Mars Dynamico Installation manual

This page follows a manual for installing Mars Dynamico (use the following link to access the wiki page of Dynamico https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core ).

The first step is to compile DYNAMICO using the LMDZ-MARS physics. Please refer to DYNAMICO with LMDZ physics for this step.

1. Install the LMDZ Mars GCM and newstart

 a) make sure u have the datafir and all of the *.def files. 
 b) create start.nc and startfi.nc

2. Compile start2archive with SSO

 a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)>  -p mars start2archive to create start_archive
 b) run start2archive.e --add-sso
 c) cp start_archive.nc to the dynamico_runs folder

3. Create an initial condiations files for dynamico by running a dynamico simulation without the physics.

 a) Copy from ICOSA_LMDZ/bin/icosa_lmdz.exe to a dynamico_runs folder (you should have followed DYNAMICO with LMDZ physics first, to compile icosa_lmdz.exe).
 b) Copy the xml files and the start files and the def files in the dynamico_runs directory and have access to the datadir.
    input file start_archive.nc need be converted to NetCDF4 format
    nccopy -k 4 start_archive.nc start_archive_nc4.nc

4. run dynamic.

 a) In run_icosa.def change to run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false(not start_file)
 b) copy datadir to the running directory
 c) run icosa_lmdz.exe 
 d) copy the files outputed by icosa_lmdz.exe
     1. cp restartfi.nc startphy_icosa_ref.nc
     2. cp restart_icosa.nc start_icosa_ref.nc

5. move to LMDZ.mars/util/startarchive2icosa then change compile script to adapt for the right location of XIOS and run compile u should get start_archive2icosa and rearrange_startphy

 a) copy start_archive2icosa and rearrange_startphy to the dynamico_runs folder.
 b) Create surface_nc4.nc and copy it dynamico_runs folder
 c) source arch.env
 d) run  ./start_archive2icosa as a job (requires a lot of memory) and make sure that Iodef.xml is the one for compile.
 e) the script create start_icosa_prefinalize.nc and  startfi_prefinalize.nc
 f) copy icosa_finalize script form /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash to dynamico_runs folder
 g) change the XIOS and the for startfi0.nc  paths in icosa_finalize.bash and run it. It adds and changes variables in the startfiles.
 h) The scripts outputs startfi.nc and start_icosa.nc
 

6. update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc

7. Run Dynamico simulation

 a) change the iodef.xml
 b) change in run_icosa.def etat0=start_file and add etat0_start_file_colocated=true