[10279] | 1 | ********************************** |
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[10201] | 2 | On line biogeochemistry coarsening |
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[10279] | 3 | ********************************** |
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[10201] | 4 | |
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[11734] | 5 | .. todo:: |
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| 6 | |
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| 7 | |
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| 8 | |
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[10201] | 9 | .. contents:: |
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| 10 | :local: |
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| 11 | |
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| 12 | Presentation |
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[10279] | 13 | ============ |
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[10201] | 14 | |
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| 15 | A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed. |
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| 16 | This capacity allow to run 'online' a BGC model coupled to OCE-SI3 with a lower resolution, |
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| 17 | to reduce the CPU cost of the BGC model, while preserving the effective resolution of the dynamics. |
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| 18 | |
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| 19 | A presentation is available [attachment:crs_wiki_1.1.pdf here], where the methodology is presented. |
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| 20 | |
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| 21 | What is available and working for now in this version |
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[10279] | 22 | ===================================================== |
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[10201] | 23 | |
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| 24 | [To be completed] |
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| 25 | |
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| 26 | Description of the successful validation tests |
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[10279] | 27 | ============================================== |
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[10201] | 28 | |
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| 29 | [To be completed] |
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| 30 | |
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| 31 | What is not working yet with on line coarsening of biogeochemistry |
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[10279] | 32 | ================================================================== |
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[10201] | 33 | |
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| 34 | [To be completed] |
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| 35 | |
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| 36 | ''should include precise explanation on MPI decomposition problems too'' |
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| 37 | |
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| 38 | How to set up and use on line biogeochemistry |
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[10279] | 39 | ============================================= |
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[10201] | 40 | |
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[10279] | 41 | Extract the on line biogeochemistry branch |
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| 42 | ------------------------------------------ |
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[10201] | 43 | |
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[10279] | 44 | To get the appropriate source code with the on line coarsening of biogeochemistry feature: |
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| 45 | |
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| 46 | .. code-block:: console |
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| 47 | |
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| 48 | $ svn co https://forge.ipsl.jussieu.fr/nemo/browser/NEMO/branches/2018/dev_r5003_MERCATOR6_CRS |
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| 49 | |
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| 50 | |
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| 51 | How to activate coarsening? |
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| 52 | --------------------------- |
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| 53 | |
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[10201] | 54 | To activate the coarsening, ``key_crs`` should be added to list of CPP keys. |
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| 55 | This key will only activate the coarsening of dynamics. |
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| 56 | |
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| 57 | Some parameters are available in the namelist_cfg: |
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| 58 | |
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| 59 | .. code-block:: fortran |
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| 60 | |
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| 61 | ! passive tracer coarsened online simulations |
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| 62 | !----------------------------------------------------------------------- |
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| 63 | nn_factx = 3 ! Reduction factor of x-direction |
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| 64 | nn_facty = 3 ! Reduction factor of y-direction |
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| 65 | nn_msh_crs = 0 ! create (=1) a mesh file or not (=0) |
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| 66 | nn_crs_kz = 3 ! 0, volume-weighted MEAN of KZ |
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| 67 | ! 1, MAX of KZ |
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| 68 | ! 2, MIN of KZ |
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[11734] | 69 | ! 3, 10^(MEAN(LOG(KZ)) |
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| 70 | ! 4, MEDIANE of KZ |
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[10201] | 71 | ln_crs_wn = .false. ! wn coarsened (T) or computed using horizontal divergence ( F ) |
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| 72 | ! ! |
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| 73 | ln_crs_top = .true. !coarsening online for the bio |
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| 74 | / |
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| 75 | |
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| 76 | - Only ``nn_factx = 3`` is available and the coarsening only works for grids with a T-pivot point for |
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| 77 | the north-fold lateral boundary condition (ORCA025, ORCA12, ORCA36, ...). |
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| 78 | - ``nn_msh_crs = 1`` will activate the generation of the coarsened grid meshmask. |
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[11734] | 79 | - ``nn_crs_kz`` is the operator to coarsen the vertical mixing coefficient. |
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[10201] | 80 | - ``ln_crs_wn`` |
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| 81 | |
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| 82 | - when ``key_vvl`` is activated, this logical has no effect; |
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| 83 | the coarsened vertical velocities are computed using horizontal divergence. |
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| 84 | - when ``key_vvl`` is not activated, |
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| 85 | |
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[11734] | 86 | - coarsened vertical velocities are computed using horizontal divergence (``ln_crs_wn = .false.``) |
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[10201] | 87 | - or coarsened vertical velocities are computed with an average operator (``ln_crs_wn = .true.``) |
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| 88 | - ``ln_crs_top = .true.``: should be activated to run BCG model in coarsened space; |
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| 89 | so only works when ``key_top`` is in the cpp list and eventually ``key_pisces`` or ``key_my_trc``. |
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| 90 | |
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[10279] | 91 | Choice of operator to coarsene KZ |
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| 92 | --------------------------------- |
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[10201] | 93 | |
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| 94 | A sensiblity test has been done with an Age tracer to compare the different operators. |
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| 95 | The 3 and 4 options seems to provide the best results. |
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| 96 | |
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| 97 | Some results can be found [xxx here] |
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| 98 | |
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[10279] | 99 | Example of xml files to output coarsened variables with XIOS |
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| 100 | ------------------------------------------------------------ |
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[10201] | 101 | |
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| 102 | In the [attachment:iodef.xml iodef.xml] file, a "nemo" context is defined and |
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[11734] | 103 | some variable defined in [attachment:file_def.xml file_def.xml] are writted on the ocean-dynamic grid. |
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[10201] | 104 | To write variables on the coarsened grid, and in particular the passive tracers, |
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| 105 | a "nemo_crs" context should be defined in [attachment:iodef.xml iodef.xml] and |
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| 106 | the associated variable are listed in [attachment:file_crs_def.xml file_crs_def.xml ]. |
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| 107 | |
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[10279] | 108 | Passive tracers tracers initial conditions |
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| 109 | ------------------------------------------ |
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[10201] | 110 | |
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| 111 | When initial conditions are provided in NetCDF files, the field might be: |
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| 112 | |
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| 113 | - on the coarsened grid |
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| 114 | - or they can be on another grid and |
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| 115 | interpolated `on-the-fly <http://forge.ipsl.jussieu.fr/nemo/wiki/Users/SetupNewConfiguration/Weight-creator>`_. |
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| 116 | Example of namelist for PISCES : |
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[11734] | 117 | |
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[10201] | 118 | .. code-block:: fortran |
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| 119 | |
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| 120 | !----------------------------------------------------------------------- |
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| 121 | &namtrc_dta ! Initialisation from data input file |
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| 122 | !----------------------------------------------------------------------- |
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| 123 | ! |
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| 124 | sn_trcdta(1) = 'DIC_REG1' , -12 , 'DIC' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 125 | sn_trcdta(2) = 'ALK_REG1' , -12 , 'ALK' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 126 | sn_trcdta(3) = 'O2_REG1' , -1 , 'O2' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 127 | sn_trcdta(5) = 'PO4_REG1' , -1 , 'PO4' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 128 | sn_trcdta(7) = 'Si_REG1' , -1 , 'Si' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 129 | sn_trcdta(10) = 'DOC_REG1' , -12 , 'DOC' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 130 | sn_trcdta(14) = 'Fe_REG1' , -12 , 'Fe' , .false. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 131 | sn_trcdta(23) = 'NO3_REG1' , -1 , 'NO3' , .true. , .true. , 'yearly' , 'reshape_REG1toeORCA075_bilin.nc' , '' , '' |
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| 132 | rn_trfac(1) = 1.0e-06 ! multiplicative factor |
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| 133 | rn_trfac(2) = 1.0e-06 ! - - - - |
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| 134 | rn_trfac(3) = 44.6e-06 ! - - - - |
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| 135 | rn_trfac(5) = 122.0e-06 ! - - - - |
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| 136 | rn_trfac(7) = 1.0e-06 ! - - - - |
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| 137 | rn_trfac(10) = 1.0e-06 ! - - - - |
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| 138 | rn_trfac(14) = 1.0e-06 ! - - - - |
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| 139 | rn_trfac(23) = 7.6e-06 ! - - - - |
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[11734] | 140 | |
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[10201] | 141 | cn_dir = './' ! root directory for the location of the data files |
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| 142 | |
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[10279] | 143 | PISCES forcing files |
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| 144 | -------------------- |
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[10201] | 145 | |
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| 146 | They might be on the coarsened grid. |
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| 147 | |
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[10279] | 148 | Perspectives |
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| 149 | ============ |
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[10201] | 150 | |
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| 151 | For the future, a few options are on the table to implement coarsening for biogeochemistry in 4.0 and |
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| 152 | future releases. |
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| 153 | Those will be discussed in Autumn 2018 |
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