Index: NEMO/trunk/README.rst
===================================================================
--- NEMO/trunk/README.rst	(revision 10604)
+++ NEMO/trunk/README.rst	(revision 10605)
@@ -58,9 +58,9 @@
  Component   Reference Manual      Quick start
 =========== ===================== ===============
- |OPA|       |NEMO manual|_        |NEMO guide|_
+ |OPA|       |NEMO manual|_        |NEMO guide|
              :cite:`NEMO_manual`
- |SI3|       |SI3 manual|_
+ |SI3|       |SI3 manual|
              :cite:`SI3_manual`
- |TOP|       |TOP manual|_
+ |TOP|       |TOP manual|
              :cite:`TOP_manual`
 =========== ===================== ===============
@@ -97,3 +97,3 @@
 .. |NEMO strategy| replace:: multi-year development strategy
 
-.. _Special Issue: http://www.geosci-model-dev.net/special_issue40.html
+.. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html
Index: NEMO/trunk/cfgs/README.rst
===================================================================
--- NEMO/trunk/cfgs/README.rst	(revision 10604)
+++ NEMO/trunk/cfgs/README.rst	(revision 10605)
@@ -3,11 +3,44 @@
 ************************
 
-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 
-------------------------
+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).
+
+.. attention::
+
+   Concerning the configurations,
+   the NEMO System Team is only in charge of the so-called reference configurations described below.
+
+.. hint::
+
+   Configurations developed by external research projects or initiatives that
+   make use of NEMO are welcome to be publicized through the website by
+   filling up the form :website:`to add an associated project<projects/add>`.
+
+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 ``./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).
+   
+List of Configurations
+======================
+
+All forcing files listed below in the table are available from |NEMO archives URL|_
+
+.. |NEMO archives URL| image:: https://www.zenodo.org/badge/DOI/10.5281/zenodo.1472245.svg
+.. _NEMO archives URL: https://doi.org/10.5281/zenodo.1472245
+
 ====================== ===== ===== ===== ======== ======= ================================================
  Configuration                     Component(s)                            Input & Forcing File(s)
@@ -15,61 +48,63 @@
  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_
+ 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_
+ 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
 ----------
 
-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.
+``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 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 setup instead of a split explicit free surface scheme.
 
 AMM12
 -----
 
-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>`_).
+``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 :cite:`ODEA2012`).
 
 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).
+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.
+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 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.
+``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 :
+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
@@ -77,33 +112,33 @@
 - ``chlorophyll_PAPASTATION.nc`` : surface chlorophyll file from Seawifs data
 
-
 GYRE_BFM
 --------
 
-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 :forge:`browser/NEMO/trunk/cfgs/GYRE_BFM/README`.
-
+``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 ``./cfgs/GYRE_BFM/README``.
 
 GYRE_PISCES
 -----------
 
-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 :forge:`browser/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: 
+``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,
+with PISCES BGC model :cite:`gmd-8-2465-2015`.
+Analytical forcing for heat, freshwater and wind-stress fields are applied.  
+
+This configuration acts 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``:
+
+.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_cfg
+   :language: fortran
+   :lines: 34-42
+
+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 in ``./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: 
 
 =========== ========= ========== ============ ===================
@@ -117,31 +152,53 @@
 =========== ========= ========== ============ ===================
 
-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
-   
-   rn_rdt      = 1200.     !  time step for the dynamics
-
-Differently from previous versions of NEMO, the code uses by default  the time-splitting scheme and internally computes the number of sub-steps. 
-
+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 ``rn_rdt = 1200`` should be set to 1200 seconds
+
+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
 ----------------
 
-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`_
+``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
+
+this configuration uses the three components 
+
+- |OPA|, the ocean dynamical core 
+- |SI3|, the thermodynamic-dynamic sea ice model.
+- |TOP|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015`
 
 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**
+The model is forced with CORE-II normal year atmospheric forcing and
+it uses the NCAR bulk formulae.
+
+In this ``ORCA2_ICE_PISCES`` configuration,
+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'
+
+By using the input files and namelists for ``ORCA2_ICE_PISCES``,
+the AGRIF test configuration is ready to run.
+
+**Ocean Physics**
 
 - *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.
@@ -155,25 +212,9 @@
 - *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'
-
-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  shares the same general offline configuration of ORCA2_ICE_TRC, but only PISCES model is an active component of TOP.
+``ORCA2_OFF_PISCES`` shares the same general offline configuration of ``ORCA2_ICE_TRC``,
+but only PISCES model is an active component of TOP.
 
 
@@ -181,69 +222,64 @@
 -------------
 
-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):
+``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):
+
+.. literalinclude:: ../../../cfgs/GYRE_PISCES/EXPREF/namelist_ref
+   :language: fortran
+   :lines: 306-333
+
+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 ``./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
 
-  !-----------------------------------------------------------------------
-  &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 :forge:`browser/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:
+   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_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 :forge:`browser/NEMO/trunk/src/OFF/dtadyn.F90`
-
+   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 in
+the routine ``./src/OFF/dtadyn.F90``.
 
 ORCA2_SAS_ICE
 -------------
 
-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.
+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.
@@ -252,19 +288,20 @@
 -------
 
-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
-.. _INPUTS_PISCES_v4.0.tar:       http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/INPUTS_PISCES_v4.0.tar
-.. _ORCA2_OFF_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_OFF_v4.0.tar
-.. _ORCA2_ICE_v4.0.tar:           http://prodn.idris.fr/thredds/fileServer/ipsl_public/romr005/Online_forcing_archives/ORCA2_ICE_v4.0.tar
-.. _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
-.. _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`` 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.
+
+References
+==========
+
+.. bibliography:: configurations.bib
+   :all:
+   :style: unsrt
+   :labelprefix: C
+
+.. Links and substitutions
+
Index: NEMO/trunk/doc/rst/source/configurations.bib
===================================================================
--- NEMO/trunk/doc/rst/source/configurations.bib	(revision 10605)
+++ NEMO/trunk/doc/rst/source/configurations.bib	(revision 10605)
@@ -0,0 +1,25 @@
+@article{ODEA2012,
+author = {E J O’Dea and A K Arnold and K P Edwards and R Furner and P Hyder and M J Martin and J R Siddorn and D Storkey and J While and J T Holt and H Liu},
+title = {An operational ocean forecast system incorporating NEMO and SST data assimilation for the tidally driven European North-West shelf},
+journal = {Journal of Operational Oceanography},
+volume = {5},
+number = {1},
+pages = {3-17},
+year  = {2012},
+publisher = {Taylor & Francis},
+doi = {10.1080/1755876X.2012.11020128},
+URL = {https://doi.org/10.1080/1755876X.2012.11020128},
+eprint = {https://doi.org/10.1080/1755876X.2012.11020128}
+}
+
+@Article{gmd-8-2465-2015,
+AUTHOR = {Aumont, O. and Eth\'e, C. and Tagliabue, A. and Bopp, L. and Gehlen, M.},
+TITLE = {PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies},
+JOURNAL = {Geoscientific Model Development},
+VOLUME = {8},
+YEAR = {2015},
+NUMBER = {8},
+PAGES = {2465--2513},
+URL = {https://www.geosci-model-dev.net/8/2465/2015/},
+DOI = {10.5194/gmd-8-2465-2015}
+}
Index: NEMO/trunk/doc/rst/source/global.rst
===================================================================
--- NEMO/trunk/doc/rst/source/global.rst	(revision 10604)
+++ NEMO/trunk/doc/rst/source/global.rst	(revision 10605)
@@ -29,5 +29,4 @@
 .. _IOIPSL: https://forge.ipsl.jussieu.fr/igcmg/browser/IOIPSL
 .. _OASIS:  https://portal.enes.org/oasis
-.. _XIOS:   https://forge.ipsl.jussieu.fr/ioserver
 
 .. NEMO
@@ -35,6 +34,6 @@
 .. _NEMO:          https://www.nemo-ocean.eu
 .. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663
-.. _NEMO guide:    https://doi.org/10.5281/zenodo.1475325
+.. _NEMO guide:    :samp: https://doi.org/10.5281/zenodo.1475325
 .. _NEMO manual:   https://doi.org/10.5281/zenodo.1464816
-.. _SI3 manual:    https://doi.org/10.5281/zenodo.1471689
-.. _TOP manual:    https://doi.org/10.5281/zenodo.1471700
+.. _SI3 manual:    :samp: https://doi.org/10.5281/zenodo.1471689
+.. _TOP manual:    :samp: https://doi.org/10.5281/zenodo.1471700
Index: NEMO/trunk/tests/README.rst
===================================================================
--- NEMO/trunk/tests/README.rst	(revision 10604)
+++ NEMO/trunk/tests/README.rst	(revision 10605)
@@ -3,14 +3,43 @@
 **********************
 
+The complete and up-to-date set of test cases is available on
+`NEMO test cases Github repository <http://github.com/NEMO-ocean/NEMO-examples>`_.
+
+Download it directly in the ``./tests`` root directory with
+
+.. code-block:: console
+
+   $ git clone http://github.com/NEMO-ocean/NEMO-examples
+
 .. contents::
 	:local:
 
-List
-====
+Procedure
+=========
 
-  The description below is a brief description of the test cases available in NEMO. 
+Compile test cases
+------------------
+
+The compilation of the test cases is very similar to the manner the reference configurations are compiled.
+If you are not familiar on how to compile NEMO, it is first recomended to read :doc:`the instructions <install>`
+
+| In the same manner as the ref. cfg are compiled with '-r' option, test cases can be compile by the use of makenemo with '-a' option.
+| Here an example to compile a copy named WAD2 of the wetting and drying test case (WAD) on the macport_osx architecture on 4 cores:
+
+.. code-block:: console
+
+   $ ./makenemo -n 'WAD2' -a 'WAD' -m 'macport_osx' -j '4'
+
+Run and analyse the test cases
+------------------------------
+
+There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly. 
+For detailed description and Jupyter notebook, the reader is directed on
+the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_
+
+The description below is a brief advertisement of some test cases.
 
 ICE_AGRIF
----------
+=========
   
   This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel
@@ -24,5 +53,5 @@
 
 VORTEX
-------
+======
   
   This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom.
@@ -37,5 +66,5 @@
 
 ISOMIP
-------
+======
 
   The purpose of this test case is to evaluate the impact of various schemes and new development with the iceshelf cavities circulation and melt.
@@ -48,5 +77,5 @@
 
 LOCK_EXCHANGE
--------------
+=============
 
   The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted
@@ -61,5 +90,5 @@
 
 OVERFLOW
---------
+========
 
   The OVERFLOW experiment illustrates the impact of different choices of numerical schemes 
@@ -74,5 +103,5 @@
 
 WAD
----
+===
 
   A set of simple closed basin geometries for testing the Wetting and drying capabilities. 
@@ -86,5 +115,5 @@
 
 CANAL
------
+=====
 
   East-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex).
@@ -93,5 +122,5 @@
 
 ICE_ADV2D
----------
+=========
   
   This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel
@@ -104,5 +133,5 @@
 
 ICE_ADV1D
----------
+=========
   
   This experiment is the classical Schar & Smolarkiewicz (1996) test case :cite:`SCHAR1996`,
@@ -112,29 +141,5 @@
   The purpose of this configuration is to test the caracteristics of advection schemes available in the sea-ice code
   (for now, Prather and Ultimate-Macho from 1st to 5th order),
-  especially the constitency between concentration, thickness and volume, and the preservation of initial shapes.
-  
-  
-
-  
-Compile test cases
-==================
-
-The compilation of the test cases is very similar to the manner the reference configurations are compiled.
-If you are not familiar on how to compile NEMO, it is first recomended to read :doc:`the instructions <install>`
-
-| In the same manner as the ref. cfg are compiled with '-r' option, test cases can be compile by the use of makenemo with '-a' option.
-
-| Here an example to compile a copy named WAD2 of the wetting and drying test case (WAD) on the macport_osx architecture on 4 cores:
-
-.. code-block:: console
- 
-	$ ./makenemo -n WAD2 -a WAD -m macport_osx -j 4
-
-Run and analyse the test cases
-==============================
-
-There no requirement of specific input file for the test_cases presented here. The XIOS xml input files and namelist are already setup correctly. 
-For detailed description and Jupyter notebook, the reader is directed on
-the `NEMO test cases repository <http://github.com/NEMO-ocean/NEMO-examples>`_
+  especially the constitency between concentration, thickness and volume, and the preservation of initial shapes.  
 
 References
