumes a mono-processor calculation. For
- calculation. For multiprocessor calculations see section on parallel
+   multiprocessor calculations see section on parallel implementation.)
- implementation.)
+ \item[grid] \
- \begin{itemize}
- \item grid
+   Three different grids are available: cartesian, spherical polar, and
- \end{itemize}
+   curvilinear (including the cubed sphere). The grid is set through
+   the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
- Three different grids are available: cartesian, spherical polar, and
+     usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
- curvilinear (including the cubed sphere). The grid is set through the
+     usingCurvilinearGrid}\textit{. }In the case of spherical and
- logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
+   curvilinear grids, the southern boundary is defined through the
- usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
+   variable \textbf{phiMin} \textit{\ }which corresponds to the
- usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
+   latitude of the southern most cell face (in degrees). The resolution
- grids, the southern boundary is defined through the variable \textbf{phiMin}%
+   along the x and y directions is controlled by the 1D arrays
- \textit{\ }which corresponds to the latitude of the southern most cell face
+   \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
- (in degrees). The resolution along the x and y directions is controlled by
+   the case of a cartesian grid, in degrees otherwise). The vertical
- the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters
+   grid spacing is set through the 1D array \textbf{delz }for the ocean
- in the case of a cartesian grid, in degrees otherwise). The vertical grid
+   (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
- spacing is set through the 1D array \textbf{delz }for the ocean (in meters)
+   The variable \textbf{ Ro\_SeaLevel} represents the standard position
- or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%
+   of Sea-Level in ''R'' coordinate. This is typically set to 0m for
- Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''
+   the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
- coordinate. This is typically set to 0m for the ocean (default value) and 10$%
+   the atmosphere, also set the logical variable \textbf{groundAtK1} to
- ^{5}$Pa for the atmosphere. For the atmosphere, also set the logical
+   '.\texttt{TRUE}.'. which put the first level (k=1) at the lower
- variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level
+   boundary (ground).
- (k=1) at the lower boundary (ground).
+   For the cartesian grid case, the Coriolis parameter $f$ is set
- For the cartesian grid case, the Coriolis parameter $f$ is set through the
+   through the variables \textbf{f0}\textit{\ }and
- variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond
+   \textbf{beta}\textit{\ }which correspond to the reference Coriolis
- to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%
+   parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
- \partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%
+   m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
- is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
+   to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
- southern edge of the domain.
+   southern edge of the domain.
- \begin{itemize}
+ \item[topography - full and partial cells] \
- \item topography - full and partial cells
- \end{itemize}
+   The domain bathymetry is read from a file that contains a 2D (x,y)
+   map of depths (in m) for the ocean or pressures (in Pa) for the
- The domain bathymetry is read from a file that contains a 2D (x,y) map of
+   atmosphere. The file name is represented by the variable
- depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The
+   \textbf{bathyFile}\textit{. }The file is assumed to contain binary
- file name is represented by the variable \textbf{bathyFile}\textit{. }The
+   numbers giving the depth (pressure) of the model at each grid cell,
- file is assumed to contain binary numbers giving the depth (pressure) of the
+   ordered with the x coordinate varying fastest. The points are
- model at each grid cell, ordered with the x coordinate varying fastest. The
+   ordered from low coordinate to high coordinate for both axes. The
- points are ordered from low coordinate to high coordinate for both axes. The
+   model code applies without modification to enclosed, periodic, and
- model code applies without modification to enclosed, periodic, and double
+   double periodic domains. Periodicity is assumed by default and is
- periodic domains. Periodicity is assumed by default and is suppressed by
+   suppressed by setting the depths to 0m for the cells at the limits
- setting the depths to 0m for the cells at the limits of the computational
+   of the computational domain (note: not sure this is the case for the
- domain (note: not sure this is the case for the atmosphere). The precision
+   atmosphere). The precision with which to read the binary data is
- with which to read the binary data is controlled by the integer variable
+   controlled by the integer variable \textbf{readBinaryPrec }which can
- \textbf{readBinaryPrec }which can take the value \texttt{32} (single
+   take the value \texttt{32} (single precision) or \texttt{64} (double
- precision) or \texttt{64} (double precision). See the matlab program \textit{%
+   precision). See the matlab program \textit{ gendata.m }in the
- gendata.m }in the \textit{input }directories under \textit{verification }to
+   \textit{input }directories under \textit{verification }to see how
- see how the bathymetry files are generated for the case study experiments.
+   the bathymetry files are generated for the case study experiments.
- To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%
+   To use the partial cell capability, the variable
- needs to be set to a value between 0 and 1 (it is set to 1 by default)
+   \textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and
- corresponding to the minimum fractional size of the cell. For example if the
+(it is set to 1 by default) corresponding to the minimum
- bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the
+   fractional size of the cell. For example if the bottom cell is 500m
- actual thickness of the cell (i.e. used in the code) can cover a range of
+   thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
- discrete values 50m apart from 50m to 500m depending on the value of the
+   thickness of the cell (i.e. used in the code) can cover a range of
- bottom depth (in \textbf{bathyFile}) at this point.
+   discrete values 50m apart from 50m to 500m depending on the value of
+   the bottom depth (in \textbf{bathyFile}) at this point.
- Note that the bottom depths (or pressures) need not coincide with the models
- levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%
+   Note that the bottom depths (or pressures) need not coincide with
- \textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
+   the models levels as deduced from \textbf{delz}\textit{\
- \textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
+   }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
- \ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
+   the numbers in \textbf{bathyFile} \textit{\ }so that they match the
+   levels obtained from \textbf{delz}\textit{ \ }or\textit{\
- (Note: the atmospheric case is a bit more complicated than what is written
+   }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
- here I think. To come soon...)
+   (Note: the atmospheric case is a bit more complicated than what is
+   written here I think. To come soon...)
+ \item[time-discretization] \
+   The time steps are set through the real variables \textbf{deltaTMom}
+   and \textbf{deltaTtracer} (in s) which represent the time step for
+   the momentum and tracer equations, respectively. For synchronous
+   integrations, simply set the two variables to the same value (or you
+   can prescribe one time step only through the variable
+   \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
+   through the variable \textbf{abEps} (dimensionless). The stagger
+   baroclinic time stepping can be activated by setting the logical
+   variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
- \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 1076 
 useCoriolis, momPressureForcing, momStep
+Line 1101 
 useCoriolis, momPressureForcing, momStep
  Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
  these variables.
- \begin{itemize}
+ \begin{description}
- \item initialization
+ \item[initialization] \
- \end{itemize}
+   The velocity components are initialized to 0 unless the simulation
- The velocity components are initialized to 0 unless the simulation is
+   is starting from a pickup file (see section on simulation control
- starting from a pickup file (see section on simulation control parameters).
+   parameters).
- \begin{itemize}
+ \item[forcing] \
- \item forcing
- \end{itemize}
+   This section only applies to the ocean. You need to generate
+   wind-stress data into two files \textbf{zonalWindFile}\textit{\ }and
- This section only applies to the ocean. You need to generate wind-stress
+   \textbf{ meridWindFile }corresponding to the zonal and meridional
- data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
+   components of the wind stress, respectively (if you want the stress
- meridWindFile }corresponding to the zonal and meridional components of the
+   to be along the direction of only one of the model horizontal axes,
- wind stress, respectively (if you want the stress to be along the direction
+   you only need to generate one file). The format of the files is
- of only one of the model horizontal axes, you only need to generate one
+   similar to the bathymetry file. The zonal (meridional) stress data
- file). The format of the files is similar to the bathymetry file. The zonal
+   are assumed to be in Pa and located at U-points (V-points). As for
- (meridional) stress data are assumed to be in Pa and located at U-points
+   the bathymetry, the precision with which to read the binary data is
- (V-points). As for the bathymetry, the precision with which to read the
+   controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See
- binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
+   the matlab program \textit{gendata.m }in the \textit{input
- See the matlab program \textit{gendata.m }in the \textit{input }directories
+   }directories under \textit{verification }to see how simple
- under \textit{verification }to see how simple analytical wind forcing data
+   analytical wind forcing data are generated for the case study
- are generated for the case study experiments.
+   experiments.
- There is also the possibility of prescribing time-dependent periodic
+   There is also the possibility of prescribing time-dependent periodic
- forcing. To do this, concatenate the successive time records into a single
+   forcing. To do this, concatenate the successive time records into a
- file (for each stress component) ordered in a (x, y, t) fashion and set the
+   single file (for each stress component) ordered in a (x, y, t)
- following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+   fashion and set the following variables:
- \textbf{externForcingPeriod }to the period (in s) of which the forcing
+   \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
- varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
+   \textbf{externForcingPeriod }to the period (in s) of which the
- time (in s) of the forcing (typically 1 year -- note: \textbf{%
+   forcing varies (typically 1 month), and \textbf{externForcingCycle
- externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
+   }to the repeat time (in s) of the forcing (typically 1 year -- note:
- With these variables set up, the model will interpolate the forcing linearly
+   \textbf{ externForcingCycle }must be a multiple of
- at each iteration.
+   \textbf{externForcingPeriod}).  With these variables set up, the
+   model will interpolate the forcing linearly at each iteration.
- \begin{itemize}
- \item dissipation
+ \item[dissipation] \
- \end{itemize}
+   The lateral eddy viscosity coefficient is specified through the
- The lateral eddy viscosity coefficient is specified through the variable
+   variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The
- \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
+   vertical eddy viscosity coefficient is specified through the
- coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
+   variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and
- ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
+   \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.
- for the atmosphere. The vertical diffusive fluxes can be computed implicitly
+   The vertical diffusive fluxes can be computed implicitly by setting
- by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
+   the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}
- .'. In addition, biharmonic mixing can be added as well through the variable
+   .'. In addition, biharmonic mixing can be added as well through the
- \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
+   variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a
- you might also need to set the variable \textbf{cosPower} which is set to 0
+   spherical polar grid, you might also need to set the variable
- by default and which represents the power of cosine of latitude to multiply
+   \textbf{cosPower} which is set to 0 by default and which represents
- viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
+   the power of cosine of latitude to multiply viscosity. Slip or
- specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
+   no-slip conditions at lateral and bottom boundaries are specified
- and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
+   through the logical variables \textbf{no\_slip\_sides}\textit{\ }
- boundary conditions are applied. If no-slip boundary conditions are applied
+   and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',
- at the bottom, a bottom drag can be applied as well. Two forms are
+   free-slip boundary conditions are applied. If no-slip boundary
- available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
+   conditions are applied at the bottom, a bottom drag can be applied
- ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
+   as well. Two forms are available: linear (set the variable
- \ }in m$^{-1}$).
+   \textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set
+   the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$).
- The Fourier and Shapiro filters are described elsewhere.
+   The Fourier and Shapiro filters are described elsewhere.
- \begin{itemize}
- \item C-D scheme
+ \item[C-D scheme] \
- \end{itemize}
+   If you run at a sufficiently coarse resolution, you will need the
+   C-D scheme for the computation of the Coriolis terms. The
+   variable\textbf{\ tauCD}, which represents the C-D scheme coupling
+   timescale (in s) needs to be set.
+ \item[calculation of pressure/geopotential] \
+   First, to run a non-hydrostatic ocean simulation, set the logical
+   variable \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure
+   field is then inverted through a 3D elliptic equation. (Note: this
+   capability is not available for the atmosphere yet.) By default, a
+   hydrostatic simulation is assumed and a 2D elliptic equation is used
+   to invert the pressure field. The parameters controlling the
+   behaviour of the elliptic solvers are the variables
+   \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual } for
+   the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{
+     cg3dTargetResidual }for the 3D case. You probably won't need to
+   alter the default values (are we sure of this?).
+   For the calculation of the surface pressure (for the ocean) or
+   surface geopotential (for the atmosphere) you need to set the
+   logical variables \textbf{rigidLid} and
+   \textbf{implicitFreeSurface}\textit{\ }(set one to '.
+   \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how
+   you want to deal with the ocean upper or atmosphere lower boundary).
- If you run at a sufficiently coarse resolution, you will need the C-D scheme
+ \end{description}
- for the computation of the Coriolis terms. The variable\textbf{\ tauCD},
- which represents the C-D scheme coupling timescale (in s) needs to be set.
- \begin{itemize}
- \item calculation of pressure/geopotential
- \end{itemize}
- First, to run a non-hydrostatic ocean simulation, set the logical variable
- \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then
- inverted through a 3D elliptic equation. (Note: this capability is not
- available for the atmosphere yet.) By default, a hydrostatic simulation is
- assumed and a 2D elliptic equation is used to invert the pressure field. The
- parameters controlling the behaviour of the elliptic solvers are the
- variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }%
- for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{%
- cg3dTargetResidual }for the 3D case. You probably won't need to alter the
- default values (are we sure of this?).
- For the calculation of the surface pressure (for the ocean) or surface
- geopotential (for the atmosphere) you need to set the logical variables
- \textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.%
- \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
- want to deal with the ocean upper or atmosphere lower boundary).
  \subsection{Tracer equations}
-Line 1171 
 This section covers the tracer equations
+Line 1198 
 This section covers the tracer equations
  equation and the salinity (for the ocean) or specific humidity (for the
  atmosphere) equation. As for the momentum equations, we only describe for
  now the parameters that you are likely to change. The logical variables
- \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%
+ \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{
  tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off
  terms in the temperature equation (same thing for salinity or specific
- humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{%
+ humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{
  saltAdvection}\textit{\ }etc). These variables are all assumed here to be
  set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a
  precise definition.
- \begin{itemize}
+ \begin{description}
- \item initialization
+ \item[initialization] \
- \end{itemize}
+   The initial tracer data can be contained in the binary files
- The initial tracer data can be contained in the binary files \textbf{%
+   \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files
- hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D
+   should contain 3D data ordered in an (x, y, r) fashion with k=1 as
- data ordered in an (x, y, r) fashion with k=1 as the first vertical level.
+   the first vertical level.  If no file names are provided, the
- If no file names are provided, the tracers are then initialized with the
+   tracers are then initialized with the values of \textbf{tRef }and
- values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation
+   \textbf{sRef }mentioned above (in the equation of state section). In
- of state section). In this case, the initial tracer data are uniform in x
+   this case, the initial tracer data are uniform in x and y for each
- and y for each depth level.
+   depth level.
- \begin{itemize}
+ \item[forcing] \
- \item forcing
- \end{itemize}
+   This part is more relevant for the ocean, the procedure for the
+   atmosphere not being completely stabilized at the moment.
- This part is more relevant for the ocean, the procedure for the atmosphere
- not being completely stabilized at the moment.
+   A combination of fluxes data and relaxation terms can be used for
+   driving the tracer equations. \ For potential temperature, heat flux
- A combination of fluxes data and relaxation terms can be used for driving
+   data (in W/m$ ^{2}$) can be stored in the 2D binary file
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
+   \textbf{surfQfile}\textit{. }  Alternatively or in addition, the
- ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
+   forcing can be specified through a relaxation term. The SST data to
- Alternatively or in addition, the forcing can be specified through a
+   which the model surface temperatures are restored to are supposed to
- relaxation term. The SST data to which the model surface temperatures are
+   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
- restored to are supposed to be stored in the 2D binary file \textbf{%
+   }The corresponding relaxation time scale coefficient is set through
- thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
+   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
- is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
+   procedure applies for salinity with the variable names
- same procedure applies for salinity with the variable names \textbf{EmPmRfile%
+   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
- }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
+   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
- \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
+   and surface salinity (in ppt) data files and relaxation time scale
- files and relaxation time scale coefficient (in s), respectively. Also for
+   coefficient (in s), respectively. Also for salinity, if the CPP key
- salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
+   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
- boundary conditions are applied i.e. when computing the surface salinity
+   are applied i.e. when computing the surface salinity tendency, the
- tendency, the freshwater flux is multiplied by the model surface salinity
+   freshwater flux is multiplied by the model surface salinity instead
- instead of a constant salinity value.
+   of a constant salinity value.
- As for the other input files, the precision with which to read the data is
+   As for the other input files, the precision with which to read the
- controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
+   data is controlled by the variable \textbf{readBinaryPrec}.
- forcing can be applied as well following the same procedure used for the
+   Time-dependent, periodic forcing can be applied as well following
- wind forcing data (see above).
+   the same procedure used for the wind forcing data (see above).
- \begin{itemize}
+ \item[dissipation] \
- \item dissipation
- \end{itemize}
+   Lateral eddy diffusivities for temperature and salinity/specific
+   humidity are specified through the variables \textbf{diffKhT }and
- Lateral eddy diffusivities for temperature and salinity/specific humidity
+   \textbf{diffKhS } (in m$^{2}$/s). Vertical eddy diffusivities are
- are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
+   specified through the variables \textbf{diffKzT }and \textbf{diffKzS
- (in m$^{2}$/s). Vertical eddy diffusivities are specified through the
+   }(in m$^{2}$/s) for the ocean and \textbf{diffKpT }and
- variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean
+   \textbf{diffKpS }(in Pa$^{2}$/s) for the atmosphere. The vertical
- and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the
+   diffusive fluxes can be computed implicitly by setting the logical
- atmosphere. The vertical diffusive fluxes can be computed implicitly by
+   variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'. In
- setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
+   addition, biharmonic diffusivities can be specified as well through
- .'. In addition, biharmonic diffusivities can be specified as well through
+   the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in
- the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note
+   m$^{4}$/s). Note that the cosine power scaling (specified through
- that the cosine power scaling (specified through \textbf{cosPower }- see the
+   \textbf{cosPower }- see the momentum equations section) is applied
- momentum equations section) is applied to the tracer diffusivities
+   to the tracer diffusivities (Laplacian and biharmonic) as well. The
- (Laplacian and biharmonic) as well. The Gent and McWilliams parameterization
+   Gent and McWilliams parameterization for oceanic tracers is
- for oceanic tracers is described in the package section. Finally, note that
+   described in the package section. Finally, note that tracers can be
- tracers can be also subject to Fourier and Shapiro filtering (see the
+   also subject to Fourier and Shapiro filtering (see the corresponding
- corresponding section on these filters).
+   section on these filters).
- \begin{itemize}
+ \item[ocean convection] \
- \item ocean convection
- \end{itemize}
+   Two options are available to parameterize ocean convection: one is
+   to use the convective adjustment scheme. In this case, you need to
+   set the variable \textbf{cadjFreq}, which represents the frequency
+   (in s) with which the adjustment algorithm is called, to a non-zero
+   value (if set to a negative value by the user, the model will set it
+   to the tracer time step). The other option is to parameterize
+   convection with implicit vertical diffusion. To do this, set the
+   logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'
+   and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have
+   non-zero value.
- Two options are available to parameterize ocean convection: one is to use
+ \end{description}
- the convective adjustment scheme. In this case, you need to set the variable
- \textbf{cadjFreq}, which represents the frequency (in s) with which the
- adjustment algorithm is called, to a non-zero value (if set to a negative
- value by the user, the model will set it to the tracer time step). The other
- option is to parameterize convection with implicit vertical diffusion. To do
- this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{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}
-Line 1265 
 Typically, you will set it to the tracer
+Line 1294 
 Typically, you will set it to the tracer
  Frequency of checkpointing and dumping of the model state are referenced to
  this clock (see below).
- \begin{itemize}
+ \begin{description}
- \item run duration
+ \item[run duration] \
- \end{itemize}
+   The beginning of a simulation is set by specifying a start time (in
- The beginning of a simulation is set by specifying a start time (in s)
+   s) through the real variable \textbf{startTime }or by specifying an
- through the real variable \textbf{startTime }or by specifying an initial
+   initial iteration number through the integer variable
- iteration number through the integer variable \textbf{nIter0}. If these
+   \textbf{nIter0}. If these variables are set to nonzero values, the
- variables are set to nonzero values, the model will look for a ''pickup''
+   model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to
- file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end
+   restart the integration\textit{. }The end of a simulation is set
- of a simulation is set through the real variable \textbf{endTime }(in s).
+   through the real variable \textbf{endTime }(in s).  Alternatively,
- Alternatively, you can specify instead the number of time steps to execute
+   you can specify instead the number of time steps to execute through
- through the integer variable \textbf{nTimeSteps}.
+   the integer variable \textbf{nTimeSteps}.
+ \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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