/[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 1.18 by edhill,
Thu Jan 29 19:22:35 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, 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 1041 
 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 1059 
 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 1085 
 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
- starting from a pickup file (see section on simulation control parameters).
- \begin{itemize}
+ \begin{description}
- \item forcing
+ \item[initialization] \
- \end{itemize}
+   The velocity components are initialized to 0 unless the simulation
- This section only applies to the ocean. You need to generate wind-stress
+   is starting from a pickup file (see section on simulation control
- data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
+   parameters).
- meridWindFile }corresponding to the zonal and meridional components of the
- wind stress, respectively (if you want the stress to be along the direction
+ \item[forcing] \
- of only one of the model horizontal axes, you only need to generate one
- file). The format of the files is similar to the bathymetry file. The zonal
+   This section only applies to the ocean. You need to generate
- (meridional) stress data are assumed to be in Pa and located at U-points
+   wind-stress data into two files \textbf{zonalWindFile} and
- (V-points). As for the bathymetry, the precision with which to read the
+   \textbf{meridWindFile} corresponding to the zonal and meridional
- binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
+   components of the wind stress, respectively (if you want the stress
- See the matlab program \textit{gendata.m }in the \textit{input }directories
+   to be along the direction of only one of the model horizontal axes,
- under \textit{verification }to see how simple analytical wind forcing data
+   you only need to generate one file). The format of the files is
- are generated for the case study experiments.
+   similar to the bathymetry file. The zonal (meridional) stress data
+   are assumed to be in Pa and located at U-points (V-points). As for
- There is also the possibility of prescribing time-dependent periodic
+   the bathymetry, the precision with which to read the binary data is
- forcing. To do this, concatenate the successive time records into a single
+   controlled by the variable \textbf{readBinaryPrec}.  See the matlab
- file (for each stress component) ordered in a (x, y, t) fashion and set the
+   program \textit{gendata.m} in the \textit{input} directories under
- following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+   \textit{verification} to see how simple analytical wind forcing data
- \textbf{externForcingPeriod }to the period (in s) of which the forcing
+   are generated for the case study experiments.
- varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
- time (in s) of the forcing (typically 1 year -- note: \textbf{%
+   There is also the possibility of prescribing time-dependent periodic
- externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
+   forcing. To do this, concatenate the successive time records into a
- With these variables set up, the model will interpolate the forcing linearly
+   single file (for each stress component) ordered in a (x,y,t) fashion
- at each iteration.
+   and set the following variables: \textbf{periodicExternalForcing }to
+   \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)
- \begin{itemize}
+   of which the forcing varies (typically 1 month), and
- \item dissipation
+   \textbf{externForcingCycle} to the repeat time (in s) of the forcing
- \end{itemize}
+   (typically 1 year -- note: \textbf{ externForcingCycle} must be a
+   multiple of \textbf{externForcingPeriod}).  With these variables set
- The lateral eddy viscosity coefficient is specified through the variable
+   up, the model will interpolate the forcing linearly at each
- \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
+   iteration.
- coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
- ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
+ \item[dissipation] \
- for the atmosphere. The vertical diffusive fluxes can be computed implicitly
- by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
+   The lateral eddy viscosity coefficient is specified through the
- .'. In addition, biharmonic mixing can be added as well through the variable
+   variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy
- \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
+   viscosity coefficient is specified through the variable
- you might also need to set the variable \textbf{cosPower} which is set to 0
+   \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and
- by default and which represents the power of cosine of latitude to multiply
+   \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The
- viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
+   vertical diffusive fluxes can be computed implicitly by setting the
- specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
+   logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.
- and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
+   In addition, biharmonic mixing can be added as well through the
- boundary conditions are applied. If no-slip boundary conditions are applied
+   variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar
- at the bottom, a bottom drag can be applied as well. Two forms are
+   grid, you might also need to set the variable \textbf{cosPower}
- available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
+   which is set to 0 by default and which represents the power of
- ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
+   cosine of latitude to multiply viscosity. Slip or no-slip conditions
- \ }in m$^{-1}$).
+   at lateral and bottom boundaries are specified through the logical
+   variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If
- The Fourier and Shapiro filters are described elsewhere.
+   set to \texttt{'.FALSE.'}, free-slip boundary conditions are
+   applied. If no-slip boundary conditions are applied at the bottom, a
- \begin{itemize}
+   bottom drag can be applied as well. Two forms are available: linear
- \item C-D scheme
+   (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
- \end{itemize}
+   quadratic (set the variable \textbf{bottomDragQuadratic} in
+   m$^{-1}$).
+   The Fourier and Shapiro filters are described elsewhere.
+ \item[C-D scheme] \
+   If you run at a sufficiently coarse resolution, you will need the
+   C-D scheme for the computation of the Coriolis terms. The
+   variable\textbf{\ tauCD}, which represents the C-D scheme coupling
+   timescale (in s) needs to be set.
+ \item[calculation of pressure/geopotential] \
+   First, to run a non-hydrostatic ocean simulation, set the logical
+   variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure
+   field is then inverted through a 3D elliptic equation. (Note: this
+   capability is not available for the atmosphere yet.) By default, a
+   hydrostatic simulation is assumed and a 2D elliptic equation is used
+   to invert the pressure field. The parameters controlling the
+   behaviour of the elliptic solvers are the variables
+   \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for
+   the 2D case and \textbf{cg3dMaxIters} and
+   \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to
+   alter the default values (are we sure of this?).
+   For the calculation of the surface pressure (for the ocean) or
+   surface geopotential (for the atmosphere) you need to set the
+   logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}
+   (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}
+   depending on how you want to deal with the ocean upper or atmosphere
+   lower boundary).
- 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
- not being completely stabilized at the moment.
- A combination of fluxes data and relaxation terms can be used for driving
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
- ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
- Alternatively or in addition, the forcing can be specified through a
- relaxation term. The SST data to which the model surface temperatures are
- restored to are supposed to be stored in the 2D binary file \textbf{%
- thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
- is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
- same procedure applies for salinity with the variable names \textbf{EmPmRfile%
- }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
- \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
- files and relaxation time scale coefficient (in s), respectively. Also for
- salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
- boundary conditions are applied i.e. when computing the surface salinity
- tendency, the freshwater flux is multiplied by the model surface salinity
- instead of a constant salinity value.
- As for the other input files, the precision with which to read the data is
- controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
- forcing can be applied as well following the same procedure used for the
- wind forcing data (see above).
- \begin{itemize}
- \item dissipation
- \end{itemize}
- Lateral eddy diffusivities for temperature and salinity/specific humidity
- are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
- (in m$^{2}$/s). Vertical eddy diffusivities are specified through the
- variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean
- and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the
- atmosphere. The vertical diffusive fluxes can be computed implicitly by
- setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .'. In addition, biharmonic diffusivities can be specified as well through
- the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note
- that the cosine power scaling (specified through \textbf{cosPower }- see the
- momentum equations section) is applied to the tracer diffusivities
- (Laplacian and biharmonic) as well. The Gent and McWilliams parameterization
- for oceanic tracers is described in the package section. Finally, note that
- tracers can be also subject to Fourier and Shapiro filtering (see the
- corresponding section on these filters).
- \begin{itemize}
+ \begin{description}
- \item ocean convection
+ \item[initialization] \
- \end{itemize}
+   The initial tracer data can be contained in the binary files
+   \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files
+   should contain 3D data ordered in an (x,y,r) fashion with k=1 as the
+   first vertical level.  If no file names are provided, the tracers
+   are then initialized with the values of \textbf{tRef} and
+   \textbf{sRef} mentioned above (in the equation of state section). In
+   this case, the initial tracer data are uniform in x and y for each
+   depth level.
+ \item[forcing] \
+   This part is more relevant for the ocean, the procedure for the
+   atmosphere not being completely stabilized at the moment.
+   A combination of fluxes data and relaxation terms can be used for
+   driving the tracer equations.  For potential temperature, heat flux
+   data (in W/m$ ^{2}$) can be stored in the 2D binary file
+   \textbf{surfQfile}.  Alternatively or in addition, the forcing can
+   be specified through a relaxation term. The SST data to which the
+   model surface temperatures are restored to are supposed to be stored
+   in the 2D binary file \textbf{thetaClimFile}. The corresponding
+   relaxation time scale coefficient is set through the variable
+   \textbf{tauThetaClimRelax} (in s). The same procedure applies for
+   salinity with the variable names \textbf{EmPmRfile},
+   \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater
+   flux (in m/s) and surface salinity (in ppt) data files and
+   relaxation time scale coefficient (in s), respectively. Also for
+   salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on,
+   natural boundary conditions are applied i.e. when computing the
+   surface salinity tendency, the freshwater flux is multiplied by the
+   model surface salinity instead of a constant salinity value.
+   As for the other input files, the precision with which to read the
+   data is controlled by the variable \textbf{readBinaryPrec}.
+   Time-dependent, periodic forcing can be applied as well following
+   the same procedure used for the wind forcing data (see above).
+ \item[dissipation] \
+   Lateral eddy diffusivities for temperature and salinity/specific
+   humidity are specified through the variables \textbf{diffKhT} and
+   \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are
+   specified through the variables \textbf{diffKzT} and
+   \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT
+   }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The
+   vertical diffusive fluxes can be computed implicitly by setting the
+   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}.
+   In addition, biharmonic diffusivities can be specified as well
+   through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in
+   m$^{4}$/s). Note that the cosine power scaling (specified through
+   \textbf{cosPower}---see the momentum equations section) is applied to
+   the tracer diffusivities (Laplacian and biharmonic) as well. The
+   Gent and McWilliams parameterization for oceanic tracers is
+   described in the package section. Finally, note that tracers can be
+   also subject to Fourier and Shapiro filtering (see the corresponding
+   section on these filters).
+ \item[ocean convection] \
+   Two options are available to parameterize ocean convection: one is
+   to use the convective adjustment scheme. In this case, you need to
+   set the variable \textbf{cadjFreq}, which represents the frequency
+   (in s) with which the adjustment algorithm is called, to a non-zero
+   value (if set to a negative value by the user, the model will set it
+   to the tracer time step). The other option is to parameterize
+   convection with implicit vertical diffusion. To do this, set the
+   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}
+   and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero
+   value.
- Two options are available to parameterize ocean convection: one is to use
+ \end{description}
- the convective adjustment scheme. In this case, you need to set the variable
- \textbf{cadjFreq}, which represents the frequency (in s) with which the
- adjustment algorithm is called, to a non-zero value (if set to a negative
- value by the user, the model will set it to the tracer time step). The other
- option is to parameterize convection with implicit vertical diffusion. To do
- this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{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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