LMDZ to DYNAMICO start files

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This page explains how to convert a start.nc startfi.nc to a Dynamico There is a wiki page specific for Dynamico just in case: https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/The_DYNAMICO_dynamical_core ).

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

1. Get start.nc and startfi.nc from your simulation via newstart or the PCM.

2. Get an archive file using start2archive 

 a) run : makelmdz_fcm -arch <archive> -d <dimensions (lonxlatxalt)>  -p pluto start2archive to create start_archive
 b) run start2archive.e 
 c) Copy start archive to your new dynamico simulation folder

 cp start_archive.nc dynamico_runs

 d) Convert the start archive to netCDF4

 nccopy -k 4 start_archive.nc start_archive_nc4.nc

3. Follow DYNAMICO with LMDZ physics, to compile icosa_lmdz.exe.

4. Create an initial conditions files for dynamico by running a dynamico simulation without an initial physics file (startphy_file=false). 

 a) In run.def change the following variables (adapt to your case) : run_length=1500, etat_isothermal_temp=200, etat=isothermal and startphy_file=false
 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. Convert the start LMDZ files to the DYNAMCIO grid. 

 a) Compile the files in LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa (where YOUR_PHYSICS is MARS/PLUTO/...) with the compile script, which will create start_archive2icosa and rearrange_startphy. Copy all the files in your simulation folder, but WARNING: there are some xml files that could overwrite your own files (like iodef.xml).
 b) Create a surface_nc4.nc based on your topography (could be a symbolic link)
 d) run start_archive2icosa as a job (requires a lot of memory) and make sure that iodef.xml is the one from the startarchive2icosa folder.
 e) the script creates start_icosa_prefinalize.nc and  startfi_prefinalize.nc
 f) run icosa_finalize.bash
 g) TODO 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 to the one in deftank/dynamico
 b) change in run.def etat0=start_file and add etat0_start_file_colocated=true
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