View source for LMDZ to DYNAMICO start files

This page explains how to convert a start.nc startfi.nc to a [[The DYNAMICO dynamical core|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 ).

== Compilation ==

* The first step is to compile DYNAMICO using the LMDZ physics. Please refer to [[DYNAMICO with LMDZ physics]] for this step. This implies the compilation of [[IOIPSL]], [[XIOS]], [[DYNAMICO]] and [[Quick Install and Run|LMDZ package]] (Generic, Mars, Pluto, ...). It will create the executable '''icosa_lmdz.exe''' in your '''[[ICOSA_LMDZ]]/bin''' directory.

* Compile '''start_archive.e''' using the following command. Replace architecture, dimensions and <your_physics> by your package (mars/pluto/...)
<pre>
makelmdz_fcm -arch <architecture> -d <dimensions (lonxlatxalt)>  -p <your_physics> start2archive 
</pre>

* 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. 

== Preliminary steps == 

To convert your lmdz files to dynamico files, you will need to go through the [[#startarchive2icosa]] script, which requires the following files:

* start_archive_nc4.nc
* startphy_icosa_ref.nc
* start_icosa_ref.nc
* surface_nc4.nc

To get these files, follow the following procedure:

1. Get start.nc and startfi.nc from your simulation via newstart or the PCM and create an archive file using '''start2archive''', and convert it to netcdf4:

<pre>
start2archive.e
nccopy -k 4 start_archive.nc start_archive_nc4.nc
</pre>

2. Create an initial conditions files for dynamico by running a  dynamico simulation without an initial physics file (startphy_file=false).
*a) In '''run_icosa.def''' change the following variables (adapt to your case) : 
<pre>

# short run
run_length=1500
# isothermal could a bad initial state, you can try  etat0=temperature_profile, which reads a 'profile.in' file.
etat=isothermal
etat_isothermal_temp=200
# use LMDZ physics
physics = phys_external
# do not use startfi.nc
startphy_file=false
</pre>

*b) run '''icosa_lmdz.exe''' (fingers crossed it run smoothly) and copy its output files. 
<pre>
icosa_lmdz.exe 
cp restartfi.nc startphy_icosa_ref.nc
cp restart.nc start_icosa_ref.nc
</pre>

3) Create a '''surface_nc4.nc''' based on your topography (could be a symbolic link). 

It may fail if the format is netCDF 3. You can convert the file with '''nc3tonc4''' or '''nccopy -k 4'''.

== startarchive2icosa ==

This script will convert the LMDZ start files to the DYNAMCIO grid.

1) Gather:
* start_archive_nc4.nc
* startphy_icosa_ref.nc
* start_icosa_ref.nc
* surface_nc4.nc
* xml files for DYNAMICO (in deftank/ hopefully)

2) Then get executable files (*.e)  from path/to/LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa/* 
<pre>
ln -s path/to/LMDZ.<YOUR_PHYSICS>/util/startarchive2icosa/
cp -r startarchive2icosa/*.e startarchive2icosa/*.def startarchive2icosa/*.xml startarchive2icosa/job* startarchive2icosa/*sh .
</pre>

3) run '''start_archive2icosa''' as a job (requires a lot of memory). Make sure that '''iodef.xml''' is the one from the '''startarchive2icosa''' folder.
<pre>
sbatch job_start_archive_2icosa
</pre>
The script creates '''start_icosa_prefinalize.nc''' and  '''startfi_prefinalize.nc'''.

4) You will need to run a final script:
<pre>
./icosa_finalize.bash
</pre>

There could be an issue with the location of the LMDZ root folder. Please change the icosa_finalize.bash file accordingly or set the '''LMDZ''' variable in your environment.
The script creates a folder '''icosa_starts/''' with the dynamico '''startfi.nc and start.nc'''.

5. NOT NEEDED? update the tracer name in startfi for each tracer for example: ncrename -v ccn_number_surf,ccn_number startfi.nc. 

== Run Dynamico simulation == 

Create another folder, with the xml and def files from '''deftank/dynamico'''.

In run.def, be sure to have :
<pre>
etat0=start_file 
etat0_start_file_colocated=true
</pre>
Make sure the run.def also lists '''llm''' equal to your start.nc '''lev''' count. If you encounter an error about '''n_glo''' not being equal to your model '''n_glo''', change '''llm''' to match '''lev'''.

Copy in your folder the '''startfi.nc and start.nc''' from the '''icosa_starts/''' folder generated by [[#start_archive2icosa]] and icosa_finalize.bash scripts.

<pre>
mv icosa_starts/start*nc your_dynamico_folder/
</pre>

[[Category:DYNAMICO]]
[[Category:Pluto-DYNAMICO]]