Changeset 220 for trunk/MESOSCALE_DEV/MANUAL/SRC

Timestamp:

Jul 13, 2011, 10:33:31 PM (13 years ago)

Author:

aslmd

Message:

MESOSCALE: user manual. started chapter about preprocessing steps.

Location:

trunk/MESOSCALE_DEV/MANUAL/SRC

Files:

• compile_exec.tex (modified) (4 diffs)
• installation.tex (modified) (1 diff)
• keep (modified) (1 diff)
• parameters.tex (modified) (2 diffs)
• preproc.tex (added)
• user_manual.tex (modified) (1 diff)
• user_manual_txt.tex (modified) (1 diff)

trunk/MESOSCALE_DEV/MANUAL/SRC/compile_exec.tex

@@ -23 +23 @@
 
 \sk
-In this chapter, the general method to perform steps 0 and 4 is reviewed. Other steps are reviewed in the next chapter. Here the model will be compiled and run in a test case with precomputed sample files for preprocessing steps 1, 2, 3. 
+In this chapter, the general method to perform steps 0 and 4 is reviewed. Other steps are reviewed in chapter~\ref{zepreproc}. Here the model will be compiled and run in a test case with precomputed sample files for preprocessing steps 1, 2, 3. 
 
 \sk
@@ -31 +31 @@
 Please take the time to check the contents of the \ttt{LMD\_MM\_MARS} directories\footnote{If you used method~$2$, you will probably notice that other directories than~\ttt{LMD\_MM\_MARS} are present in \ttt{\$LMDMOD}, but those are not important at this stage.} and sub-directories through the following command lines:
 \begin{verbatim}
-ls $MMM
-ls $MMM/*
+ls $MMM ; ls $MMM/*
 \end{verbatim}
 
@@ -62 +61 @@
 \item \ttt{runmeso}: this is a \ttt{bash} script that can be used once the model and preprocessing systems are installed; it prepares and runs a mesoscale simulation by going from step~1 to~4. 
 \item \ttt{RUN}: this is a directory containing various files and scripts useful for advanced simulations.
-\item \ttt{DEF}: this is a directory containing many examples for parameter files to be used in the LMD Martian Mesoscale Model simulations.
+\item \ttt{DEF}: this is a directory containing many examples of parameter files for simulations.
 \end{citemize}
 
@@ -94 +93 @@
 \item calculate the total number of horizontal grid points handled by the LMD physics;
 \item duplicate LMD physical sources if nesting is activated;
+\pagebreak
 \item compile the LMD physical packages with the appropriate \ttt{makegcm} command
 and collect the compiled objects in the library \ttt{liblmd.a};

trunk/MESOSCALE_DEV/MANUAL/SRC/installation.tex

@@ -35 +35 @@
 \sk
 \begin{finger}
-\item 
-You might also find useful -- though not mandatory -- to install on your system the following software:
+\item If you want the environment variables to be persistent in your system, please copy the \ttt{declare} command lines spread in this user manual in your \ttt{.bashrc} or \ttt{.bash\_profile}. 
+\item You might also find useful -- though not mandatory -- to install on your system:
 \begin{citemize}
 \item \ttt{ncview}\footnote{ \url{http://meteora.ucsd.edu/~pierce/ncview\_home\_page.html} }: tool to visualize the contents of a netCDF file;

trunk/MESOSCALE_DEV/MANUAL/SRC/keep

@@ +1 @@
+
+\footnote{And \ttt{wrfinput\_d02}, \ttt{wrfinput\_d03}, \ldots (one file per domain, see~\ref{nests}) 
+
+
+}
+
 
 %%%

trunk/MESOSCALE_DEV/MANUAL/SRC/parameters.tex

@@ -1 @@
-\chapter{Setting the simulation parameters}
+\chapter{Setting the simulation parameters}\label{zeparam}
 
 \vk
@@ -38 +38 @@
 \begin{citemize}
 \item \ttt{(r)} indicates parameters which modifications imply a new compilation\footnote{A full recompilation using the option \ttt{makemeso -f} is not needed here.} of the model using \ttt{makemeso} (step 0);
-\item \ttt{(p1)}, \ttt{(p2)}, \ttt{(p3)} mention parameters which modification implies a new processing of initial and boundary conditions (see next chapter), corresponding respectively to step~1, 2, 3; \ttt{(p1)} means the user has to carry out again steps~1 to 3 before being able to run the model at step~4; \ttt{(p2)} means the user has to carry out again steps~2 to~3 before model run at step~4; 
+\item \ttt{(p1)}, \ttt{(p2)}, \ttt{(p3)} mention parameters which modification implies a new processing of initial and boundary conditions (see chapter~\ref{zepreproc}), corresponding respectively to step~1, 2, 3; \ttt{(p1)} means the user has to carry out again steps~1 to 3 before being able to run the model at step~4; \ttt{(p2)} means the user has to carry out again steps~2 to~3 before model run at step~4; 
 \item no label means once you have modified the parameter, you can simply start directly at step~4 (running the model);
 \item \ttt{(*d)} denotes dynamical parameters which modification implies non-standard simulations -- please read \ttt{\$MMM/SRC/WRFV2/run/README.namelist} and use with caution, i.e. if you know what you are doing; after modifying those parameters you can simply start at step~4.

trunk/MESOSCALE_DEV/MANUAL/SRC/user_manual.tex

@@ -91 +91 @@
 \include{compile_exec}
 \include{parameters}
+\include{preproc}
 %\include{user_manual_txt}
+%\end{document}
 
 \backmatter

trunk/MESOSCALE_DEV/MANUAL/SRC/user_manual_txt.tex

@@ -1 +1 @@
 
 
-\mk
-\chapter{Preprocessing utilities}
-
-\mk
-In the previous chapter, we decribed the simulation settings
-in the \ttt{namelist.input} file.
-%
-We saw that any modification of the parameters
-labelled with \ttt{(p1)}, \ttt{(p2)} or \ttt{(p3)} 
-implies the initial and boundary conditions
-and/or the domain definition to be recomputed prior to running the model again.
-%
-As a result, you were probably unable to change many of the parameters 
-of the Arsia Mons test case (proposed in section \ref{sc:arsia}) in which 
-the initial and boundary conditions -- as well as the domain of 
-simulation -- were predefined.
-
-\mk
-\marge In this chapter, we describe the installation and use of the preprocessing tools to 
-define the domain of simulation, calculate an initial atmospheric state
-and prepare the boundary conditions for the chosen simulation time.
-%
-This necessary step would eventually allow you to run your own simulations at the specific season and region
-you are interested in, with a complete ability to modify any of the parameters in \ttt{namelist.input}.
-
-\mk
-\section{Installing the preprocessing utilities}
-
-\mk
-First and foremost, since the preprocessing utilities could generate 
-(or involve) files of quite significant sizes, it is necessary
-to define a directory where these files would be stored.
-%
-Such a directory (e.g. \ttt{/bigdisk/user}) must be linked as follows
-%
-\begin{verbatim}
-ln -sf /bigdisk/user $LMDMOD/TMPDIR
-\end{verbatim}
-
-\mk
-\marge A second prerequisite to the installation of the preprocessing tools is that the LMD Martian
-Mesoscale Model was compiled at least once.
-%
-If this is not the case, please compile
-the model with the \ttt{makemeso} command 
-(see section \ref{sc:makemeso}).
-
-\mk
-\marge The compilation process created an
-installation directory adapted to your
-particular choice of compiler$+$machine.
-%
-The preprocessing tools will also
-be installed in this directory.
-%
-Please type the following commands:
-%
-\begin{verbatim}
-cd $LMDMOD/LMD_MM_MARS/g95_32_single/   ## or any install directory
-ln -sf ../prepare_ini .
-./prepare_ini
-\end{verbatim}
-
-\mk
-\marge The script \ttt{prepare\_ini} plays with the preprocessing tools 
-an equivalent role as the \ttt{copy\_model} with the model sources :
-files are simply linked to their actual location in the \ttt{SRC} folder.
-%
-Once you have executed \ttt{prepare\_ini}, please check that
-two folders were generated: \ttt{PREP\_MARS} and \ttt{WPS}. 
-
-\mk
-\marge In the \ttt{PREP\_MARS} directory, please compile
-the programs \ttt{create\_readmeteo.exe} and \ttt{readmeteo.exe}, 
-using the compiler mentionned in the name of the current
-installation directory: 
-%
-\begin{verbatim}
-echo $PWD
-cd PREP_MARS/
-./compile [or] ./compile_g95
-ls -lt create_readmeteo.exe readmeteo.exe
-cd ..
-\end{verbatim}
-
-\mk
-\marge In the \ttt{WPS} directory, please compile
-the programs \ttt{geogrid.exe} and \ttt{metgrid.exe}:
-\begin{verbatim}
-cd WPS/   
-./configure   ## select your compiler + 'NO GRIB2' option
-./compile
-ls -lt geogrid.exe metgrid.exe
-\end{verbatim}
-
-\mk
-\marge Apart from the executables you just compiled,
-the preprocessing utilities include \ttt{real.exe}, 
-which was compiled by the \ttt{makemeso} script
-along with the mesoscale model executable \ttt{wrf.exe}.
-%
-\ttt{real.exe} should be copied or linked in the 
-simulation directory (e.g. \ttt{TESTCASE} for the
-Arsia Mons test case) to be at the same level than
-\ttt{namelist.input}.
-
-\begin{finger}
-\item Even though the name of the executable writes 
-e.g. \ttt{real\_x61\_y61\_z61\_d1\_t1\_p1.exe}, such program
-is not related to the specific \ttt{makemeso} 
-parameters -- contrary to the \ttt{wrf.exe} executable.
-%
-We just found that renaming the (possibly similar
-if the model sources were not modified) 
-\ttt{real.exe} was a practical way not to confuse
-between executables compiled at different moments. 
-\end{finger}
-
-\mk
-\section{Running the preprocessing utilities}
-
-\mk
-When you run a simulation with \ttt{wrf.exe},
-the program attempts to read the initial state 
-in the files 
-\ttt{wrfinput\_d01}, 
-\ttt{wrfinput\_d02}, \ldots 
-(one file per domain)
-and the parent domain boundary conditions
-in \ttt{wrfbdy\_d01}.
-%
-The whole chain of data conversion and
-interpolation needed to generate those
-files is summarized in the diagram next 
-page.
-%
-Three distinct preprocessing steps are
-necessary to generate the final files. 
-%
-As is described in the previous section,
-some modifications in the \ttt{namelist.input} file
-[e.g. start/end dates labelled with \ttt{(p1)}]
-requires a complete reprocessing from step $1$ to step $3$
-to successfully launch the simulation,
-whereas other changes
-[e.g. model top labelled with \ttt{(p3)}] 
-only requires a quick reprocessing at step $3$, keeping
-the files generated at the end of step $2$
-the same.
- 
-\mk
-\subsection{Input data}
-
-\mk
-\subsubsection{Static data}
-
-\mk
-All the static data 
-(topography, thermal inertia, albedo)
-needed to initialize the model
-are included in the \ttt{\$LMDMOD/LMD\_MM\_MARS/WPS\_GEOG} directory.
-%
-By default, only coarse-resolution datasets\footnote{ 
-%%%
-Corresponding to the fields stored in the
-file \ttt{surface.nc} known by LMD-MGCM users:
-\url{http://web.lmd.jussieu.fr/~forget/datagcm/datafile/surface.nc}
-%%%
-} are available, but the directory also contains sources and scripts
-to install finer resolution datasets:
-\begin{citemize}
-\item 32 and/or 64 pixel-per-degree (ppd) MOLA topography [\textit{Smith et al.}, 2001]\nocite{Smit:01mola},
-\item 8 ppd MGS/Thermal Emission Spectrometer (TES) albedo [\textit{Christensen et al.}, 2001]\nocite{Chri:01},
-\item 20 ppd TES thermal inertia [\textit{Putzig and Mellon}, 2007]\nocite{Putz:07} 
-\end{citemize}
-\pagebreak
-\includepdf[pages=1,offset=25mm -20mm]{diagramme.pdf}
-
-\mk
-\marge The role of the \ttt{build\_static} script is to
-automatically download these datasets from the web
-(namely PDS archives) and convert them to an 
-acceptable format for a future use by the 
-preprocessing utilities:
-%
-\begin{verbatim}
-cd $LMDMOD/LMD_MM_MARS
-./build_static
-\end{verbatim}
-%
-\begin{finger}
-\item Please install the \ttt{octave}
-free software\footnote{
-%%%
-Available at \url{http://www.gnu.org/software/octave}
-%%%
-} on your system to be able to use the
-\ttt{build\_static} script.
-%
-Another solution is to browse into each of the
-directories contained within \ttt{WPS\_GEOG}, download the
-data with the shell scripts and execute the \ttt{.m} scripts with either
-\ttt{octave} or the commercial software \ttt{matlab}
-(just replace \ttt{\#} by \ttt{\%}).
-%
-\item If you do not manage to execute the \ttt{build\_static} script, 
-converted ready-to-use datafiles are available upon request.
-%
-\item The building of the MOLA 64ppd topographical 
-database can be quite long. Thus, such a process is
-not performed by default by the \ttt{build\_static} script.
-If the user would like to build this database,
-please remove the \ttt{exit} command in the script, just above
-the commands related to the MOLA 64ppd.
-%
-\item The resulting \ttt{WPS\_GEOG} can reach a size
-of several hundreds of Mo. 
-%
-You might move such a folder in a place 
-with more disk space available, but then be
-sure to create in \ttt{\$LMDMOD/LMD\_MM\_MARS}
-a link to the new location
-of the directory.
-\end{finger}
-
-\mk
-\subsubsection{Meteorological data}
-
-\mk
-The preprocessing tools generate initial and boundary conditions
-from the \ttt{diagfi.nc} outputs of LMD-MGCM simulations.
-%
-If you would like to run a mesoscale simulation at a given
-season, you need to first run a GCM simulation and output
-the meteorological fields at the considered season.
-%
-For optimal forcing at the boundaries, we advise you
-to write the meteorological fields to the 
-\ttt{diagfi.nc} file at least each two hours.
-%
-Please also make sure that the following fields
-are stored in the NETCDF \ttt{diagfi.nc} file:
-
-\footnotesize
-\codesource{contents_diagfi}
-
-\normalsize
-\begin{finger}
-\item If the fields 
-\ttt{emis}, 
-\ttt{co2ice}, 
-\ttt{q01}, 
-\ttt{q02}, 
-\ttt{tsoil} 
-are missing in the \ttt{diagfi.nc} file, 
-they are replaced by respective default 
-values $0.95$, $0$, $0$, $0$, tsurf.
-\end{finger}
-
-\mk
-\marge An example of input meteorological file 
-\ttt{diagfi.nc} file can be downloaded
-at \url{http://web.lmd.jussieu.fr/~aslmd/LMD_MM_MARS/diagfi.nc.tar.gz}.
-%
-Please deflate the archive and copy the \ttt{diagfi.nc} file
-in \ttt{\$LMDMOD/TMPDIR/GCMINI}.
-%
-Such a file can then be used to define the initial
-and boundary conditions, and we will go 
-through the three preprocessing steps.
-
-\mk
-\subsection{Preprocessing steps} 
-
-\mk
-\subsubsection{Step 1: Converting GCM data}
-
-\mk
-\section{Running your own GCM simulations}
-
-\begin{remarque}
-To be completed
-\end{remarque}
-
-\mk
-The programs in the \ttt{PREP\_MARS} directory
-convert the data from the NETCDF \ttt{diagfi.nc}
-file into separated binary datafiles for each
-date contained in \ttt{diagfi.nc}, according to
-the formatting needed by the 
-preprocessing programs at step 2.
-%
-These programs can be executed by the following
-commands: 
-\begin{verbatim}
-cd $LMDMOD/LMD_MM_MARS/your_install_dir/PREP\_MARS
-echo 1 | ./create_readmeteo.exe     # drop the "echo 1 |" if you want control
-./readmeteo.exe < readmeteo.def
-\end{verbatim}
-%
-\marge If every went well with the conversion,
-the directory \ttt{\$LMDMOD/TMPDIR/WPSFEED}
-should contain files named \ttt{LMD:}.
-
-\mk
-\subsubsection{2: Interpolation on the regional domain}
-
-\mk
-In the \ttt{WPS} directory, the \ttt{geogrid.exe} program allows 
-you to define the mesoscale simulation domain
-to horizontally interpolate the topography, 
-thermal inertia and albedo fields at the domain
-resolution and to calculate useful fields
-such as topographical slopes.%\pagebreak
-
-\mk
-\marge Please execute the commands:
-%
-\begin{verbatim}
-cd $LMDMOD/LMD_MM_MARS/your_install_dir/WPS
-ln -sf ../../TESTCASE/namelist.wps .   # test case
-./geogrid.exe
-\end{verbatim}
-%
-\marge The result of \ttt{geogrid.exe} 
--- and thus the definition of the mesoscale
-domain -- can be checked in the NETCDF
-file \ttt{geo\_em.d01.nc}.
-%
-A quick check can be performed using the command line
-\begin{verbatim}
-ncview geo_em.d01.nc
-\end{verbatim} 
-\marge if \ttt{ncview} is installed, or the \ttt{IDL}
-script \ttt{out\_geo.pro}
-\begin{verbatim}
-idl
-IDL> out_geo, field1='TOPO'
-IDL> out_geo, field1='TI'
-IDL> SPAWN, 'ghostview geo_em.d01_HGT_M.ps &'
-IDL> SPAWN, 'ghostview geo_em.d01_THERMAL_INERTIA.ps &'
-IDL> exit
-\end{verbatim}
-\marge if the demo version of \ttt{IDL} is installed.
-%
-Of course if your favorite graphical tool supports
-the NETCDF standard, you might use it to check the
-domain definition in \ttt{geo\_em.d01.nc}.
-
-\mk
-\marge If you are unhappy with the results or
-you want to change 
-the location of the mesoscale domain on the planet, 
-the horizontal resolution,
-the number of grid points \ldots,
-please modify the parameter
-file \ttt{namelist.wps} and execute again \ttt{geogrid.exe}.
-%
-Here are the contents of \ttt{namelist.wps}:
-%
-\codesource{namelist.wps_TEST} 
-
-\begin{finger}
-%
-\item No input meteorological data 
-are actually needed to execute \ttt{geogrid.exe}.
-%
-\item More details about the database and
-more options of interpolation could be
-found in the file \ttt{geogrid/GEOGRID.TBL}.
-%
-\item Defining several domains yields
-distinct files 
-\ttt{geo\_em.d01.nc},
-\ttt{geo\_em.d02.nc},
-\ttt{geo\_em.d03.nc}\ldots
-\end{finger}
-
-\mk
-\marge Once the \ttt{geo\_em} file(s) are generated,
-the \ttt{metgrid.exe} program performs
-a similar horizontal interpolation 
-of the meteorological fields to the mesoscale 
-domain as the one performed by \ttt{geogrid.exe} 
-for the surface data.
-%
-Then the program writes the results in
-\ttt{met\_em} files and also collects
-the static fields and domain parameters
-included in the \ttt{geo\_em} file(s)
-%
-Please type the following commands:
-\begin{verbatim}
-cd $LMDMOD/LMD_MM_MARS/your_install_dir/WPS
-./metgrid.exe
-\end{verbatim}
-%
-\marge If every went well,
-the directory \ttt{\$LMDMOD/TMPDIR/WRFFEED}
-should contain the \ttt{met\_em.*} files.
-
-\mk
-\subsubsection{Step 3: Vertical interpolation on mesoscale levels}
-
-\mk
-\marge The last step is to execute \ttt{real.exe}
-to perform the interpolation from the vertical
-levels of the GCM to the vertical levels 
-defined in the mesoscale model.
-%
-This program also prepares the final initial
-state for the simulation in files called
-\ttt{wrfinput} and the boundary conditions
-in files called \ttt{wrfbdy}.
-
-\mk
-\marge To successfully execute \ttt{real.exe}, 
-you need the \ttt{met\_em.*} files
-and the \ttt{namelist.input} file
-to be in the same directory as \ttt{real.exe}.
-%
-Parameters in \ttt{namelist.input} 
-controlling the behavior of the vertical interpolation 
-are those labelled with \ttt{(p3)} in the detailed
-list introduced in the previous chapter.
-
-\mk
-\marge Please type the following commands
-to prepare files for the Arsia Mons test case
-(or your personal test case if you changed
-the parameters in \ttt{namelist.wps}):
-\begin{verbatim}
-cd $LMDMOD/TESTCASE
-ln -sf $LMDMOD/WRFFEED/met_em* .
-./real.exe
-\end{verbatim}
-
-\mk
-\marge The final message of the \ttt{real.exe}
-should claim the success of the processes and you
-are now ready to launch the integrations
-of the LMD Martian Mesoscale Model again
-with the \ttt{wrf.exe} command as in section
-\ref{sc:arsia}.
-
-\begin{finger}
-\item When you modify either 
-\ttt{namelist.wps} or \ttt{namelist.input},
-make sure that the common parameters
-are exactly similar in both files
-(especially when running nested simulations)
-otherwise either \ttt{real.exe} or \ttt{wrf.exe}
-command will exit with an error message.
-\end{finger}
-%\pagebreak