Trough grid refinement (AGRIF nesting & coarsening)

Last edition: Wikinfo(changed_ts)? by Wikinfo(changed_by)?

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 developed 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 NEMO_3.6 , but is available in a specific branch of the 3.6 stable. This branch is regularly phased with the NEMO_3.6. An associated ticket to follow evolution is here.

A presentation is available here​, where the methodology is presented. PdfImg(crs_wiki_1.1.pdf)?

How to activate coarsening ?

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:

! 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 coarsen 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 iodef.xml​ file, a "nemo" context is defined and some variable defined in 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 iodef.xml​ and the associated variable are listed in file_crs_def.xml ​.

Passive tracers tracers initial conditions

When initial conditions are provided in NetCDF files, the field might be:

• on the coarsened grid
• or they can be on another grid and interpolated on-the-fly . Example of namelist for PISCES :

!-----------------------------------------------------------------------
&namtrc_dta      !    Initialisation from data input file
!-----------------------------------------------------------------------
!
   sn_trcdta(1)  = 'DIC_REG1'        ,        -12        ,  'DIC'     ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(2)  = 'ALK_REG1'        ,        -12        ,  'ALK'     ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(3)  = 'O2_REG1'         ,        -1         ,  'O2'      ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(5)  = 'PO4_REG1'        ,        -1         ,  'PO4'     ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(7)  = 'Si_REG1'         ,        -1         ,  'Si'      ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(10) = 'DOC_REG1'        ,        -12        ,  'DOC'     ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(14) = 'Fe_REG1'         ,        -12        ,  'Fe'      ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   sn_trcdta(23) = 'NO3_REG1'        ,        -1         ,  'NO3'     ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
   rn_trfac(1)   =   1.0e-06  !  multiplicative factor
   rn_trfac(2)   =   1.0e-06  !  -      -      -     -
   rn_trfac(3)   =  44.6e-06  !  -      -      -     -
   rn_trfac(5)   = 122.0e-06  !  -      -      -     -
   rn_trfac(7)   =   1.0e-06  !  -      -      -     -
   rn_trfac(10)  =   1.0e-06  !  -      -      -     -
   rn_trfac(14)  =   1.0e-06  !  -      -      -     -
   rn_trfac(23)  =   7.6e-06  !  -      -      -     -

   cn_dir        =  './'      !  root directory for the location of the data files

PISCES forcing files

They might be on the coarsened grid.