Changeset 10541


Ignore:
Timestamp:
2019-01-17T15:08:27+01:00 (18 months ago)
Author:
lovato
Message:

Update configuration description file - 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 +----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     1REFERENCE CONFIGURATIONS 
     2======================== 
     3 
     4NEMO 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 
     7Configurations 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 
     9Available 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 
     30A 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 
     37A 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 
     39Then it will be possible to launch the execution of the model through a runscript (opportunely adapted to the user system). 
    4340 
    4441AGRIF_DEMO 
    4542---------- 
    4643 
    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 
     44AGRIF_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 
     46The 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 
     48The 1:1 grid can be used alone as a benchmark to check that the model solution is not corrupted by grid exchanges.  
     49Note 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. 
    7350 
    7451AMM12 
    7552----- 
    7653 
    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. 
     54AMM12 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 
     56This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.  
     57In particular, AMM12  accounts for vertical s-coordinates system, GLS turbulence scheme, tidal lateral boundary conditions using a flather scheme (see more in BDY). 
     58Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``. 
     59 
     60Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run (AMM12_v4.0.tar_). 
     61 
     62Note 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. 
    9563 
    9664C1D_PAPA 
    9765-------- 
    9866 
    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. 
     67C1D_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 
     69The 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 
     71This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae. 
     72Data 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 
    12078 
    12179GYRE_BFM 
    12280-------- 
    12381 
    124 ``GYRE_BFM`` is the same configuration as `GYRE_PISCES`_, except that PISCES is replaced by 
    125 BFM biogeochemichal model in coupled mode. 
     82GYRE_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 
    12684 
    12785GYRE_PISCES 
    12886----------- 
    12987 
    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`) 
     88GYRE_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 
     90This 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 
     102Note 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 
     106GYRE 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 
     118Note 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 
     120For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, the timestep should be set to 1200 seconds 
    168121 
    169122.. code-block:: fortran 
     
    171124   rn_rdt      = 1200.     !  time step for the dynamics 
    172125 
    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 
     126Differently from previous versions of NEMO, the code uses by default  the time-splitting scheme and internally computes the number of sub-steps.  
     127 
    197128 
    198129ORCA2_ICE_PISCES 
    199130---------------- 
    200131 
    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. 
     132ORCA2_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. 
     133ORCA 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 
     135In 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 
     140All components share the same grid. 
     141 
     142The 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. 
    241151  The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes. 
    242152  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 
     160From the ORCA2_ICE_PISCES configuration, a demonstrator using AGRIF nesting can be activated that includes a nested grid in the Agulhas region. 
     161 
     162To set up this configuration, after extracting NEMO: 
     163 
     164Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated: 
    266165 
    267166.. code-block:: console 
    268167                 
    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 
     170By using the input files and namelists for ORCA2_ICE_PISCES, the AGRIF test configuration is ready to run. 
     171 
    283172 
    284173ORCA2_OFF_PISCES 
    285174---------------- 
    286175 
    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. 
     176ORCA2_OFF_PISCES  shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP. 
     177 
    294178 
    295179ORCA2_OFF_TRC 
    296180------------- 
    297181 
    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. 
     182ORCA2_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 
     184This 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 
     186Pre-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 
     215Input 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 
     217Note 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 
     219It 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 
     221In addition, the offline module (OFF) allows for the provision of further fields: 
     222 
     2231. **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 
     2292. **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 
     237More details can be found by inspecting the offline data manager at :trac:`source:/NEMO/trunk/src/OFF/dtadyn.F90` 
     238 
    308239 
    309240ORCA2_SAS_ICE 
    310241------------- 
    311242 
    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`_. 
     243ORCA2_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 
     245The standalone surface module allows surface elements such as sea-ice, iceberg drift, and surface fluxes to be run using prescribed model state fields. 
     246It can profitably be used to compare different bulk formulae or adjust the parameters of a given bulk formula. 
     247 
     248More informations about SAS can be found in NEMO manual. 
    324249 
    325250SPITZ12 
    326251------- 
    327252 
    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 
     253SPITZ12 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 
     255This 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 
    339259.. _AMM12_v4.0.tar:               http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar 
    340260.. _PISCES biogeochemical model:  http://www.geosci-model-dev.net/8/2465/2015 
     
    344264.. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar 
    345265.. _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 
    347268.. _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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