On line biogeochemistry coarsening

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

Work in progress

Presentation

A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed in NEMO_3.6, in an associated branch. 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 3_6 release itself, but is available in a specific associated branch. 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.

What is available and working for now in this version

To be completed

Description of the successful validation tests

To be completed

What is not working yet with on line coarsening of biogeochemistry

To be completed

should include precise explanation on MPI decomposition problems too

How to set up and use on line biogeochemistry

Extract the on line biogeochemistry branch

To get the appropriate source code with the on line coarsening of biogeochemistry feature:

svn co https://forge.ipsl.jussieu.fr/nemo/browser/NEMO/branches/2018/dev_r5003_MERCATOR6_CRS

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.

Perspectives

For the future, a few options are on the table to implement coarsening for biogeochemistry in 4.0 and future releases. Those will be discussed in Autumn 2018