.. _doc.manual.procedure:

MARS procedure  (Step by Step) 
===============================

How to set up a new configuration 
------------------------------------
See first :ref:`doc.environment.setup`
and :ref:`doc.envir_newconfig`

  * The grid size is defined in parameters.F90[_rank*] with imin=0, jmin=0,imax=***,jmax=***,kmax=***,
  * The rank is noted in parameters.F90[_rank*] with no=*
  * And the "nrac" of the configuration (4 letters) is defined parameters.F90[_rank*] (same as configuration name usually)

Compilation with ranks 
------------------------
Each rank is compiled by modifying *makefile* :
::

  cd $UDIR/CONF/CONF-CASE
  vi makefile, RANK = 0
  gmake clean ; gmake
  vi makefile, RANK = 1
  gmake clean ; gmake

Choice of parametrization 
---------------------------
* 1. **cd $RDIR/CONF/CONF-CASE**

    * Choice parameters and options in namelists files (:ref:`doc_namelistfiles`)
        * :ref:`doc.paramain` and :ref:`doc.paracom` are the same whatever the rank
        * :ref:`doc.paraspec` changes for each rank
             + date_startshift (if negative, date_startshift decreases as the number of the rank increases)
             + l_tide_harmcompo=.true. Only for rank 0
             + l_bathy_meanlev=.true. Except for the rank 0 (because taken into account in the bathymetry file)
        * **open boundary management** in :ref:`doc.paraspec`;  
             + Look at your domain, and specify where are the open boundaries
                . l_obc_east=.true./.false. (if open/closed boundary)
                . l_obc_west=….
             + Specify the file containing the obc fields issued from an ogcm and extract executable
                . file_obc_n='../../inputs/obc_north.nc‘
                . file_obc_e=…
             + Which ogcm variables do you want to read and use at open boundaries ? Specify :
                . l_obc_ogcm_rssh=.false.	! Read the sea surface height
                . l_obc_ogcm_rs=.false.		! Read the salinity
                . l_obc_ogcm_rt=.false.		! Read the temperature
                . l_obc_ogcm_ruv=.false.		! Read the barotropic velocities
                . l_obc_ogcm_ruvz=.false.	! Read the 3d velocities
             + To relax the salinity and temperature towards the ogcm values over a bandwidth specified by obc_width 
                . l_obc_ogcm_relax=.true.
                . obc_coef_relax=0.7e-06  (time relaxation in s-1)
             + others
                . dtmax=1000.d0
                . l_tide_harmcompo=.true.
             + What kind of physics do you want to introduce through the open boundaries ?
                . l_obc_ogcm=.true. 	! If nested with an ogcm
                . l_obc_tide=.true.	! If tide and nested with a previous rank
             + Which operator do you want to use ? Choose one of the following items
                . l_obc_diri=.false.	! Dirichlet
                . l_obc_mars	! Zero gradient of velocities

    * Choice of options and parameters definig outputs files in **output.dat** (:ref:`doc_outputdat`)

    * Build a file **mpi.txt** (for MPI purpose if you want to divide the domain along X AND Y) (:ref:`doc_mpidecomp`)

Choice of inputs data 
---------------------------
* 2. **cd $RDIR/CONF/inputs**

    * modify **head.CONF** (keep the same format !!!) (:ref:`doc_head`)
    * add the **input files** (like bathymetry, initial condition, open boundary conditions, meteo …)
    * modify all default .dat files read by the simulation before any use and add the good path in namelists (ex river.dat, trajec2d*.dat, outflow.dat, variables.dat)

Starting the run 
------------------
* 3. **cd $RDIR/CONF/CONF-CASE**

    * Run directly if small et rapid tests with **mars_exe** 
    * or with *batch_seq*, *batch_omp*, *runmpi_connect* (which uses batch_mpi and batch_connect(bydate) ),
    * or *runmpt_connect…* depending of your choice (:ref:`doc.manual.run`)