Changeset 10541 for NEMO/trunk/cfgs/README.rst
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NEMO/trunk/cfgs/README.rst
r10460 r10541 1 *************************** 2 Run built-in configurations 3 *************************** 4 5 .. contents:: 6 :local: 7 :depth: 1 8 9 Official configurations 10 ======================= 11 12 | NEMO is distributed with some reference configurations allowing both the user to set up a first application and 13 the developer to validate their developments. 14 | :underline:`The NEMO System Team is in charge of these configurations`. 15 16 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 17 | | OPA | SI3 | TOP | PISCES | AGRIF | Inputs | 18 +======================+=====+=====+=====+========+=======+==========================+ 19 | `AGRIF_DEMO`_ | X | X | | | X | - AGRIF_DEMO_v4.0.tar | 20 | | | | | | | - ORCA2_ICE_v4.0.tar | 21 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 22 | `AMM12`_ | X | | | | | AMM12_v4.0.tar | 23 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 24 | `C1D_PAPA`_ | X | | | | | INPUTS_C1D_PAPA_v4.0.tar | 25 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 26 | `GYRE_BFM`_ | X | | X | | | ``-`` | 27 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 28 | `GYRE_PISCES`_ | X | | X | X | | ``-`` | 29 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 30 | `ORCA2_ICE_PISCES`_ | X | X | X | X | | - ORCA2_ICE_v4.0.tar | 31 | | | | | | | - INPUTS_PISCES_v4.0.tar | 32 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 33 | `ORCA2_OFF_PISCES`_ | | | X | X | | - INPUTS_PISCES_v4.0.tar | 34 | | | | | | | - ORCA2_OFF_v4.0.tar | 35 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 36 | `ORCA2_OFF_TRC`_ | | | X | | | ORCA2_OFF_v4.0.tar | 37 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 38 | `ORCA2_SAS_ICE`_ | | X | | | | - ORCA2_ICE_v4.0.tar | 39 | | | | | | | - INPUTS_SAS_v4.0.tar | 40 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 41 | `SPITZ12`_ | X | X | | | | SPITZ12_v4.0.tar | 42 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 1 REFERENCE CONFIGURATIONS 2 ======================== 3 4 NEMO is distributed with a set of reference configurations allowing both the user to set up his own first applications and the developer to test/validate his NEMO developments (using SETTE package). 5 *The NEMO System Team is in charge only for these configurations.* 6 7 Configurations developed by external research projects or initiatives that make use of NEMO are welcome to be publicized also through the NEMO website by filling up the form `Add project <http://www.nemo-ocean.eu/projects/add>`_ 8 9 Available Configurations 10 ------------------------ 11 ====================== ===== ===== ===== ======== ======= ================================================ 12 Configuration Component(s) Input & Forcing File(s) 13 ---------------------- ---------------------------------- ------------------------------------------------ 14 Name OPA SI3 TOP PISCES AGRIF 15 ====================== ===== ===== ===== ======== ======= ================================================ 16 AGRIF_DEMO_ X X X AGRIF_DEMO_v4.0.tar_, ORCA2_ICE_v4.0.tar_ 17 AMM12_ X AMM12_v4.0.tar_ 18 C1D_PAPA_ X INPUTS_C1D_PAPA_v4.0.tar_ 19 GYRE_BFM_ X X *none* 20 GYRE_PISCES_ X X X *none* 21 ORCA2_ICE_PISCES_ X X X X ORCA2_ICE_v4.0.tar_, INPUTS_PISCES_v4.0.tar_ 22 ORCA2_OFF_PISCES_ X X ORCA2_OFF_v4.0.tar_, INPUTS_PISCES_v4.0.tar_ 23 ORCA2_OFF_TRC_ X ORCA2_OFF_v4.0.tar_ 24 ORCA2_SAS_ICE_ X ORCA2_ICE_v4.0.tar_, INPUTS_SAS_v4.0.tar_ 25 SPITZ12_ X X SPITZ12_v4.0.tar_ 26 ====================== ===== ===== ===== ======== ======= ================================================ 27 28 **How to compile an experiment from a reference configuration** 29 30 A user who wants to compile the ORCA2_ICE_PISCES_ reference configuration using makenemo should use the following, by selecting among available architecture file or providing a user defined one: 31 32 33 .. code-block:: console 34 35 $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4' 36 37 A new EXP00 folder will be created within the selected reference configurations, namely ``trunk/cfgs/ORCA2_ICE_PISCES/EXP00``, where it will be necessary to uncompress the Input & Forcing Files listed in the above table. 38 39 Then it will be possible to launch the execution of the model through a runscript (opportunely adapted to the user system). 43 40 44 41 AGRIF_DEMO 45 42 ---------- 46 43 47 .. image:: _static/AGRIF_DEMO.jpg 48 49 ``AGRIF_DEMO`` is based on the ``ORCA2_LIM3_PISCES`` global 2° configuration but 50 it includes 3 online nested grids that demonstrate the overall capabilities of AGRIF in a realistic context, 51 including nesting sea ice models. 52 53 The configuration includes a 1:1 grid in the Pacific and two successively nested grids with odd and 54 even refinement ratios over the Arctic ocean. 55 The finest grid spanning the whole Svalbard archipelago is of particular interest to check that 56 sea ice coupling is done properly. 57 The 1:1 grid, used alone, is used as a benchmark to check that the solution is not corrupted by grid exchanges. 58 59 Note that since grids interact only at the baroclinic time level, 60 numerically exact results can not be achieved in the 1:1 case. 61 One has to switch to a fully explicit in place of a split explicit free surface scheme in order to 62 retrieve perfect reproducibility. 63 64 Corresponding ``AGRIF_FixedGrids.in`` file is given by:: 65 66 2 67 42 82 49 91 1 1 1 68 122 153 110 143 4 4 4 69 0 70 1 71 38 80 71 111 3 3 3 72 0 44 AGRIF_DEMO is based on the ORCA2_ICE_PISCES_ global configuration at 2° of resolution with the inclusion of 3 online nested grids to demonstrate the overall capabilities of AGRIF (Adaptive Grid Refinement In Fortran) in a realistic context (including the nesting of sea ice models). 45 46 The configuration includes a 1:1 grid in the Pacific and two successively nested grids with odd and even refinement ratios over the Arctic ocean, with the finest grid spanning the whole Svalbard archipelago that is of particular interest to test sea ice coupling. 47 48 The 1:1 grid can be used alone as a benchmark to check that the model solution is not corrupted by grid exchanges. 49 Note that since grids interact only at the baroclinic time level, numerically exact results can not be achieved in the 1:1 case. Perfect reproducibility is obtained only by switching to a fully explicit setip instead of a split explicit free surface scheme. 73 50 74 51 AMM12 75 52 ----- 76 53 77 ``AMM12`` for *Atlantic Margin Model 12kms* is a `regional model`_ covering the Northwest European Shelf domain on 78 a regular lat-lon grid at approximately 12km horizontal resolution. 79 The key ``key_amm_12km`` is used to create the correct dimensions of the AMM domain. 80 81 | This configuration tests several features of NEMO functionality specific to the shelf seas. 82 | In particular, the AMM uses s-coordinates in the vertical rather than z-coordinates and is forced with 83 tidal lateral boundary conditions using a flather boundary condition from the BDY module (``key_bdy``). 84 85 The AMM configuration uses the GLS (``key_zdfgls``) turbulence scheme, 86 the VVL non-linear free surface (``key_vvl``) and time-splitting (``key_dynspg_ts``). 87 88 In addition to the tidal boundary condition, the model may also take open boundary conditions from 89 a North Atlantic model. 90 Boundaries may be completely ommited by removing the BDY key (key_bdy) in ``./cfgs/AMM12/cpp_AMM12_fcm``. 91 92 Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run. 93 The Baltic boundary is included within the river input file and is specified as a river source. 94 Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 54 AMM12 stands for *Atlantic Margin Model at 12 km* that is a regional configuration covering the Northwest European Shelf domain on a regular horizontal grid of ~12 km of resolution (see `O'Dea et al., 2012 <http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128>`_). 55 56 This configuration allows to tests several features of NEMO specifically addressed to the shelf seas. 57 In particular, AMM12 accounts for vertical s-coordinates system, GLS turbulence scheme, tidal lateral boundary conditions using a flather scheme (see more in BDY). 58 Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``. 59 60 Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run (AMM12_v4.0.tar_). 61 62 Note that, the Baltic boundary is included within the river input file and is specified as a river source, but unlike ordinary river points the Baltic inputs also include salinity and temperature data. 95 63 96 64 C1D_PAPA 97 65 -------- 98 66 99 ``C1D_PAPA`` is a 1D configuration (one water column called NEMO1D, activated with CPP key ``key_c1d``), 100 located at the `PAPA station 145W-50N <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_. 101 102 | NEMO1D is useful to test vertical physics in NEMO 103 (turbulent closure scheme, solar penetration, interaction ocean/atmosphere.,...) 104 | Size of the horizontal domain is 3x3 grid points. 105 106 This reference configuration uses a 75 vertical levels grid (1m at the surface), 107 the GLS (key_zdfgls) turbulence scheme with K-epsilon closure and the CORE BULK formulae. 108 The atmospheric forcing comes from ECMWF operational analysis with a modification of the long and short waves flux. 109 This set has been rescaled at a frequency of 1h. 1 year is simulated in outputs, 110 see below (June,15 2010 to June,14 2011) 111 112 `Reffray 2015`_ describes some tests on vertical physic using this configuration. 113 114 The inputs tar file includes: 115 116 - forcing files covering the years 2010 and 2011 (``forcing_PAPASTATION_1h_y201*.nc``) 117 - initialization file for June,15 2010 deduced from observed data and Levitus 2009 climatology 118 (``init_PAPASTATION_m06d15.nc``) 119 - surface chlorophyll file (``chlorophyll_PAPASTATION.nc``) deduced from Seawifs data. 67 C1D_PAPA is a 1D configuration for the `PAPA station <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_ located in the northern-eastern Pacific Ocean at 50.1°N, 144.9°W. See `Reffray et al. (2015) <http://www.geosci-model-dev.net/8/69/2015>`_ for the description of its physical and numerical turbulent-mixing behaviour. 68 69 The water column setup, called NEMO1D, is activated with the inclusion of the CPP key ``key_c1d`` and has a horizontal domain of 3x3 grid points. 70 71 This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae. 72 Data provided with INPUTS_C1D_PAPA_v4.0.tar_ file account for : 73 74 - ``forcing_PAPASTATION_1h_y201[0-1].nc`` : ECMWF operational analysis atmospheric forcing rescaled to 1h (with long and short waves flux correction) for years 2010 and 2011 75 - ``init_PAPASTATION_m06d15.nc`` : Initial Conditions from observed data and Levitus 2009 climatology 76 - ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data 77 120 78 121 79 GYRE_BFM 122 80 -------- 123 81 124 ``GYRE_BFM`` is the same configuration as `GYRE_PISCES`_, except that PISCES is replaced by 125 BFM biogeochemichal model in coupled mode. 82 GYRE_BFM shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in :trac:`source:/NEMO/trunk/cfgs/GYRE_BFM/README`. 83 126 84 127 85 GYRE_PISCES 128 86 ----------- 129 87 130 | Idealized configuration representing double gyres in the North hemisphere, Beta-plane with 131 a regular grid spacing at 1° horizontal resolution (and possible use as a benchmark by 132 easily inscreasing grid size), 101 vertical levels, forced with analytical heat, freshwater and 133 wind-stress fields. 134 | This configuration is coupled to `PISCES biogeochemical model`_. 135 136 Running GYRE as a benchmark 137 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 138 139 This simple configuration can be used as a benchmark since it is easy to increase resolution 140 (and in this case no physical meaning of outputs): 141 142 1. Choose the grid size 143 144 In ``./cfgs/GYRE/EXP00``, edit your ``namelist_cfg`` file to change the ``jp_cfg``, ``jpi``, ``jpj``, 145 ``jpk`` variables in &namcfg: 146 147 +------------+---------+---------+---------+------------------+---------------+ 148 | ``jp_cfg`` | ``jpi`` | ``jpj`` | ``jpk`` | Number of points | Equivalent to | 149 +============+=========+=========+=========+==================+===============+ 150 | 1 | 30 | 20 | 101 | 60600 | GYRE 1° | 151 +------------+---------+---------+---------+------------------+---------------+ 152 | 25 | 750 | 500 | 101 | 37875000 | ORCA 1/2° | 153 +------------+---------+---------+---------+------------------+---------------+ 154 | 50 | 1500 | 1000 | 101 | 151500000 | ORCA 1/4° | 155 +------------+---------+---------+---------+------------------+---------------+ 156 | 150 | 4500 | 3000 | 101 | 1363500000 | ORCA 1/12° | 157 +------------+---------+---------+---------+------------------+---------------+ 158 | 200 | 6000 | 4000 | 101 | 2424000000 | ORCA 1/16° | 159 +------------+---------+---------+---------+------------------+---------------+ 160 161 2. In `namelist_cfg` again, avoid problems in the physics (and results will not be meaningful in terms of physics) by setting `nn_bench = 1` in &namctl 162 163 .. code-block:: fortran 164 165 nn_bench = 1 ! Bench mode (1/0): CAUTION use zero except for bench 166 167 3. If you increase domain size, you may need to decrease time-step (for stability) by changing `rn_rdt` value in &namdom (i.e. for `jp_cfg = 150`, ORCA12 equivalent, use `rn_rdt = 1200`) 88 GYRE_PISCES is an idealized configuration representing a Northern hemisphere double gyres system, in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels, which is coupled with `PISCES biogeochemical model`_. Analytical forcing for heat, freshwater and wind-stress fields are applied. 89 90 This configuration act also as demonstrator of the **USER DEFINED setup** (``ln_read_cfg = .false.``) and grid setting are handled through the ``&namusr_def`` controls in namelist_cfg: 91 92 .. code-block:: fortran 93 94 !----------------------------------------------------------------------- 95 &namusr_def ! GYRE user defined namelist 96 !----------------------------------------------------------------------- 97 nn_GYRE = 1 ! GYRE resolution [1/degrees] 98 ln_bench = .false. ! ! =T benchmark with gyre: the gridsize is kept constant 99 jpkglo = 31 ! number of model levels 100 / 101 102 Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and vertical levels are set by ``jpkglo``. The specific code changes can be inspected at :trac:`source:/NEMO/trunk/src/OCE/USR` 103 104 **Running GYRE as a benchmark** : this simple configuration can be used as a benchmark since it is easy to increase resolution, with the drawback of getting results that have a very limited physical meaning. 105 106 GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE`` (integer multiplier scaling factor), as described in the following table: 107 108 =========== ========= ========== ============ =================== 109 ``nn_GYRE`` *jpiglo* *jpjglo* ``jpkglo`` **Equivalent to** 110 =========== ========= ========== ============ =================== 111 1 30 20 31 GYRE 1° 112 25 750 500 101 ORCA 1/2° 113 50 1500 1000 101 ORCA 1/4° 114 150 4500 3000 101 ORCA 1/12° 115 200 6000 4000 101 ORCA 1/16° 116 =========== ========= ========== ============ =================== 117 118 Note that, it is necessary to set ``ln_bench = .true.`` in ``namusr_def`` to avoid problems in the physics computation and that the model timestep should be adequately rescaled. 119 120 For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, the timestep should be set to 1200 seconds 168 121 169 122 .. code-block:: fortran … … 171 124 rn_rdt = 1200. ! time step for the dynamics 172 125 173 4. Optional, in order to increase the number of MPI communication for benchmark purposes: 174 you can change the number of sub-timesteps computed in the time-splitting scheme each iteration. 175 First change the list of active CPP keys for your experiment, 176 in `cfgs/"your configuration name"/cpp_"your configuration name".fcm`: 177 replace ``key_dynspg_flt by key_dynspg_ts`` and recompile/create your executable again 178 179 .. code-block:: fortran 180 181 makenemo [...] add_key 'key_dynspg_ts' del_key 'key_dynspg_flt' 182 183 In your ``namelist_cfg`` file, edit the &namsplit namelist by adding the following line: 184 185 .. code-block:: fortran 186 187 nn_baro = 30 ! Number of iterations of barotropic mode/ 188 189 ``nn_baro = 30`` is a kind of minimum (we usually use 30 to 60). 190 So than increasing the ``nn_baro`` value will increase the number of MPI communications. 191 192 The GYRE CPP keys, namelists and scripts can be explored in the ``GYRE`` configuration directory 193 (``./cfgs/GYRE`` and ``./cfgs/GYRE/EXP00``). 194 195 Find monthly mean outputs of 1 year run here: 196 http://prodn.idris.fr/thredds/catalog/ipsl_public/reee451/NEMO_OUT/GYRE/catalog.html 126 Differently from previous versions of NEMO, the code uses by default the time-splitting scheme and internally computes the number of sub-steps. 127 197 128 198 129 ORCA2_ICE_PISCES 199 130 ---------------- 200 131 201 ORCA is the generic name given to global ocean configurations. 202 Its specificity lies on the horizontal curvilinear mesh used to overcome the North Pole singularity found for 203 geographical meshes. 204 SI3 (Sea Ice Integrated Initiative) is a thermodynamic-dynamic sea ice model specifically designed for 205 climate studies. 206 A brief description of the model is given here. 207 208 :underline:`Space-time domain` 209 210 The horizontal resolution available through the standard configuration is ORCA2. 211 It is based on a 2 degrees Mercator mesh, (i.e. variation of meridian scale factor as cosinus of the latitude). 212 In the northern hemisphere the mesh has two poles so that the ratio of anisotropy is nearly one everywhere. 213 The mean grid spacing is about 2/3 of the nominal value: for example it is 1.3 degrees for ORCA2. 214 Other resolutions (ORCA4, ORCA05 and ORCA025) are running or under development within specific projects. 215 In the coarse resolution version (i.e. ORCA2 and ORCA4) the meridional grid spacing is increased near 216 the equator to improve the equatorial dynamics. 217 Figures in pdf format of mesh and bathymetry can be found and downloaded here. 218 The sea-ice model runs on the same grid. 219 220 The vertical domain spreads from the surface to a depth of 5000m. 221 There are 31 levels, with 10 levels in the top 100m. 222 The vertical mesh is deduced from a mathematical function of z ([[AttachmentNum(1)]]). 223 The ocean surface corresponds to the w-level k=1, and the ocean bottom to the w-level k=31. 224 The last T-level (k=31) is thus always in the ground.The depths of the vertical levels and 225 the associated scale factors can be viewed. 226 Higher vertical resolution is used in ORCA025 and ORCA12 (see `DRAKKAR project <http://www.drakkar-ocean.eu>`_). 227 228 The time step depends on the resolution. It is 1h36' for ORCA2 so that there is 15 time steps in one day. 229 230 :underline:`Ocean Physics (for ORCA2)` 231 232 - horizontal diffusion on momentum: the eddy viscosity coefficient depends on the geographical position. 233 It is taken as 40000 $m^2/s$, reduced in the equator regions (2000 $m^2/s$) excepted near the western boundaries. 234 - isopycnal diffusion on tracers: the diffusion acts along the isopycnal surfaces (neutral surface) with 235 a eddy diffusivity coefficient of 2000 $m^2/s$. 236 - Eddy induced velocity parametrization with a coefficient that depends on the growth rate of 237 baroclinic instabilities (it usually varies from 15 $m^2/s$ to 3000 $m^2/s$). 238 - lateral boundary conditions : zero fluxes of heat and salt and no-slip conditions are applied through 239 lateral solid boundaries. 240 - bottom boundary condition : zero fluxes of heat and salt are applied through the ocean bottom. 132 ORCA2_ICE_PISCES is a reference configuration for the global ocean with a 2°x2° curvilinear horizontal mesh and 31 vertical levels, distributed using z-coordinate system and with 10 levels in the top 100m. 133 ORCA is the generic name given to global ocean Mercator mesh, (i.e. variation of meridian scale factor as cosinus of the latitude), with two poles in the northern hemisphere so that the ratio of anisotropy is nearly one everywhere 134 135 In this configuration, the ocean dynamical core is coupled to 136 137 - **ICE**, namely SI3 (Sea Ice Integrated Initiative) a thermodynamic-dynamic sea ice model specifically designed for climate studies. 138 - **TOP**, passive tracer transport module and `PISCES biogeochemical model`_ 139 140 All components share the same grid. 141 142 The model is forced with CORE-II normal year atmospheric forcing and it uses the NCAR bulk formulae. 143 144 **Ocean Physics configuration** 145 146 - *horizontal diffusion on momentum*: the eddy viscosity coefficient depends on the geographical position. It is taken as 40000 m^2/s, reduced in the equator regions (2000 m^2/s) excepted near the western boundaries. 147 - *isopycnal diffusion on tracers*: the diffusion acts along the isopycnal surfaces (neutral surface) with an eddy diffusivity coefficient of 2000 m^2/s. 148 - *Eddy induced velocity parametrization* with a coefficient that depends on the growth rate of baroclinic instabilities (it usually varies from 15 m^2/s to 3000 m^2/s). 149 - *lateral boundary conditions* : zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries. 150 - *bottom boundary condition* : zero fluxes of heat and salt are applied through the ocean bottom. 241 151 The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes. 242 152 A linear friction is applied on momentum. 243 - convection: the vertical eddy viscosity and diffusivity coefficients are increased to 1 $m^2/s$ in case of 244 static instability. 245 - forcings: the ocean receives heat, freshwater, and momentum fluxes from the atmosphere and/or the sea-ice. 246 The solar radiation penetrates the top meters of the ocean. 247 The downward irradiance I(z) is formulated with two extinction coefficients [Paulson and Simpson, 1977], 248 whose values correspond to a Type I water in Jerlov's classification (i.e the most transparent water) 249 250 ORCA2_ICE_PISCES is a reference configuration with the following characteristics: 251 252 - global ocean configuration 253 - based on a tri-polar ORCA grid, with a 2° horizontal resolution 254 - 31 vertical levels 255 - forced with climatological surface fields 256 - coupled to the sea-ice model SI3. 257 - coupled to TOP passive tracer transport module and `PISCES biogeochemical model`_. 258 259 :underline:`AGRIF demonstrator` 260 261 | From the ``ORCA2_ICE_PISCES`` configuration, a demonstrator using AGRIF nesting can be activated. 262 It includes the global ``ORCA2_ICE_PISCES`` configuration and a nested grid in the Agulhas region. 263 | To set up this configuration, after extracting NEMO: 264 265 - Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated: 153 - *convection*: the vertical eddy viscosity and diffusivity coefficients are increased to 1 m^2/s in case of static instability. 154 - *time step* is 5760sec (1h36') so that there is 15 time steps in one day. 155 156 157 158 **AGRIF demonstrator** 159 160 From the ORCA2_ICE_PISCES configuration, a demonstrator using AGRIF nesting can be activated that includes a nested grid in the Agulhas region. 161 162 To set up this configuration, after extracting NEMO: 163 164 Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated: 266 165 267 166 .. code-block:: console 268 167 269 $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif' 270 271 - Using the ``ORCA2_ICE_PISCES`` input files and namelist, AGRIF test configuration is ready to run 272 273 :underline:`On-The-Fly Interpolation` 274 275 | NEMO allows to use the interpolation on the fly option allowing to interpolate input data during the run. 276 If you want to use this option you need files giving informations on weights, which have been created. 277 | You can find at http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/WEIGHTS/catalog.html 278 2 weights files `bil_weights` for scalar field (bilinear interpolation) and `bic_weights` for 279 vector field (bicubic interpolation). 280 | The data files used are `COREII forcing <http://data1.gdfl.noaa.gov/nomads/forms/mom4/COREv2>`_ extrapolated on 281 continents, ready to be used for on the fly option: 282 `COREII`_ forcing files extrapolated on continents 168 $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif' 169 170 By using the input files and namelists for ORCA2_ICE_PISCES, the AGRIF test configuration is ready to run. 171 283 172 284 173 ORCA2_OFF_PISCES 285 174 ---------------- 286 175 287 ``ORCA2_OFF_PISCES`` uses the ORCA2 configuration in which the `PISCES biogeochemical model`_ has been activated in 288 standalone using the dynamical fields that are pre calculated. 289 290 See `ORCA2_ICE_PISCES`_ for general description of ORCA2. 291 292 The input files for PISCES are needed, in addition the dynamical fields are used as input. 293 They are coming from a 2000 years of an ORCA2_LIM climatological run using ERA40 atmospheric forcing. 176 ORCA2_OFF_PISCES shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP. 177 294 178 295 179 ORCA2_OFF_TRC 296 180 ------------- 297 181 298 ``ORCA2_OFF_TRC`` uses the ORCA2_LIM configuration in which the tracer passive transport module TOP has been 299 activated in standalone using the dynamical fields that are pre calculated. 300 301 See `ORCA2_ICE_PISCES`_ for general description of ORCA2. 302 303 In ``namelist_top_cfg``, different passive tracers can be activated ( cfc11, cfc12, sf6, c14, age ) or my-trc, 304 a user-defined tracer. 305 306 The dynamical fields are used as input, they are coming from a 2000 years of an ORCA2_LIM climatological run using 307 ERA40 atmospheric forcing. 182 ORCA2_OFF_TRC is based on the ORCA2 global ocean configuration (see `ORCA2_ICE_PISCES`_ for general description) along with the tracer passive transport module (TOP), but dynamical fields are pre-calculated and read with specific time frequency. 183 184 This enables for an offline coupling of TOP components, here specifically inorganic carbon compounds (cfc11, cfc12, sf6, c14) and water age module (age). See ``namelist_top_cfg`` to inspect the selection of each component with the dedicated logical keys. 185 186 Pre-calculated dynamical fields are provided to NEMO using the namelist ``&namdta_dyn`` in ``namelist_cfg``, in this case with a 5 days frequency (120 hours): 187 188 .. code-block:: fortran 189 190 !----------------------------------------------------------------------- 191 &namdta_dyn ! offline ocean input files (OFF_SRC only) 192 !----------------------------------------------------------------------- 193 ln_dynrnf = .false. ! runoffs option enabled (T) or not (F) 194 ln_dynrnf_depth = .false. ! runoffs is spread in vertical (T) or not (F) 195 cn_dir = './' ! root directory for the ocean data location 196 !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________! 197 ! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 198 ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! ! pairing ! filename ! 199 sn_tem = 'dyna_grid_T' , 120 , 'votemper' , .true. , .true. , 'yearly' , '' , '' , '' 200 sn_sal = 'dyna_grid_T' , 120 , 'vosaline' , .true. , .true. , 'yearly' , '' , '' , '' 201 sn_mld = 'dyna_grid_T' , 120 , 'somixhgt' , .true. , .true. , 'yearly' , '' , '' , '' 202 sn_emp = 'dyna_grid_T' , 120 , 'sowaflup' , .true. , .true. , 'yearly' , '' , '' , '' 203 sn_fmf = 'dyna_grid_T' , 120 , 'iowaflup' , .true. , .true. , 'yearly' , '' , '' , '' 204 sn_ice = 'dyna_grid_T' , 120 , 'soicecov' , .true. , .true. , 'yearly' , '' , '' , '' 205 sn_qsr = 'dyna_grid_T' , 120 , 'soshfldo' , .true. , .true. , 'yearly' , '' , '' , '' 206 sn_wnd = 'dyna_grid_T' , 120 , 'sowindsp' , .true. , .true. , 'yearly' , '' , '' , '' 207 sn_uwd = 'dyna_grid_U' , 120 , 'uocetr_eff', .true. , .true. , 'yearly' , '' , '' , '' 208 sn_vwd = 'dyna_grid_V' , 120 , 'vocetr_eff', .true. , .true. , 'yearly' , '' , '' , '' 209 sn_wwd = 'dyna_grid_W' , 120 , 'wocetr_eff', .true. , .true. , 'yearly' , '' , '' , '' 210 sn_avt = 'dyna_grid_W' , 120 , 'voddmavs' , .true. , .true. , 'yearly' , '' , '' , '' 211 sn_ubl = 'dyna_grid_U' , 120 , 'sobblcox' , .true. , .true. , 'yearly' , '' , '' , '' 212 sn_vbl = 'dyna_grid_V' , 120 , 'sobblcoy' , .true. , .true. , 'yearly' , '' , '' , '' 213 / 214 215 Input dynamical fields for this configuration (ORCA2_OFF_v4.0.tar_) comes from a 2000 years long climatological simulation of ORCA2_ICE using ERA40 atmospheric forcing. 216 217 Note that, this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that model mesh is not varying in time and it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that requires the provision of bbl coefficients through ``sn_ubl`` and ``sn_vbl`` fields. 218 219 It is also possible to activate PISCES model (see ORCA2_OFF_PISCES_) or a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` (and adaptation of :trac:`source:/NEMO/trunk/src/TOP/MY_TRC` routines). 220 221 In addition, the offline module (OFF) allows for the provision of further fields: 222 223 1. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and by including an input datastream similarly to the following: 224 225 .. code-block:: fortran 226 227 sn_rnf = 'dyna_grid_T' , 120 , 'sorunoff' , .true. , .true. , 'yearly' , '' , '' , '' 228 229 2. **VVL dynamical fields**, in the case input data were produced by a dyamical core using variable volume (``ln_linssh = .false.``) it necessary to provide also diverce and E-P at before timestep by including input datastreams similarly to the following 230 231 .. code-block:: fortran 232 233 sn_div = 'dyna_grid_T' , 120 , 'e3t' , .true. , .true. , 'yearly' , '' , '' , '' 234 sn_empb = 'dyna_grid_T' , 120 , 'sowaflupb' , .true. , .true. , 'yearly' , '' , '' , '' 235 236 237 More details can be found by inspecting the offline data manager at :trac:`source:/NEMO/trunk/src/OFF/dtadyn.F90` 238 308 239 309 240 ORCA2_SAS_ICE 310 241 ------------- 311 242 312 ``ORCA2_SAS_ICE`` is a demonstrator of the SAS ( Stand-alone Surface module ) based on ORCA2_LIM configuration. 313 314 The standalone surface module allows surface elements such as sea-ice, iceberg drift and surface fluxes to 315 be run using prescribed model state fields. 316 For example, it can be used to inter-compare different bulk formulae or adjust the parameters of 317 a given bulk formula 318 319 See `ORCA2_ICE_PISCES`_ for general description of ORCA2. 320 321 Same input files as `ORCA2_ICE_PISCES`_ are needed plus fields from a previous ORCA2_LIM run. 322 323 More informations on input and configuration files in `NEMO manual`_. 243 ORCA2_SAS_ICE is a demonstrator of the Stand-Alone Surface (SAS) module and it relies on ORCA2 global ocean configuration (see `ORCA2_ICE_PISCES`_ for general description). 244 245 The standalone surface module allows surface elements such as sea-ice, iceberg drift, and surface fluxes to be run using prescribed model state fields. 246 It can profitably be used to compare different bulk formulae or adjust the parameters of a given bulk formula. 247 248 More informations about SAS can be found in NEMO manual. 324 249 325 250 SPITZ12 326 251 ------- 327 252 328 ``SPITZ12`` 329 330 Unsupported configurations 331 ========================== 332 333 Other configurations are developed and used by some projects with "NEMO inside", 334 these projects are welcome to publicize it here: http://www.nemo-ocean.eu/projects/add-project 335 336 :underline:`Obviously these "projects configurations" are not under the NEMO System Team's responsibility`. 337 338 .. _regional model: http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128 253 SPITZ12 is a regional configuration around the Svalbard archipelago at 1/12° of horizontal resolution and 75 vertical levels. See `Rousset et al. (2015) <https://www.geosci-model-dev.net/8/2991/2015/>`_ for more details. 254 255 This configuration references to year 2002, with atmospheric forcing provided every 2 hours using NCAR bulk formulae, while lateral boundary conditions for dynamical fields have 3 days time frequency. 256 257 258 .. _AGRIF_DEMO_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar 339 259 .. _AMM12_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar 340 260 .. _PISCES biogeochemical model: http://www.geosci-model-dev.net/8/2465/2015 … … 344 264 .. _INPUTS_SAS_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar 345 265 .. _INPUTS_C1D_PAPA_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar 346 .. _Reffray 2015: http://www.geosci-model-dev.net/8/69/2015 266 .. _SPITZ12_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar 267 347 268 .. _COREII: http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html 348 .. _SPITZ12_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar 349 .. _AGRIF_DEMO_v4.0.tar: http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar 269
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