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

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-revision 1.17 by edhill,
Thu Jan 29 15:11:39 2004 UTC
+revision 1.24 by edhill,
Fri Apr  9 15:06:18 2004 UTC
 Line 79 
 provide easy support for maintenance upd
  \end{enumerate}
+ \subsubsection{Checkout from CVS}
+ \label{sect:cvs_checkout}
  If CVS is available on your system, we strongly encourage you to use it. CVS
  provides an efficient and elegant way of organizing your code and keeping
  track of your changes. If CVS is not available on your machine, you can also
-Line 93 
 in your .cshrc or .tcshrc file.  For bas
+Line 96 
 in your .cshrc or .tcshrc file.  For bas
  \begin{verbatim}
  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
  \end{verbatim}
- in your .profile or .bashrc file.
+ in your \texttt{.profile} or \texttt{.bashrc} file.
  To get MITgcm through CVS, first register with the MITgcm CVS server
-Line 121 
 http://mitgcm.org/source_code.html
+Line 124 
 http://mitgcm.org/source_code.html
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
+ As a convenience, the MITgcm CVS server contains aliases which are
+ named subsets of the codebase.  These aliases can be especially
+ helpful when used over slow internet connections or on machines with
+ restricted storage space.  Table \ref{tab:cvsModules} contains a list
+ of CVS aliases
+ \begin{table}[htb]
+   \centering
+   \begin{tabular}[htb]{|lp{3.25in}|}\hline
+     \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
+     \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
+     \texttt{MITgcm\_verif\_basic}
+     &  Source code plus a small set of the verification examples
+     (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
+     \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
+     \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
+     \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
+     \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
+     verification examples. \\\hline
+   \end{tabular}
+   \caption{MITgcm CVS Modules}
+   \label{tab:cvsModules}
+ \end{table}
  The checkout process creates a directory called \textit{MITgcm}. If
  the directory \textit{MITgcm} exists this command updates your code
-Line 134 
 MITgcm code can be found
+Line 159 
 MITgcm code can be found
  here
  \begin{rawhtml} </A> \end{rawhtml}
  .
+ It is important to note that the CVS aliases in Table
+ \ref{tab:cvsModules} cannot be used in conjunction with the CVS
+ \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
+ they create can be changed to a different name following the check-out:
+ \begin{verbatim}
+    %  cvs co MITgcm_verif_basic
+    %  mv MITgcm MITgcm_verif_basic
+ \end{verbatim}
- \paragraph*{Conventional download method}
+ \subsubsection{Conventional download method}
  \label{sect:conventionalDownload}
  If you do not have CVS on your system, you can download the model as a
-Line 156 
 MITgcm-support@mitgcm.org
+Line 189 
 MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
  mailing list.
- \paragraph*{Upgrading from an earlier version}
+ \subsubsection{Upgrading from an earlier version}
  If you already have an earlier version of the code you can ``upgrade''
  your copy instead of downloading the entire repository again. First,
-Line 633 
 the one experiment:
+Line 666 
 the one experiment:
  \end{verbatim}
+ \subsection{Using \texttt{genmake2}}
- \subsection{Using \textit{genmake2}}
  \label{sect:genmake}
  To compile the code, first use the program \texttt{genmake2} (located
- in the \textit{tools} directory) to generate a Makefile.
+ in the \texttt{tools} directory) to generate a Makefile.
  \texttt{genmake2} is a shell script written to work with all
  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
  Internally, \texttt{genmake2} determines the locations of needed
  files, the compiler, compiler options, libraries, and Unix tools.  It
- relies upon a number of ``optfiles'' located in the {\em
+ relies upon a number of ``optfiles'' located in the
-   tools/build\_options} directory.
+ \texttt{tools/build\_options} directory.
  The purpose of the optfiles is to provide all the compilation options
  for particular ``platforms'' (where ``platform'' roughly means the
-Line 739 
 The most important command-line options
+Line 771 
 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[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
+   set of packages to be used.  The normal order of precedence for
+   packages is as follows:
+   \begin{enumerate}
+   \item If available, the command line (\texttt{--pdefault}) settings
+     over-rule any others.
+   \item Next, \texttt{genmake2} will look for a file named
+     ``\texttt{packages.conf}'' in the local directory or in any of the
+     directories specified with the \texttt{--mods} option.
+   \item Finally, if neither of the above are available,
+     \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
+   \end{enumerate}
  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
    used for packages.
-Line 751 
 The most important command-line options
+Line 798 
 The most important command-line options
    assumed that the two packages are compatible and will function
    either with or without each other.
- \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-   set of packages to be used.
-   If not set, the default package list will be read from {\em
-     pkg/pkg\_default}
  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
    automatic differentiation options file to be used.  The file is
    analogous to the ``optfile'' defined above but it specifies
-Line 786 
 The most important command-line options
+Line 827 
 The most important command-line options
      ``-standarddirs'' option)
    \end{itemize}
+ \item[\texttt{--mpi}] This option enables certain MPI features (using
+   CPP \texttt{\#define}s) within the code and is necessary for MPI
+   builds (see Section \ref{sect:mpi-build}).
  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
    soft-links and other bugs common with the \texttt{make} versions
    provided by commercial Unix vendors, GNU \texttt{make} (sometimes
    called \texttt{gmake}) should be preferred.  This option provides a
    means for specifying the make executable to be used.
+ \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
+   machines, the ``bash'' shell is unavailable.  To run on these
+   systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
+   a Bourne, POSIX, or compatible) shell.  The syntax in these
+   circumstances is:
+   \begin{center}
+     \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
+   \end{center}
+   where \texttt{/bin/sh} can be replaced with the full path and name
+   of the desired shell.
  \end{description}
+ \subsection{Building with MPI}
+ \label{sect:mpi-build}
+ Building MITgcm to use MPI libraries can be complicated due to the
+ variety of different MPI implementations available, their dependencies
+ or interactions with different compilers, and their often ad-hoc
+ locations within file systems.  For these reasons, its generally a
+ good idea to start by finding and reading the documentation for your
+ machine(s) and, if necessary, seeking help from your local systems
+ administrator.
+ The steps for building MITgcm with MPI support are:
+ \begin{enumerate}
+ \item Determine the locations of your MPI-enabled compiler and/or MPI
+   libraries and put them into an options file as described in Section
+   \ref{sect:genmake}.  One can start with one of the examples in:
+   \begin{rawhtml} <A
+     href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
+   \end{rawhtml}
+   \begin{center}
+     \texttt{MITgcm/tools/build\_options/}
+   \end{center}
+   \begin{rawhtml} </A> \end{rawhtml}
+   such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
+   \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
+   hand.  You may need help from your user guide or local systems
+   administrator to determine the exact location of the MPI libraries.
+   If libraries are not installed, MPI implementations and related
+   tools are available including:
+   \begin{itemize}
+   \item \begin{rawhtml} <A
+       href="http://www-unix.mcs.anl.gov/mpi/mpich/">
+     \end{rawhtml}
+     MPICH
+     \begin{rawhtml} </A> \end{rawhtml}
+   \item \begin{rawhtml} <A
+       href="http://www.lam-mpi.org/">
+     \end{rawhtml}
+     LAM/MPI
+     \begin{rawhtml} </A> \end{rawhtml}
+   \item \begin{rawhtml} <A
+       href="http://www.osc.edu/~pw/mpiexec/">
+     \end{rawhtml}
+     MPIexec
+     \begin{rawhtml} </A> \end{rawhtml}
+   \end{itemize}
+ \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
+   (see Section \ref{sect:genmake}) using commands such as:
+ {\footnotesize \begin{verbatim}
+   %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
+   %  make depend
+   %  make
+ \end{verbatim} }
+ \item Run the code with the appropriate MPI ``run'' or ``exec''
+   program provided with your particular implementation of MPI.
+   Typical MPI packages such as MPICH will use something like:
+ \begin{verbatim}
+   %  mpirun -np 4 -machinefile mf ./mitgcmuv
+ \end{verbatim}
+   Sightly more complicated scripts may be needed for many machines
+   since execution of the code may be controlled by both the MPI
+   library and a job scheduling and queueing system such as PBS,
+   LoadLeveller, Condor, or any of a number of similar tools.  A few
+   example scripts (those used for our \begin{rawhtml} <A
+     href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
+   verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
+   at:
+   \begin{rawhtml} <A
+     href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
+   \end{rawhtml}
+   {\footnotesize \tt
+     http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
+   \begin{rawhtml} </A> \end{rawhtml}
+ \end{enumerate}
  \section{Running the model}
  \label{sect:runModel}
- If compilation finished succesfuully (section \ref{sect:buildModel})
+ If compilation finished succesfuully (section \ref{sect:buildingCode})
- then an executable called {\em mitgcmuv} will now exist in the local
+ then an executable called \texttt{mitgcmuv} will now exist in the
- directory.
+ local directory.
  To run the model as a single process (ie. not in parallel) simply
  type:
-Line 940 
 simulation controls.
+Line 1078 
 simulation controls.
  \begin{description}
  \item[dimensions] \
-   The number of points in the x, y,\textit{\ }and r\textit{\
+   The number of points in the x, y, and r directions are represented
-   }directions are represented by the variables \textbf{sNx}\textit{,
+   by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr}
-   }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
+   respectively which are declared and set in the file
-   which are declared and set in the file \textit{model/inc/SIZE.h.
+   \textit{model/inc/SIZE.h}.  (Again, this assumes a mono-processor
-   }(Again, this assumes a mono-processor calculation. For
+   calculation. For multiprocessor calculations see the section on
-   multiprocessor calculations see section on parallel implementation.)
+   parallel implementation.)
  \item[grid] \
    Three different grids are available: cartesian, spherical polar, and
-   curvilinear (including the cubed sphere). The grid is set through
+   curvilinear (which includes the cubed sphere). The grid is set
-   the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
+   through the logical variables \textbf{usingCartesianGrid},
-     usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
+   \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
-     usingCurvilinearGrid}\textit{. }In the case of spherical and
+   In the case of spherical and curvilinear grids, the southern
-   curvilinear grids, the southern boundary is defined through the
+   boundary is defined through the variable \textbf{phiMin} which
-   variable \textbf{phiMin} \textit{\ }which corresponds to the
+   corresponds to the latitude of the southern most cell face (in
-   latitude of the southern most cell face (in degrees). The resolution
+   degrees). The resolution along the x and y directions is controlled
-   along the x and y directions is controlled by the 1D arrays
+   by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the
-   \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
+   case of a cartesian grid, in degrees otherwise).  The vertical grid
-   the case of a cartesian grid, in degrees otherwise). The vertical
+   spacing is set through the 1D array \textbf{delz} for the ocean (in
-   grid spacing is set through the 1D array \textbf{delz }for the ocean
+   meters) or \textbf{delp} for the atmosphere (in Pa).  The variable
-   (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
+   \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level
-   The variable \textbf{ Ro\_SeaLevel} represents the standard position
+   in ``R'' coordinate. This is typically set to 0m for the ocean
-   of Sea-Level in ''R'' coordinate. This is typically set to 0m for
+   (default value) and 10$^{5}$Pa for the atmosphere. For the
-   the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
+   atmosphere, also set the logical variable \textbf{groundAtK1} to
-   the atmosphere, also set the logical variable \textbf{groundAtK1} to
+   \texttt{'.TRUE.'} which puts the first level (k=1) at the lower
-   '.\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}\textit{\ }and
+   through the variables \textbf{f0} and \textbf{beta} which correspond
-   \textbf{beta}\textit{\ }which correspond to the reference Coriolis
+   to the reference Coriolis parameter (in s$^{-1}$) and
-   parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
+   $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively.
-   m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
+   If \textbf{beta } is set to a nonzero value, \textbf{f0} is the
-   to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
+   value of $f$ at the southern edge of the domain.
-   southern edge of the domain.
  \item[topography - full and partial cells] \
    The domain bathymetry is read from a file that contains a 2D (x,y)
    map of depths (in m) for the ocean or pressures (in Pa) for the
    atmosphere. The file name is represented by the variable
-   \textbf{bathyFile}\textit{. }The file is assumed to contain binary
+   \textbf{bathyFile}. The file is assumed to contain binary numbers
-   numbers giving the depth (pressure) of the model at each grid cell,
+   giving the depth (pressure) of the model at each grid cell, ordered
-   ordered with the x coordinate varying fastest. The points are
+   with the x coordinate varying fastest. The points are ordered from
-   ordered from low coordinate to high coordinate for both axes. The
+   low coordinate to high coordinate for both axes. The model code
-   model code applies without modification to enclosed, periodic, and
+   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 setting the depths to 0m for the cells at the limits
    of the computational domain (note: not sure this is the case for the
    atmosphere). The precision with which to read the binary data is
-   controlled by the integer variable \textbf{readBinaryPrec }which can
+   controlled by the integer variable \textbf{readBinaryPrec} which can
    take the value \texttt{32} (single precision) or \texttt{64} (double
-   precision). See the matlab program \textit{ gendata.m }in the
+   precision). See the matlab program \textit{gendata.m} in the
-   \textit{input }directories under \textit{verification }to see how
+   \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
+   To use the partial cell capability, the variable \textbf{hFacMin}
-   \textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and
+   needs to be set to a value between 0 and 1 (it is set to 1 by
-(it is set to 1 by default) corresponding to the minimum
+   default) corresponding to the minimum fractional size of the cell.
-   fractional size of the cell. For example if the bottom cell is 500m
+   For example if the bottom cell is 500m thick and \textbf{hFacMin} is
-   thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
+   set to 0.1, the actual thickness of the cell (i.e. used in the code)
-   thickness of the cell (i.e. used in the code) can cover a range of
+   can cover a range of discrete values 50m apart from 50m to 500m
-   discrete values 50m apart from 50m to 500m depending on the value of
+   depending on the value of the bottom depth (in \textbf{bathyFile})
-   the bottom depth (in \textbf{bathyFile}) at this point.
+   at this point.
    Note that the bottom depths (or pressures) need not coincide with
-   the models levels as deduced from \textbf{delz}\textit{\
+   the models levels as deduced from \textbf{delz} or \textbf{delp}.
-   }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
+   The model will interpolate the numbers in \textbf{bathyFile} so that
-   the numbers in \textbf{bathyFile} \textit{\ }so that they match the
+   they match the levels obtained from \textbf{delz} or \textbf{delp}
-   levels obtained from \textbf{delz}\textit{ \ }or\textit{\
+   and \textbf{hFacMin}.
-   }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
    (Note: the atmospheric case is a bit more complicated than what is
    written here I think. To come soon...)
-Line 1026 
 simulation controls.
+Line 1161 
 simulation controls.
    \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}.'.
+   variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}.
  \end{description}
-Line 1044 
 humidity profile (in g/kg) for the atmos
+Line 1179 
 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 1063 
 they match those of your configuration).
+Line 1197 
 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 1088 
 salinity is required.
+Line 1223 
 salinity is required.
  \subsection{Momentum equations}
- In this section, we only focus for now on the parameters that you are likely
+ In this section, we only focus for now on the parameters that you are
- to change, i.e. the ones relative to forcing and dissipation for example.
+ likely to change, i.e. the ones relative to forcing and dissipation
- The details relevant to the vector-invariant form of the equations and the
+ for example.  The details relevant to the vector-invariant form of the
- various advection schemes are not covered for the moment. We assume that you
+ equations and the various advection schemes are not covered for the
- use the standard form of the momentum equations (i.e. the flux-form) with
+ moment. We assume that you use the standard form of the momentum
- the default advection scheme. Also, there are a few logical variables that
+ equations (i.e. the flux-form) with the default advection scheme.
- allow you to turn on/off various terms in the momentum equation. These
+ Also, there are a few logical variables that allow you to turn on/off
- variables are called \textbf{momViscosity, momAdvection, momForcing,
+ various terms in the momentum equation. These variables are called
- useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }%
+ \textbf{momViscosity, momAdvection, momForcing, useCoriolis,
- \textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here.
+   momPressureForcing, momStepping} and \textbf{metricTerms }and are
- Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
+ assumed to be set to \texttt{'.TRUE.'} here.  Look at the file
- these variables.
+ \textit{model/inc/PARAMS.h }for a precise definition of these
+ variables.
  \begin{description}
  \item[initialization] \
-Line 1111 
 these variables.
+Line 1247 
 these variables.
  \item[forcing] \
    This section only applies to the ocean. You need to generate
-   wind-stress data into two files \textbf{zonalWindFile}\textit{\ }and
+   wind-stress data into two files \textbf{zonalWindFile} and
-   \textbf{ meridWindFile }corresponding to the zonal and meridional
+   \textbf{meridWindFile} corresponding to the zonal and meridional
    components of the wind stress, respectively (if you want the stress
    to be along the direction of only one of the model horizontal axes,
    you only need to generate one file). The format of the files is
    similar to the bathymetry file. The zonal (meridional) stress data
    are assumed to be in Pa and located at U-points (V-points). As for
    the bathymetry, the precision with which to read the binary data is
-   controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See
+   controlled by the variable \textbf{readBinaryPrec}.  See the matlab
-   the matlab program \textit{gendata.m }in the \textit{input
+   program \textit{gendata.m} in the \textit{input} directories under
-   }directories under \textit{verification }to see how simple
+   \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
    forcing. To do this, concatenate the successive time records into a
-   single file (for each stress component) ordered in a (x, y, t)
+   single file (for each stress component) ordered in a (x,y,t) fashion
-   fashion and set the following variables:
+   and set the following variables: \textbf{periodicExternalForcing }to
-   \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+   \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)
-   \textbf{externForcingPeriod }to the period (in s) of which the
+   of which the forcing varies (typically 1 month), and
-   forcing varies (typically 1 month), and \textbf{externForcingCycle
+   \textbf{externForcingCycle} to the repeat time (in s) of the forcing
-   }to the repeat time (in s) of the forcing (typically 1 year -- note:
+   (typically 1 year -- note: \textbf{ externForcingCycle} must be a
-   \textbf{ externForcingCycle }must be a multiple of
+   multiple of \textbf{externForcingPeriod}).  With these variables set
-   \textbf{externForcingPeriod}).  With these variables set up, the
+   up, the model will interpolate the forcing linearly at each
-   model will interpolate the forcing linearly at each iteration.
+   iteration.
  \item[dissipation] \
    The lateral eddy viscosity coefficient is specified through the
-   variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The
+   variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy
-   vertical eddy viscosity coefficient is specified through the
+   viscosity coefficient is specified through the variable
-   variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and
+   \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and
-   \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.
+   \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The
-   The vertical diffusive fluxes can be computed implicitly by setting
+   vertical diffusive fluxes can be computed implicitly by setting the
-   the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}
+   logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.
-   .'. In addition, biharmonic mixing can be added as well through the
+   In addition, biharmonic mixing can be added as well through the
-   variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a
+   variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar
-   spherical polar grid, you might also need to set the variable
+   grid, you might also need to set the variable \textbf{cosPower}
-   \textbf{cosPower} which is set to 0 by default and which represents
+   which is set to 0 by default and which represents the power of
-   the power of cosine of latitude to multiply viscosity. Slip or
+   cosine of latitude to multiply viscosity. Slip or no-slip conditions
-   no-slip conditions at lateral and bottom boundaries are specified
+   at lateral and bottom boundaries are specified through the logical
-   through the logical variables \textbf{no\_slip\_sides}\textit{\ }
+   variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If
-   and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',
+   set to \texttt{'.FALSE.'}, free-slip boundary conditions are
-   free-slip boundary conditions are applied. If no-slip boundary
+   applied. If no-slip boundary conditions are applied at the bottom, a
-   conditions are applied at the bottom, a bottom drag can be applied
+   bottom drag can be applied as well. Two forms are available: linear
-   as well. Two forms are available: linear (set the variable
+   (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
-   \textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set
+   quadratic (set the variable \textbf{bottomDragQuadratic} in
-   the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$).
+   m$^{-1}$).
    The Fourier and Shapiro filters are described elsewhere.
-Line 1172 
 these variables.
+Line 1307 
 these variables.
  \item[calculation of pressure/geopotential] \
    First, to run a non-hydrostatic ocean simulation, set the logical
-   variable \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure
+   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
+   \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for
-   the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{
+   the 2D case and \textbf{cg3dMaxIters} and
-     cg3dTargetResidual }for the 3D case. You probably won't need to
+   \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
+   logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}
-   \textbf{implicitFreeSurface}\textit{\ }(set one to '.
+   (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}
-   \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how
+   depending on how you want to deal with the ocean upper or atmosphere
-   you want to deal with the ocean upper or atmosphere lower boundary).
+   lower boundary).
  \end{description}
  \subsection{Tracer equations}
- This section covers the tracer equations i.e. the potential temperature
+ This section covers the tracer equations i.e. the potential
- equation and the salinity (for the ocean) or specific humidity (for the
+ temperature equation and the salinity (for the ocean) or specific
- atmosphere) equation. As for the momentum equations, we only describe for
+ humidity (for the atmosphere) equation. As for the momentum equations,
- now the parameters that you are likely to change. The logical variables
+ we only describe for now the parameters that you are likely to change.
- \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{
+ The logical variables \textbf{tempDiffusion} \textbf{tempAdvection}
- tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off
+ \textbf{tempForcing}, and \textbf{tempStepping} allow you to turn
- terms in the temperature equation (same thing for salinity or specific
+ on/off terms in the temperature equation (same thing for salinity or
- humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{
+ specific humidity with variables \textbf{saltDiffusion},
- saltAdvection}\textit{\ }etc). These variables are all assumed here to be
+ \textbf{saltAdvection} etc.). These variables are all assumed here to
- set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a
+ be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h}
- precise definition.
+ for a precise definition.
  \begin{description}
  \item[initialization] \
    The initial tracer data can be contained in the binary files
-   \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files
+   \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files
-   should contain 3D data ordered in an (x, y, r) fashion with k=1 as
+   should contain 3D data ordered in an (x,y,r) fashion with k=1 as the
-   the first vertical level.  If no file names are provided, the
+   first vertical level.  If no file names are provided, the tracers
-   tracers are then initialized with the values of \textbf{tRef }and
+   are then initialized with the values of \textbf{tRef} and
-   \textbf{sRef }mentioned above (in the equation of state section). In
+   \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.
-Line 1224 
 precise definition.
+Line 1359 
 precise definition.
    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
+   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
+   \textbf{surfQfile}.  Alternatively or in addition, the forcing can
-   forcing can be specified through a relaxation term. The SST data to
+   be specified through a relaxation term. The SST data to which the
-   which the model surface temperatures are restored to are supposed to
+   model surface temperatures are restored to are supposed to be stored
-   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
+   in the 2D binary file \textbf{thetaClimFile}. The corresponding
-   }The corresponding relaxation time scale coefficient is set through
+   relaxation time scale coefficient is set through the variable
-   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
+   \textbf{tauThetaClimRelax} (in s). The same procedure applies for
-   procedure applies for salinity with the variable names
+   salinity with the variable names \textbf{EmPmRfile},
-   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
+   \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater
-   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
+   flux (in m/s) and surface salinity (in ppt) data files and
-   and surface salinity (in ppt) data files and relaxation time scale
+   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,
-   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
+   natural boundary conditions are applied i.e. when computing the
-   are applied i.e. when computing the surface salinity tendency, the
+   surface salinity tendency, the freshwater flux is multiplied by the
-   freshwater flux is multiplied by the model surface salinity instead
+   model surface salinity 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 controlled by the variable \textbf{readBinaryPrec}.
-Line 1250 
 precise definition.
+Line 1384 
 precise definition.
  \item[dissipation] \
    Lateral eddy diffusivities for temperature and salinity/specific
-   humidity are specified through the variables \textbf{diffKhT }and
+   humidity are specified through the variables \textbf{diffKhT} and
-   \textbf{diffKhS } (in m$^{2}$/s). Vertical eddy diffusivities are
+   \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are
-   specified through the variables \textbf{diffKzT }and \textbf{diffKzS
+   specified through the variables \textbf{diffKzT} and
-   }(in m$^{2}$/s) for the ocean and \textbf{diffKpT }and
+   \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT
-   \textbf{diffKpS }(in Pa$^{2}$/s) for the atmosphere. The vertical
+   }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The
-   diffusive fluxes can be computed implicitly by setting the logical
+   vertical diffusive fluxes can be computed implicitly by setting the
-   variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'. In
+   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}.
-   addition, biharmonic diffusivities can be specified as well through
+   In addition, biharmonic diffusivities can be specified as well
-   the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in
+   through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in
    m$^{4}$/s). Note that the cosine power scaling (specified through
-   \textbf{cosPower }- see the momentum equations section) is applied
+   \textbf{cosPower}---see the momentum equations section) is applied to
-   to the tracer diffusivities (Laplacian and biharmonic) as well. The
+   the tracer diffusivities (Laplacian and biharmonic) as well. The
    Gent and McWilliams parameterization for oceanic tracers is
    described in the package section. Finally, note that tracers can be
    also subject to Fourier and Shapiro filtering (see the corresponding
-Line 1276 
 precise definition.
+Line 1410 
 precise definition.
    value (if set to a negative value by the user, the model will set it
    to the tracer time step). The other option is to parameterize
    convection with implicit vertical diffusion. To do this, set the
-   logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'
+   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}
-   and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s)
+   and the real variable \textbf{ivdc\_kappa} to a value (in m$^{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
+   \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero
-   non-zero value.
+   value.
  \end{description}
  \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{description}
  \item[run duration] \
    The beginning of a simulation is set by specifying a start time (in
-   s) through the real variable \textbf{startTime }or by specifying an
+   s) through the real variable \textbf{startTime} or by specifying an
    initial iteration number through the integer variable
    \textbf{nIter0}. If these variables are set to nonzero values, the
-   model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to
+   model will look for a ''pickup'' file \textit{pickup.0000nIter0} to
-   restart the integration\textit{. }The end of a simulation is set
+   restart the integration. The end of a simulation is set through the
-   through the real variable \textbf{endTime }(in s).  Alternatively,
+   real variable \textbf{endTime} (in s).  Alternatively, you can
-   you can specify instead the number of time steps to execute through
+   specify instead the number of time steps to execute through the
-   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
+   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
+   saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output
-   output frequency of rolling and permanent checkpoint files,
+   frequency of rolling and permanent checkpoint files, respectively.
-   respectively. See section 1.5.1 Output files for the definition of
+   See section 1.5.1 Output files for the definition of model state and
-   model state and checkpoint files. In addition, time-averaged fields
+   checkpoint files. In addition, time-averaged fields can be written
-   can be written out by setting the variable \textbf{taveFreq} (in s).
+   out by setting the variable \textbf{taveFreq} (in s).  The precision
-   The precision with which to write the binary data is controlled by
+   with which to write the binary data is controlled by the integer
-   the integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32}
+   variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or
-   or \texttt{ 64}).
+   \texttt{64}).
  \end{description}

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