.. _mars.init.rst:

Initialization (section **init**)
=================================

* For MARS initialization, for rank_0 *date_startshift=-2* and for rank_1 *date_startshift=0*, in order to give enough time for tide to propagate correctly in rank 0. This means that rank 0 starts 2 days before rank 0, so you have to make meteo start 2 days before start date. Check in section **meteo**:

::

    #startshift = -1.0
    startshift = -2.0

* If you only want to run MARS (no post-processing), change treatments in section **treatments**:

::

  #list = ['meteo', 'obc', 'river', 'rank_0', 'rank_1', 'format_oco','demerliac','mirror_copy','finalize']
  list = ['meteo', 'obc', 'river', 'rank_0', 'rank_1']

* If you want to modify the number of processors, change **nmpi** in section **rank_0** and **rank_1** (in this case, do not forget to move **mpi.txt** if it exists !)

.. note:: In MARS run directory (**MARS/RUN_MARS/MANGAE2500/MANGAE2500-r1630/**), *paraspec.txt.init* is systematically copied at the beginning of the run in *paraspec.txt*. To change *paracom paraspec* or *output* parameters, make it directly in configuration file in subsections **[[[paracom]]]**, **[[[paraspec]]]** or **[[[output]]]**.

::

    [[[paracom]]]
      #file_meteo = '../../inputs/mangae_meteo.nc'
      file_meteo = 'my_file.nc'
    [[[paraspec]]]
      l_out_nc4par='.false.'
    [[[output]]]
      time_startout = '00:00:00'
      l_out_ubt = '.false.'
      pasor = 0.25

* To initialize a MARS run from 01/01/2014 to 03/01/2014: 

::

    launch_mangae config_mangae.cfg -s 2014-01-01,00:00 -e 2014-01-03,00:00 --init

* To follow if the run is OK
   * check if sections are **OK** in **f1-mangae.xml**
   * in case of problem, check the log files **./logs/MANGAE2500-r1630/20140101_20140103/*.log**

* Output files:
    * init file: **./inputs/MANGAE-2500-r1630/init/mangae_init.nc**
    * MARS results and save files in RDIR **./MARS/RUN_MARS/MANGAE2500/MANGAE2500-r1630/**:

      * **rank_0/champs_r1630.nc**
      * **rank_0/save_20140102000000.nc**
      * **rank_0/save_20140103000000.nc**
      * **rank_1/champs_r1630.nc**
      * **rank_1/save_20140102000000.nc**
      * **rank_1/save_20140103000000.nc**

* Section **init** allows to create init file for MARS with *extract*, it is automatically launched with options **--init**

::

  #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  # Section init
  # Préparation des conditions initiales
  # Entrées disponibles :
  #     depend       : liste contenant les noms des traitements dont dépend le traitement courant, liste vide si aucune dépendance
  #     description  : description du traitement (récupéré via l'option --list du script launcher.py)
  #     name         : nom du job soumis sur le calculateur (!!!! ne pas dépasser 15 caractères !!!)
  #     launch       : procédure de lancement associée 
  #     startshift   : optionnel, réél indiquant le décalage en jours du début du traitement par rapport �|  la date de démarrage de référence
  #     lon_to_ni    : optionnel, logique permettant d'activer le renommage des dimensions (considéré comme False si absent)
  # Sous-sections :
  #     options      : sous-section contenant les arguments optionnels de la fonction de récupération des fichiers OBC (retrieve) 
  #     extract      : sous-section concernant l'exécution du programme Extract, contient les entrées suivantes
  #       ogcm_model   : modèle de données OGCM
  #       extract_dir  : emplacement du répertoire Extract
  #       exe          : chemin complet vers l'exécutable Extract
  #       namelist_ref : chemin complet vers la namelist de référence d'Extract qui sera modifiée par la chaîne
  #       namelist     : sous-section d'édition de la namelist de référence     
  #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  
  [[init]]
    depend = []
    description = 'Preparation of initial conditions'
    name = 'mang25_init'
    launch = 'tools.obc.launch_obc'
    lon_to_ni = False
    [[[options]]]
      lonmin = -20
      lonmax = 11
      latmin = 39
      latmax = 57
      verbose = True
    [[[extract]]]
      ogcm_model = 'mercator_psy2v4'
      extract_dir =  '/work/lpineaug/FORMATION_CHAINOP/CHAINOP/tools_fortran/Extract/'
      exe = '%(extract_dir)s/extract_exe'
      namelist_ref = '%(extract_dir)s/IN/namelist_ref'
      [[[[namelist]]]]
        l_extract_ic = '.true.'
        file_coarse = 'MERCATOR_PSY2V4.nc'
        file_ic = 'mangae_init.nc'

* Section **init** parameters are similar to OBC parameters, see OBC section for more details.

.. note:: In MARS run directory (**MARS/RUN_MARS/MANGAE2500/MANGAE2500-r1630/**), *paraspec.txt.init* is systematically copied at the beginning of the run in *paraspec.txt*. To change *paracom paraspec* or *output* parameters, make it directly in configuration file in subsections **[[[paracom]]]**, **[[[paraspec]]]** or **[[[output]]]**.