********************************** On line biogeochemistry coarsening ********************************** .. todo:: .. contents:: :local: Presentation ============ A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed. This capacity allow to run 'online' a BGC model coupled to OCE-SI3 with a lower resolution, to reduce the CPU cost of the BGC model, while preserving the effective resolution of the dynamics. A presentation is available [attachment:crs_wiki_1.1.pdf​ 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: .. code-block:: console $ 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: .. code-block:: fortran ! 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 = 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 [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 ]. 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 : .. code-block:: fortran !----------------------------------------------------------------------- &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