= 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 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: {{{#!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 ]. == Passive tracers tracers initial conditions == When initial conditions are provided in netcdf files, the field might be:[[BR]] - on the coarsened grid [[BR]] - or they can be on another grid and interpolated [browser:Users/SetupNewConfiguration/Weight-creator 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 ==