Tool Box
Contents
Pre-processing Tools
newstart: a fortran program to modify start files
Newstart is an interactive tool to modify the start files (start.nc and startfi.nc).
To be usable, newstart should be compile in the LMDZ.COMMON directory by using the following command line:
./makelmdz_fcm -arch my_arch_file -p std -d 64x48x30 newstart
In the example, my_arch_file is the name the arch files (see | arch ) and 64x48x30 is the resolution of the physical grid. Then copy the executable from the LMDZ.COMMON/bin directory to your bench directory.
When you execute newstart, you can use both a start2archive file or the start files (start.nc and startfi.nc). Then the interactive interface will propose to modify several physical quantities such as the gravity, the surface pressure or the rotation of the planet. At the end of the procedure, two files are created: restart.nc and restartfi.nc. They can be renamed and used as start files to initialize a new simulation.
start2archive
description of start2archive
- TBD by Guillaume
other third party scripts and tools
TO BE COMPLETED
Post-processing tools
zrecast
With this program you can recast atmospheric (i.e.: 4D-dimentional longitude-latitude-altitude-time) data from GCM outputs (e.g. as given in diagfi.nc files) onto either pressure or altitude above areoid vertical coordinates. Since integrating the hydrostatic equation is required to recast the data, the input file must contain surface pressure and atmospheric temperature, as well as the ground geopotential. If recasting data onto pressure coordinates, then the output file name is given by the input file name to which _P.nc will be appened. If recasting data onto altitude above areoid coordinates, then a _A.nc will be appened.
mass stream function
The mass stream function (and the total angular momentum) can be computed from a diagfi.nc or a stats.nc, using the streamfunction.F90 script. The script is located at
trunk/LMDZ.GENERIC/utilities
To compile the script, open the compile file in the same directory and do the following:
- Replace "pgf90" with your favorite fortran compiler
- replace "/distrib/local/netcdf/pgi_7.1-6_32/lib" with the lib address and directory that contains your NetCDF library (file libnetcdf.a).
- Replace "/distrib/local/netcdf/pgi_7.1-6_32/include" with the address of the directory that contains the NetCDF include file (netcdf.inc).
- You can mess with the compiling options but it is not mandatory.
Once the script is compiled, copy it in the same directory as your .nc file and run
./streamfunction.e
The script will ask you for the name of your .nc file, and will run and produce a new nameofyourfile_stream.nc file.
Be careful : In this new file, all fields are temporally and zonally averaged.
If you want to use python instead of fortran, you can take a look at this repo. It hosts a tool to perform dynamical analysis of GCM simulations (and therefore, it computes the mass stream function and a lot of other stuff), but it is tailored for Dynamico only. This repo also takes care of recasting (it does the job of both zrecast.F90 and streamfunction.F90)
Continuing Simulations
manually
At the end of a simulation, the model generates restart files (files 'restart.nc' and 'restartfi.nc') which contain the final state of the model. The 'restart.nc' and 'restartfi.nc' files have the same format as the 'start.nc' and 'startfi.nc' files, respectively.
These files can in fact be used as initial states to continue the simulation, using the following renaming command lines:
mv restart.nc start.nc
mv restartfi.nc startfi.nc
Running a simulation with these start files will in fact resume the simulation from where the previous run ended.
with bash scripts
We have set up very simple bash scripts to automatize the launching of chain simulations. Here is an example of bash script that does the job:
#!/bin/bash
###########################################################################
# Script to perform several chained LMD Mars GCM simulations
# SET HERE the maximum total number of simulations
nummax=100
###########################################################################
echo "---------------------------------------------------------"
echo "STARTING LOOP RUN"
echo "---------------------------------------------------------"
dir=`pwd`
machine=`hostname`
address=`whoami`
# Look for file "num_run" which should contain
# the value of the previously computed season
# (defaults to 0 if file "num_run" does not exist)
if [[ -r num_run ]] ; then
echo "found file num_run"
numold=`cat num_run`
else
numold=0
fi
echo "numold is set to" ${numold}
# Set value of current season
(( numnew = ${numold} + 1 ))
echo "numnew is set to" ${numnew}
# Look for initialization data files (exit if none found)
if [[ ( -r start${numold}.nc && -r startfi${numold}.nc ) ]] ; then
\cp -f start${numold}.nc start.nc
\cp -f startfi${numold}.nc startfi.nc
else
if (( ${numold} == 99999 )) ; then
echo "No run because previous run crashed ! (99999 in num_run)"
exit
else
echo "Where is file start"${numold}".nc??"
exit
fi
fi
# Run GCM -- THIS LINE NEEDS TO BE MODIFIED WITH THE CORRECT GCM EXECUTION COMMAND
mpirun -np 8 gcm_64x48x26_phystd_para.e < diagfi.def > lrun${numnew}
# Check if run ended normaly and copy datafiles
if [[ ( -r restartfi.nc && -r restart.nc ) ]] ; then
echo "Run seems to have ended normaly"
\mv -f restart.nc start${numnew}.nc
\mv -f restartfi.nc startfi${numnew}.nc
else
if [[ -r num_run ]] ; then
\mv -f num_run num_run.crash
else
echo "No file num_run to build num_run.crash from !!"
# Impose a default value of 0 for num_run
echo 0 > num_run.crash
fi
echo 99999 > num_run
exit
fi
# Copy other datafiles that may have been generated
if [[ -r diagfi.nc ]] ; then
\mv -f diagfi.nc diagfi${numnew}.nc
fi
if [[ -r diagsoil.nc ]] ; then
\mv -f diagsoil.nc diagsoil${numnew}.nc
fi
if [[ -r stats.nc ]] ; then
\mv -f stats.nc stats${numnew}.nc
fi
if [[ -f profiles.dat ]] ; then
\mv -f profiles.dat profiles${numnew}.dat
\mv -f profiles.hdr profiles${numnew}.hdr
fi
# Prepare things for upcoming runs by writing
# value of computed season in file num_run
echo ${numnew} > num_run
# If we are over nummax : stop
if (( $numnew + 1 > $nummax )) ; then
exit
else
\cp -f run_gnome exe_mars
./exe_mars
fi
Summary of what this bash script does:
- It reads the file 'num_run' which contains the step of the simulation.
If num_run is
5
then the script expects to read start5.nc and startfi5.nc.
- It modifies start5.nc and startfi5.nc into start.nc and startfi.nc, respectively.
- It runs the GCM.
- It modifies restart.nc and restartfi.nc into start6.nc and startfi6.nc
- It rewrite num_run as follows:
6
- It restarts the loop until num_run reaches the value (defined in nummax):
100
Visualization software
Panoply
Panoply is a user-friendly tool for viewing raw NetCDF data, available here: https://www.giss.nasa.gov/tools/panoply/
Planetoplot
Planetoplot is a in-house, python based library developped to vizualize LMDG data.
The code and documentation can be found at: https://nbviewer.org/github/aymeric-spiga/planetoplot/blob/master/tutorial/planetoplot_tutorial.ipynb
ncview
Command line tool to visualize NetCDF data.
- Installation on Linux:
sudo apt install ncview
paraview
python scripts
The xarray python library is a very good tool to easily load and plot netcdf data.
TBD
