Changeset 2569


Ignore:
Timestamp:
Oct 19, 2021, 10:14:36 AM (3 years ago)
Author:
emillour
Message:

Mars GCM: update documentation (mostly better handling of http links)
EM

Location:
trunk/LMDZ.MARS
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/LMDZ.MARS/doc/compilation.tex

    r1954 r2569  
    4848\end{verbatim}
    4949
    50 
     50obtain
    5151\section{Organization of the model source files}
    5252\index{Organization of the model source files}
  • trunk/LMDZ.MARS/doc/main.tex

    r1954 r2569  
    55\usepackage{pstricks}
    66\usepackage[round]{natbib}
    7 
     7\usepackage{hyperref}
    88\usepackage{makeidx}
    99\usepackage{a4}
     
    3939\author{Ehouarn MILLOUR, Fran\c{c}ois FORGET  \\ \it{Contributors to earlier versions}: Karine DASSAS, \\ Christophe HOURDIN, Fr\'ed\'eric HOURDIN, \\  and Yann WANHERDRICK}
    4040%\date{\today}
    41 \date{June 20, 2018}
     41\date{October 18, 2021}
    4242
    4343\maketitle
  • trunk/LMDZ.MARS/doc/make_documentation.bash

    r1954 r2569  
    88cd input
    99echo '\begin{verbatim}' > z2sig.tex
    10 cat ../../deftank/z2sig.def >> z2sig.tex
     10cat ../../deftank/z2sig.def.MCD5 >> z2sig.tex
    1111echo '\end{verbatim}' >> z2sig.tex
    1212
  • trunk/LMDZ.MARS/doc/run.tex

    r2206 r2569  
    3939If you are not on the LMD machines, you will also need to download a
    4040set of files available online at:\\
    41 {\verb+http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir+}\\
     41\url{http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir}\\
    4242(preserve the file names and subdirectory structure).
    4343This directory contains input files (topography, dust scenarios,
     
    5050To run the model, you will also need some initial condition files that
    5151can be downloaded from:\\
    52 {\verb+http://www.lmd.jussieu.fr/~lmdz/planets/mars/starts+}
     52\url{http://www.lmd.jussieu.fr/~lmdz/planets/mars/starts}
    5353(see section \ref{sc:inputfiles}).
    5454
     
    6161 compiler suite (e.g. gfortran and gcc, or ifort and icc) that you will use
    6262 to compile the model. The latest version of the NetCDF package is available
    63  on the web at the following address:
    64   \begin{verbatim}
    65   http://www.unidata.ucar.edu/software/netcdf
    66   \end{verbatim}
     63 on the web at the following address:\\
     64  \url{https://www.unidata.ucar.edu/software/netcdf} \\
     65
    6766  along with instructions for building (or downloading precompiled
    6867  binaries of) the library.\\
     
    7372\item Some software to load and display NetCDF files such as
    7473   \begin{itemize}
    75    \item Ferret {\tt http://ferret.wrc.noaa.gov/Ferret}
    76    \item Panoply {\tt https://www.giss.nasa.gov/tools/panoply}
    77    \item GrAdS {\tt http://grads.iges.org/grads}
    78    \item ncview {\tt http://meteora.ucsd.edu/\~pierce/ncview\_home\_page.html}
     74   \item Ferret \url{http://ferret.wrc.noaa.gov/Ferret}
     75   \item Panoply \url{https://www.giss.nasa.gov/tools/panoply}
     76   \item GrAdS \url{http://grads.iges.org/grads}
     77   \item ncview \url{http://meteora.ucsd.edu/~pierce/ncview_home_page.html}
    7978   \end{itemize}
    8079   among others, should be installed on your system.
    8180\item The {\tt fcm} utility must be installed on your system.
    82   If it is not already so, it may be obtained by the following svn command:\\
    83   {\tt svn checkout http://forge.ipsl.jussieu.fr/fcm/svn/PATCHED/FCM\_V1.2}\\
     81  If it is not already so, it may be obtained by the following svn command line:\\
     82  {\verb+ svn checkout http://forge.ipsl.jussieu.fr/fcm/svn/PATCHED/FCM_V1.2+}\\
    8483  And add its {\tt bin} subdirectory to your {\tt PATH} environment variable
    8584  to make the {\tt fcm} command available from anywhere.
     
    168167stndard scenarios and which can thus be used
    169168to check if the model is installed correctly) stored on the LMD website at
    170 \verb+http://www.lmd.jussieu.fr/~lmdz/planets/mars/starts+.
     169\url{http://www.lmd.jussieu.fr/~lmdz/planets/mars/starts}.
    171170See section~\ref{sc:newstart} for a description of how to proceed to
    172171extract {\bf start} files from {\bf start\_archives}.
     
    190189Where {\tt /path/to/datafile} is the full path to the directory which
    191190contains the set of files downloaded from:\\
    192 \verb+http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir+
     191\url{http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir} \\
     192To ease downloading, a tar file of this directory can be obtained at: \\
     193\url{http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir.tar.gz}
    193194}
    194195a simulation:
     
    338339display and the information about the run.
    339340
    340 {\it NOTE:} to restart a series of simulations after a first series
     341To carry on simulations after a first series
    341342(for example, starting from {\tt start5 and  startfi5}), just write the
    342 index of the initial files (e.g. 5) in the file named {\tt num\_run}.
     343index of the initial files (e.g. 5) in the file {\tt num\_run}.
    343344If {\tt num\_run} exists, the model will start from the index written in
    344345{\tt num\_run}. If not it will start from, {\tt start0 and startfi0}.
     
    350351{\tt deftank}).
    351352This script functions with script run0. Just set the number of simulations to
    352 1 in run0. Then copy run.def into run.def.ref and set nday to 9999 in this
     3531 in run0. Then copy {\tt run.def} into {\tt run.def.ref} and set nday to 9999 in this
    353354file. To start from startN.c, edit the file run\_mcd and comment
    354355(with a \#) the N months already created and describe N in {\tt num\_run}.
    355356Then run  {\bf \tt run\_mcd}.
    356357
     358Some scripts similar to {\tt run\_mcd}, but including dedicated handling of job schedulers for the Occigen and Ciclad supercomputers can be found in the {\tt ciclad} and {\tt occigen} subdirectories of {\tt deftank}. Check out the {\tt README} files there.
    357359
    358360\section{Creating and modifying initial states}
     
    463465\end{itemize}
    464466
    465 If you want to create starts files with tarcers for 49 layers using a
     467If you want to create starts files with tracers for 49 layers using a
    466468{\tt start\_archive.nc} obtained for 32 layers, do not forget to use the
    467469\verb+ ini_q+ option in newstart in order to correctly initialize tracers
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