diff --git a/doc/rst/source/unpub/crs.rst b/doc/rst/source/unpub/crs.rst deleted file mode 120000 index afcd1994fe6a61fe00029d01df37b120a9b29c5e..0000000000000000000000000000000000000000 --- a/doc/rst/source/unpub/crs.rst +++ /dev/null @@ -1 +0,0 @@ -../../../../src/OCE/CRS/README.rst \ No newline at end of file diff --git a/doc/rst/source/unpub/crs.rst b/doc/rst/source/unpub/crs.rst new file mode 100644 index 0000000000000000000000000000000000000000..8633dbeb339fd6d61d4f191a6d453c7936d430f8 --- /dev/null +++ b/doc/rst/source/unpub/crs.rst @@ -0,0 +1,153 @@ +********************************** +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 <http://forge.ipsl.jussieu.fr/nemo/wiki/Users/SetupNewConfiguration/Weight-creator>`_. + 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 diff --git a/doc/rst/source/unpub/src.rst b/doc/rst/source/unpub/src.rst deleted file mode 120000 index 683e1231d688ec36297546a00c9068da332237d8..0000000000000000000000000000000000000000 --- a/doc/rst/source/unpub/src.rst +++ /dev/null @@ -1 +0,0 @@ -../../../../src/README.rst \ No newline at end of file diff --git a/doc/rst/source/unpub/src.rst b/doc/rst/source/unpub/src.rst new file mode 100644 index 0000000000000000000000000000000000000000..4ea8114d03b3688ffee7fdda1f82a76942756356 --- /dev/null +++ b/doc/rst/source/unpub/src.rst @@ -0,0 +1,15 @@ +******* +Sources +******* + +.. todo:: + + + +:file:`ICE`: |NEMO-ICE| + +:file:`NST`: AGRIF for embedded zooms + +:file:`OCE`: |NEMO-OCE| + +:file:`TOP`: |NEMO-MBG|