= Trough grid refinement (AGRIF nesting & coarsening)

Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]'''

{{{#!div class="important"
'''Work in progress'''
}}}

= Coarsening of physics for biogeochemistery model =

== Presentation ==

A capacity of coarsening physics to force a BGC model coupled to NEMO has been developped in NEMO_3.6. This capacity allow to run 'online' a BGC model coupled to OPA-LIM with a lower resolution, to reduce the CPU coast of the BGC model, while preserving the effective resolution of the dynamics.


This capacity is not included in the [browser:branches/2015/nemo_v3_6_STABLE/NEMOGCM NEMO_3.6] , but is available in a specific [browser:branches/2015/dev_r5003_MERCATOR6_CRS branch] of the 3.6 stable. This branch is regularly phazed with the NEMO_3.6.
An associated ticket to follow evolution is  [ticket:1426 here].

A presentation is available [attachment:crs_wiki_1.1.pdf​ here], where the methodology is presented.


== How to ? ==

To activate the coarsening, key_crs should be added to list of cpp keys. This key will only activate the coarsening of dynamics.

Some parameters are available in the namelist_cfg:


{{{#!f
               !   passive tracer coarsened online simulations
!-----------------------------------------------------------------------
   nn_factx    = 3         !  Reduction factor of x-direction
   nn_facty    = 3         !  Reduction factor of y-direction
   nn_msh_crs  = 0         !  create (=1) a mesh file or not (=0)
   nn_crs_kz   = 3         ! 0, volume-weighted MEAN of KZ
                           ! 1, MAX of KZ
                           ! 2, MIN of KZ
                           ! 3, 10^(MEAN(LOG(KZ)) 
                           ! 4, MEDIANE of KZ 
   ln_crs_wn   = .false.   ! wn coarsened (T) or computed using horizontal divergence ( F )
                           !                           !
   ln_crs_top = .true.     !coarsening online for the bio
/
}}}

- '''Only nn_factx = nn_facty = 3''' is available and the coarsening only works for grids with a T-pivot point for the north-fold lateral boundary condition( ORCA025, ORCA12,ORCA36,...).

- '''nn_msh_crs  = 1''' : will activate the generation of the coarsened grid meshmask.

- '''nn_crs_kz''' : is the operator to coarsene the vertical mixing coefficient. 

- '''ln_crs_wn''' : when key_vvl is activated, this logical has no effect;  the coarsened vertical velocities are computed using horizontal divergence.
              when key_vvl is not activated, coarsened vertical velocities are computed using horizontal divergence ( ln_crs_wn   = .false ) 
                                             or coarsened vertical velocities are computed with an average operator ( ln_crs_wn   = .true. )
- '''ln_crs_top = .true''': should be activated to run BCG model in coarsened space; so only works when key_top is in the cpp list and eventually key_pisces or key_my_trc.


== Choice of operator to coarsene KZ == 

A sensiblity test has been done with an Age tracer to compare the different operators. The 3 and 4 options seems to provide the best results.

Some results can be found [xxx here]

== Example of xml files to output coarsened variables with XIOS == 


In the [attachment:iodef.xml iodef.xml]  file, a "nemo" context is defined and some variable defined in [attachment:file_def.xml file_def.xml] are writted on the ocean-dynamic grid.  
To write variables on the coarsened grid, and in particular the passive tracers, a "nemo_crs" context should be defined in  [attachment:iodef.xml iodef.xml] and the associated variable are listed in [attachment:file_crs_def.xml file_crs_def.xml ].