Index: /NEMO/trunk/cfgs/README.rst
===================================================================
--- /NEMO/trunk/cfgs/README.rst	(revision 10540)
+++ /NEMO/trunk/cfgs/README.rst	(revision 10541)
@@ -1,169 +1,122 @@
-***************************
-Run built-in configurations
-***************************
-
-.. contents::
-	:local:
-	:depth: 1
-      
-Official configurations
-=======================
-
-| NEMO is distributed with some reference configurations allowing both the user to set up a first application and
-  the developer to validate their developments.
-| :underline:`The NEMO System Team is in charge of these configurations`.
-
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-|                      | OPA | SI3 | TOP | PISCES | AGRIF | Inputs                   |
-+======================+=====+=====+=====+========+=======+==========================+
-| `AGRIF_DEMO`_        |  X  |  X  |     |        |   X   | - AGRIF_DEMO_v4.0.tar    |
-|                      |     |     |     |        |       | - ORCA2_ICE_v4.0.tar     |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `AMM12`_             |  X  |     |     |        |       | AMM12_v4.0.tar           |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `C1D_PAPA`_          |  X  |     |     |        |       | INPUTS_C1D_PAPA_v4.0.tar |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `GYRE_BFM`_          |  X  |     |  X  |        |       | ``-``                    |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `GYRE_PISCES`_       |  X  |     |  X  |   X    |       | ``-``                    |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `ORCA2_ICE_PISCES`_  |  X  |  X  |  X  |   X    |       | - ORCA2_ICE_v4.0.tar     |
-|                      |     |     |     |        |       | - INPUTS_PISCES_v4.0.tar |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `ORCA2_OFF_PISCES`_  |     |     |  X  |   X    |       | - INPUTS_PISCES_v4.0.tar |
-|                      |     |     |     |        |       | - ORCA2_OFF_v4.0.tar     |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `ORCA2_OFF_TRC`_     |     |     |  X  |        |       | ORCA2_OFF_v4.0.tar       |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `ORCA2_SAS_ICE`_     |     |  X  |     |        |       | - ORCA2_ICE_v4.0.tar     |
-|                      |     |     |     |        |       | - INPUTS_SAS_v4.0.tar    |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
-| `SPITZ12`_           |  X  |  X  |     |        |       | SPITZ12_v4.0.tar         |
-+----------------------+-----+-----+-----+--------+-------+--------------------------+
+REFERENCE CONFIGURATIONS
+========================
+
+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).
+*The NEMO System Team is in charge only for these configurations.*
+
+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>`_
+
+Available Configurations 
+------------------------
+====================== ===== ===== ===== ======== ======= ================================================
+ Configuration                     Component(s)                            Input & Forcing File(s)
+---------------------- ---------------------------------- ------------------------------------------------
+ Name                   OPA   SI3   TOP   PISCES   AGRIF
+====================== ===== ===== ===== ======== ======= ================================================
+ AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar_, ORCA2_ICE_v4.0.tar_
+ AMM12_                  X                                 AMM12_v4.0.tar_
+ C1D_PAPA_               X                                 INPUTS_C1D_PAPA_v4.0.tar_
+ GYRE_BFM_               X           X                     *none*
+ GYRE_PISCES_            X           X      X              *none*
+ ORCA2_ICE_PISCES_       X     X     X      X              ORCA2_ICE_v4.0.tar_, INPUTS_PISCES_v4.0.tar_
+ ORCA2_OFF_PISCES_                   X      X              ORCA2_OFF_v4.0.tar_, INPUTS_PISCES_v4.0.tar_
+ ORCA2_OFF_TRC_                      X                     ORCA2_OFF_v4.0.tar_
+ ORCA2_SAS_ICE_                X                           ORCA2_ICE_v4.0.tar_, INPUTS_SAS_v4.0.tar_
+ SPITZ12_                X     X                           SPITZ12_v4.0.tar_
+====================== ===== ===== ===== ======== ======= ================================================
+
+**How to compile an experiment from a reference configuration**
+
+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:
+
+
+.. code-block:: console
+                
+        $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4'
+
+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.
+
+Then it will be possible to launch the execution of the model through a runscript (opportunely adapted to the user system).
 
 AGRIF_DEMO
 ----------
 
-.. image:: _static/AGRIF_DEMO.jpg
-
-``AGRIF_DEMO`` is based on the ``ORCA2_LIM3_PISCES`` global 2° configuration but
-it includes 3 online nested grids that demonstrate the overall capabilities of AGRIF in a realistic context,
-including nesting sea ice models.
-
-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.
-The finest grid spanning the whole Svalbard archipelago is of particular interest to check that
-sea ice coupling is done properly.
-The 1:1 grid, used alone, is used as a benchmark to check that the solution is not corrupted by grid exchanges.
-
-Note that since grids interact only at the baroclinic time level,
-numerically exact results can not be achieved in the 1:1 case.
-One has to switch to a fully explicit in place of a split explicit free surface scheme in order to
-retrieve perfect reproducibility.
-
-Corresponding ``AGRIF_FixedGrids.in`` file is given by::
-
-	2
-	42 82 49 91 1 1 1
-	122 153 110 143 4 4 4
-	0
-	1
-	38 80 71 111 3 3 3
-	0
+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).
+
+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.
+
+The 1:1 grid can be used alone as a benchmark to check that the model solution is not corrupted by grid exchanges. 
+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.
 
 AMM12
 -----
 
-``AMM12`` for *Atlantic Margin Model 12kms* is a `regional model`_ covering the Northwest European Shelf domain on
-a regular lat-lon grid at approximately 12km horizontal resolution.
-The key ``key_amm_12km`` is used to create the correct dimensions of the AMM domain.
-
-| This configuration tests several features of NEMO functionality specific to the shelf seas.
-| In particular, the AMM uses s-coordinates in the vertical rather than z-coordinates and is forced with
-  tidal lateral boundary conditions using a flather boundary condition from the BDY module (``key_bdy``).
-
-The AMM configuration uses the GLS (``key_zdfgls``) turbulence scheme,
-the VVL non-linear free surface (``key_vvl``) and time-splitting (``key_dynspg_ts``).
-
-In addition to the tidal boundary condition, the model may also take open boundary conditions from
-a North Atlantic model.
-Boundaries may be completely ommited by removing the BDY key (key_bdy) in ``./cfgs/AMM12/cpp_AMM12_fcm``.
-
-Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
-The Baltic boundary is included within the river input file and is specified as a river source.
-Unlike ordinary river points the Baltic inputs also include salinity and temperature data.
+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>`_).
+
+This configuration allows to tests several features of NEMO specifically addressed to the shelf seas. 
+In particular, AMM12  accounts for vertical s-coordinates system, GLS turbulence scheme, tidal lateral boundary conditions using a flather scheme (see more in BDY).
+Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.
+
+Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run (AMM12_v4.0.tar_).
+
+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.
 
 C1D_PAPA
 --------
 
-``C1D_PAPA`` is a 1D configuration (one water column called NEMO1D, activated with CPP key ``key_c1d``),
-located at the `PAPA station 145W-50N <http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml>`_.
-
-| NEMO1D is useful to test vertical physics in NEMO
-  (turbulent closure scheme, solar penetration, interaction ocean/atmosphere.,...)
-| Size of the horizontal domain is 3x3 grid points.
-
-This reference configuration uses a 75 vertical levels grid (1m at the surface),
-the GLS (key_zdfgls) turbulence scheme with K-epsilon closure and the CORE BULK formulae.
-The atmospheric forcing comes from ECMWF operational analysis with a modification of the long and short waves flux.
-This set has been rescaled at a frequency of 1h. 1 year is simulated in outputs,
-see below (June,15 2010 to June,14 2011)
-
-`Reffray 2015`_ describes some tests on vertical physic using this configuration.
-
-The inputs tar file includes:
-
-- forcing files covering the years 2010 and 2011 (``forcing_PAPASTATION_1h_y201*.nc``)
-- initialization file for June,15 2010 deduced from observed data and Levitus 2009 climatology
-  (``init_PAPASTATION_m06d15.nc``)
-- surface chlorophyll file (``chlorophyll_PAPASTATION.nc``) deduced from Seawifs data.
+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.
+
+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.
+
+This reference configuration uses 75 vertical levels grid (1m at the surface), GLS turbulence scheme with K-epsilon closure and the NCAR bulk formulae.
+Data provided with INPUTS_C1D_PAPA_v4.0.tar_ file account for :
+
+- ``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
+- ``init_PAPASTATION_m06d15.nc`` : Initial Conditions from observed data and Levitus 2009 climatology
+- ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data
+
 
 GYRE_BFM
 --------
 
-``GYRE_BFM`` is the same configuration as `GYRE_PISCES`_, except that PISCES is replaced by
-BFM biogeochemichal model in coupled mode.
+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`.
+
 
 GYRE_PISCES
 -----------
 
-| Idealized configuration representing double gyres in the North hemisphere, Beta-plane with
-  a regular grid spacing at 1° horizontal resolution (and possible use as a benchmark by
-  easily inscreasing grid size), 101 vertical levels, forced with analytical heat, freshwater and
-  wind-stress fields.
-| This configuration is coupled to `PISCES biogeochemical model`_.
-
-Running GYRE as a benchmark
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-This simple configuration can be used as a benchmark since it is easy to increase resolution
-(and in this case no physical meaning of outputs):
-
-1. Choose the grid size
-
-   In ``./cfgs/GYRE/EXP00``, edit your ``namelist_cfg`` file to change the ``jp_cfg``, ``jpi``, ``jpj``,
-   ``jpk`` variables in &namcfg:
-
-	+------------+---------+---------+---------+------------------+---------------+
-	| ``jp_cfg`` | ``jpi`` | ``jpj`` | ``jpk`` | Number of points | Equivalent to |
-	+============+=========+=========+=========+==================+===============+
-	| 1          | 30      | 20      | 101     | 60600            | GYRE 1°       |
-	+------------+---------+---------+---------+------------------+---------------+
-	| 25         | 750     | 500     | 101     | 37875000         | ORCA 1/2°     |
-	+------------+---------+---------+---------+------------------+---------------+
-	| 50         | 1500    | 1000    | 101     | 151500000        | ORCA 1/4°     |
-	+------------+---------+---------+---------+------------------+---------------+
-	| 150        | 4500    | 3000    | 101     | 1363500000       | ORCA 1/12°    |
-	+------------+---------+---------+---------+------------------+---------------+
-	| 200        | 6000    | 4000    | 101     | 2424000000       | ORCA 1/16°    |
-	+------------+---------+---------+---------+------------------+---------------+
-
-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
-
-.. code-block:: fortran
-   
-   nn_bench    =    1     !  Bench mode (1/0): CAUTION use zero except for bench
-
-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`)
+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.  
+
+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:
+
+.. code-block:: fortran
+
+  !-----------------------------------------------------------------------
+  &namusr_def    !   GYRE user defined namelist
+  !-----------------------------------------------------------------------
+     nn_GYRE     =     1     !  GYRE resolution [1/degrees]
+     ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant
+     jpkglo      =    31     !  number of model levels
+  /
+
+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` 
+
+**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.
+
+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: 
+
+=========== ========= ========== ============ ===================
+``nn_GYRE``  *jpiglo*  *jpjglo*   ``jpkglo``   **Equivalent to**
+=========== ========= ========== ============ ===================
+ 1           30        20         31           GYRE 1°
+ 25          750       500        101          ORCA 1/2°
+ 50          1500      1000       101          ORCA 1/4°
+ 150         4500      3000       101          ORCA 1/12°
+ 200         6000      4000       101          ORCA 1/16°
+=========== ========= ========== ============ ===================
+
+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. 
+
+For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, the timestep should be set to 1200 seconds
 
 .. code-block:: fortran
@@ -171,170 +124,137 @@
    rn_rdt      = 1200.     !  time step for the dynamics
 
-4. Optional, in order to increase the number of MPI communication for benchmark purposes:
-   you can change the number of sub-timesteps computed in the time-splitting scheme each iteration.
-   First change the list of active CPP keys for your experiment,
-   in `cfgs/"your configuration name"/cpp_"your configuration name".fcm`:
-   replace ``key_dynspg_flt by key_dynspg_ts`` and recompile/create your executable again
-   
-   .. code-block:: fortran
-   
-   makenemo [...] add_key 'key_dynspg_ts' del_key 'key_dynspg_flt'
-
-In your ``namelist_cfg`` file, edit the &namsplit namelist by adding the following line: 
-
-.. code-block:: fortran
-   
-   nn_baro       =    30               !  Number of iterations of barotropic mode/
-
-``nn_baro = 30`` is a kind of minimum (we usually use 30 to 60).
-So than increasing the ``nn_baro`` value will increase the number of MPI communications.
-
-The GYRE CPP keys, namelists and scripts can be explored in the ``GYRE`` configuration directory
-(``./cfgs/GYRE`` and ``./cfgs/GYRE/EXP00``).
-
-Find monthly mean outputs of 1 year run here:
-http://prodn.idris.fr/thredds/catalog/ipsl_public/reee451/NEMO_OUT/GYRE/catalog.html
+Differently from previous versions of NEMO, the code uses by default  the time-splitting scheme and internally computes the number of sub-steps. 
+
 
 ORCA2_ICE_PISCES
 ----------------
 
-ORCA is the generic name given to global ocean configurations.
-Its specificity lies on the horizontal curvilinear mesh used to overcome the North Pole singularity found for
-geographical meshes.
-SI3 (Sea Ice Integrated Initiative) is a thermodynamic-dynamic sea ice model specifically designed for
-climate studies.
-A brief description of the model is given here.
-
-:underline:`Space-time domain`
-
-The horizontal resolution available through the standard configuration is ORCA2.
-It is based on a 2 degrees Mercator mesh, (i.e. variation of meridian scale factor as cosinus of the latitude).
-In the northern hemisphere the mesh has two poles so that the ratio of anisotropy is nearly one everywhere.
-The mean grid spacing is about 2/3 of the nominal value: for example it is 1.3 degrees for ORCA2.
-Other resolutions (ORCA4, ORCA05 and ORCA025) are running or under development within specific projects.
-In the coarse resolution version (i.e. ORCA2 and ORCA4) the meridional grid spacing is increased near
-the equator to improve the equatorial dynamics.
-Figures in pdf format of mesh and bathymetry can be found and downloaded here.
-The sea-ice model runs on the same grid.
-
-The vertical domain spreads from the surface to a depth of 5000m.
-There are 31 levels, with 10 levels in the top 100m.
-The vertical mesh is deduced from a mathematical function of z ([[AttachmentNum(1)]]).
-The ocean surface corresponds to the w-level k=1, and the ocean bottom to the w-level k=31.
-The last T-level (k=31) is thus always in the ground.The depths of the vertical levels and
-the associated scale factors can be viewed.
-Higher vertical resolution is used in ORCA025 and ORCA12 (see `DRAKKAR project <http://www.drakkar-ocean.eu>`_).
-
-The time step depends on the resolution. It is 1h36' for ORCA2 so that there is 15 time steps in one day.
-
-:underline:`Ocean Physics (for ORCA2)`
-
-- 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.
-- isopycnal diffusion on tracers: the diffusion acts along the isopycnal surfaces (neutral surface) with
-  a eddy diffusivity coefficient of 2000 $m^2/s$.
-- 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 $m^2/s$).
-- lateral boundary conditions : zero fluxes of heat and salt and no-slip conditions are applied through
-  lateral solid boundaries.
-- bottom boundary condition : zero fluxes of heat and salt are applied through the ocean bottom.
+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.
+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
+
+In this configuration, the ocean dynamical core  is coupled to  
+
+- **ICE**, namely SI3 (Sea Ice Integrated Initiative) a thermodynamic-dynamic sea ice model specifically designed for climate studies.
+- **TOP**, passive tracer transport module and `PISCES biogeochemical model`_
+
+All components share the same grid.
+
+The model is forced with CORE-II normal year atmospheric forcing and it uses the NCAR bulk formulae.
+
+**Ocean Physics configuration**
+
+- *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.
+- *isopycnal diffusion on tracers*: the diffusion acts along the isopycnal surfaces (neutral surface) with an eddy diffusivity coefficient of 2000 m^2/s.
+- *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).
+- *lateral boundary conditions* : zero fluxes of heat and salt and no-slip conditions are applied through lateral solid boundaries.
+- *bottom boundary condition* : zero fluxes of heat and salt are applied through the ocean bottom.
   The Beckmann [19XX] simple bottom boundary layer parameterization is applied along continental slopes.
   A linear friction is applied on momentum.
-- convection: the vertical eddy viscosity and diffusivity coefficients are increased to 1 $m^2/s$ in case of
-  static instability.
-- forcings: the ocean receives heat, freshwater, and momentum fluxes from the atmosphere and/or the sea-ice.
-  The solar radiation penetrates the top meters of the ocean.
-  The downward irradiance I(z) is formulated with two extinction coefficients [Paulson and Simpson, 1977],
-  whose values correspond to a Type I water in Jerlov's classification (i.e the most transparent water)
-
-ORCA2_ICE_PISCES is a reference configuration with the following characteristics:
-
-- global ocean configuration
-- based on a tri-polar ORCA grid, with a 2° horizontal resolution
-- 31 vertical levels
-- forced with climatological surface fields
-- coupled to the sea-ice model SI3.
-- coupled to TOP passive tracer transport module and `PISCES biogeochemical model`_.
-
-:underline:`AGRIF demonstrator`
-
-| From the ``ORCA2_ICE_PISCES`` configuration, a demonstrator using AGRIF nesting can be activated.
-  It includes the global ``ORCA2_ICE_PISCES`` configuration and a nested grid in the Agulhas region.
-| To set up this configuration, after extracting NEMO:
-
-- Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated:
+- *convection*: the vertical eddy viscosity and diffusivity coefficients are increased to 1 m^2/s in case of static instability.
+- *time step* is 5760sec (1h36') so that there is 15 time steps in one day.
+
+
+
+**AGRIF demonstrator**
+
+From the ORCA2_ICE_PISCES configuration, a demonstrator using AGRIF nesting can be activated that includes a nested grid in the Agulhas region.
+
+To set up this configuration, after extracting NEMO:
+
+Build your AGRIF configuration directory from ORCA2_ICE_PISCES, with the key_agrif CPP key activated:
 
 .. code-block:: console
                 
-	$ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif'
-
-- Using the ``ORCA2_ICE_PISCES`` input files and namelist, AGRIF test configuration is ready to run
-
-:underline:`On-The-Fly Interpolation`
-
-| NEMO allows to use the interpolation on the fly option allowing to interpolate input data during the run.
-  If you want to use this option you need files giving informations on weights, which have been created.
-| You can find at http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/WEIGHTS/catalog.html
-  2 weights files `bil_weights` for scalar field (bilinear interpolation) and `bic_weights` for
-  vector field (bicubic interpolation).
-| The data files used are `COREII forcing <http://data1.gdfl.noaa.gov/nomads/forms/mom4/COREv2>`_ extrapolated on
-  continents, ready to be used for on the fly option:
-  `COREII`_ forcing files extrapolated on continents
+        $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif'
+
+By using the input files and namelists for ORCA2_ICE_PISCES, the AGRIF test configuration is ready to run.
+
 
 ORCA2_OFF_PISCES
 ----------------
 
-``ORCA2_OFF_PISCES`` uses the ORCA2 configuration in which the `PISCES biogeochemical model`_ has been activated in
-standalone using the dynamical fields that are pre calculated.
-
-See `ORCA2_ICE_PISCES`_ for general description of ORCA2.
-
-The input files for PISCES are needed, in addition the dynamical fields are used as input.
-They are coming from a 2000 years of an ORCA2_LIM climatological run using ERA40 atmospheric forcing.
+ORCA2_OFF_PISCES  shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP.
+
 
 ORCA2_OFF_TRC
 -------------
 
-``ORCA2_OFF_TRC`` uses the ORCA2_LIM configuration in which the tracer passive transport module TOP has been
-activated in standalone using the dynamical fields that are pre calculated.
-
-See `ORCA2_ICE_PISCES`_ for general description of ORCA2.
-
-In ``namelist_top_cfg``, different passive tracers can be activated ( cfc11, cfc12, sf6, c14, age ) or my-trc,
-a user-defined tracer.
-
-The dynamical fields are used as input, they are coming from a 2000 years of an ORCA2_LIM climatological run using
-ERA40 atmospheric forcing.
+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.
+
+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.
+
+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):
+
+.. code-block:: fortran
+
+  !-----------------------------------------------------------------------
+  &namdta_dyn    !   offline ocean input files                            (OFF_SRC only)
+  !-----------------------------------------------------------------------
+     ln_dynrnf       =  .false.    !  runoffs option enabled (T) or not (F)
+     ln_dynrnf_depth =  .false.    !  runoffs is spread in vertical (T) or not (F)
+     cn_dir      = './'      !  root directory for the ocean data location
+     !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
+     !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask !
+     !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   !
+     sn_tem      = 'dyna_grid_T'           ,       120         , 'votemper'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_sal      = 'dyna_grid_T'           ,       120         , 'vosaline'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_mld      = 'dyna_grid_T'           ,       120         , 'somixhgt'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_emp      = 'dyna_grid_T'           ,       120         , 'sowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_fmf      = 'dyna_grid_T'           ,       120         , 'iowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_ice      = 'dyna_grid_T'           ,       120         , 'soicecov'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_qsr      = 'dyna_grid_T'           ,       120         , 'soshfldo'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_wnd      = 'dyna_grid_T'           ,       120         , 'sowindsp'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_uwd      = 'dyna_grid_U'           ,       120         , 'uocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_vwd      = 'dyna_grid_V'           ,       120         , 'vocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_wwd      = 'dyna_grid_W'           ,       120         , 'wocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_avt      = 'dyna_grid_W'           ,       120         , 'voddmavs'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_ubl      = 'dyna_grid_U'           ,       120         , 'sobblcox'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_vbl      = 'dyna_grid_V'           ,       120         , 'sobblcoy'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+  /
+
+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.
+
+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.
+
+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).
+
+In addition, the offline module (OFF) allows for the provision of further fields:
+
+1. **River runoff** can be provided to TOP components by setting ``ln_dynrnf = .true.`` and by including an input datastream similarly to the following:
+
+.. code-block:: fortran
+
+     sn_rnf      = 'dyna_grid_T'           ,       120         , 'sorunoff'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+
+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
+
+.. code-block:: fortran
+
+     sn_div       = 'dyna_grid_T'           ,       120         ,    'e3t'     ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+     sn_empb      = 'dyna_grid_T'           ,       120         , 'sowaflupb'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , ''
+
+
+More details can be found by inspecting the offline data manager at :trac:`source:/NEMO/trunk/src/OFF/dtadyn.F90`
+
 
 ORCA2_SAS_ICE
 -------------
 
-``ORCA2_SAS_ICE`` is a demonstrator of the SAS ( Stand-alone Surface module ) based on ORCA2_LIM configuration.
-
-The standalone surface module allows surface elements such as sea-ice, iceberg drift and surface fluxes to
-be run using prescribed model state fields.
-For example, it can be used to inter-compare different bulk formulae or adjust the parameters of
-a given bulk formula
-
-See `ORCA2_ICE_PISCES`_ for general description of ORCA2.
-
-Same input files as `ORCA2_ICE_PISCES`_ are needed plus fields from a previous ORCA2_LIM run.
-
-More informations on input and configuration files in `NEMO manual`_.
+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).
+
+The standalone surface module allows surface elements such as sea-ice, iceberg drift, and surface fluxes to be run using prescribed model state fields.
+It can profitably be used to compare different bulk formulae or adjust the parameters of a given bulk formula.
+
+More informations about SAS can be found in NEMO manual.
 
 SPITZ12
 -------
 
-``SPITZ12``
-
-Unsupported configurations
-==========================
-
-Other configurations are developed and used by some projects with "NEMO inside",
-these projects are welcome to publicize it here: http://www.nemo-ocean.eu/projects/add-project
-
-:underline:`Obviously these "projects configurations" are not under the NEMO System Team's responsibility`.
-
-.. _regional model:               http://www.tandfonline.com/doi/pdf/10.1080/1755876X.2012.11020128
+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.
+
+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.
+
+
+.. _AGRIF_DEMO_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar
 .. _AMM12_v4.0.tar:               http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AMM12_v4.0.tar
 .. _PISCES biogeochemical model:  http://www.geosci-model-dev.net/8/2465/2015
@@ -344,6 +264,6 @@
 .. _INPUTS_SAS_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_SAS_v4.0.tar
 .. _INPUTS_C1D_PAPA_v4.0.tar:     http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_C1D_PAPA_v4.0.tar
-.. _Reffray 2015:                 http://www.geosci-model-dev.net/8/69/2015
+.. _SPITZ12_v4.0.tar:             http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar
+
 .. _COREII:                       http://prodn.idris.fr/thredds/catalog/ipsl_public/reee512/ORCA2_ONTHEFLY/FILLED_FILES/catalog.html
-.. _SPITZ12_v4.0.tar:             http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/SPITZ12_v4.0.tar
-.. _AGRIF_DEMO_v4.0.tar:          http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/AGRIF_DEMO_v4.0.tar
+
