Index: NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/AGRIF_DEMO/EXPREF/namelist_ice_cfg
===================================================================
--- NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/AGRIF_DEMO/EXPREF/namelist_ice_cfg	(revision 11777)
+++ NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/AGRIF_DEMO/EXPREF/namelist_ice_cfg	(revision 11836)
@@ -38,4 +38,5 @@
 &namdyn_rhg     !   Ice rheology
 !------------------------------------------------------------------------------
+      ln_aEVP       = .false.          !     adaptive rheology (Kimmritz et al. 2016 & 2017)
 /
 !------------------------------------------------------------------------------
Index: NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/AGRIF_DEMO/README.rst
===================================================================
--- NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/AGRIF_DEMO/README.rst	(revision 11777)
+++ NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/AGRIF_DEMO/README.rst	(revision 11836)
@@ -13,11 +13,13 @@
 ========
 
-AGRIF (Adaptive Grid Refinement In Fortran) is a library that allows the seamless space and time refinement over
-rectangular regions in NEMO.
+AGRIF (Adaptive Grid Refinement In Fortran) is a library that
+allows the seamless space and time refinement over rectangular regions in NEMO.
 Refinement factors can be odd or even (usually lower than 5 to maintain stability).
-Interaction between grid is "two-ways" in the sense that the parent grid feeds the child grid open boundaries and
-the child grid provides volume averages of prognostic variables once a given number of time step is completed.
+Interaction between grid is "two-ways" in the sense that
+the parent grid feeds the child grid open boundaries and
+the child grid provides volume averages of prognostic variables once
+a given number of time step is completed.
 These pages provide guidelines how to use AGRIF in NEMO.
-For a more technical description of the library itself, please refer to http://agrif.imag.fr.
+For a more technical description of the library itself, please refer to AGRIF_.
 
 Compilation
@@ -28,9 +30,9 @@
 .. code-block:: sh
 
-	./makenemo add_key 'key_agrif'
+   ./makenemo [...] add_key 'key_agrif'
 
-Although this is transparent to users, the way the code is processed during compilation is different from
-the standard case:
-a preprocessing stage (the so called "conv" program) translates the actual code so that
+Although this is transparent to users,
+the way the code is processed during compilation is different from the standard case:
+a preprocessing stage (the so called ``conv`` program) translates the actual code so that
 saved arrays may be switched in memory space from one domain to an other.
 
@@ -38,25 +40,26 @@
 ================================
 
-An additional text file ``AGRIF_FixedGrids.in`` is required at run time.
+An additional text file :file:`AGRIF_FixedGrids.in` is required at run time.
 This is where the grid hierarchy is defined.
-An example of such a file, here taken from the ``ICEDYN`` test case, is given below::
+An example of such a file, here taken from the ``ICEDYN`` test case, is given below
 
-	1
-	34 63 34 63 3 3 3
-	0
+.. literalinclude:: ../../../tests/ICE_AGRIF/EXPREF/AGRIF_FixedGrids.in
 
 The first line indicates the number of zooms (1).
 The second line contains the starting and ending indices in both directions on the root grid
-(imin=34 imax=63 jmin=34 jmax=63) followed by the space and time refinement factors (3 3 3).
+(``imin=34 imax=63 jmin=34 jmax=63``) followed by the space and time refinement factors (3 3 3).
 The last line is the number of child grid nested in the refined region (0).
 A more complex example with telescoping grids can be found below and
-in the ``AGRIF_DEMO`` reference configuration directory.
+in the :file:`AGRIF_DEMO` reference configuration directory.
 
-[Add some plots here with grid staggering and positioning ?]
+.. todo::
 
-When creating the nested domain, one must keep in mind that the child domain is shifted toward north-east and
-depends on the number of ghost cells as illustrated by the (attempted) drawing below for nbghostcells=1 and
-nbghostcells=3.
-The grid refinement is 3 and nxfin is the number of child grid points in i-direction.
+   Add some plots here with grid staggering and positioning?
+
+When creating the nested domain, one must keep in mind that
+the child domain is shifted toward north-east and
+depends on the number of ghost cells as illustrated by
+the *attempted* drawing below for ``nbghostcells=1`` and ``nbghostcells=3``.
+The grid refinement is 3 and ``nxfin`` is the number of child grid points in i-direction.
 
 .. image:: _static/agrif_grid_position.jpg
@@ -71,9 +74,10 @@
 =============
 
-Knowing the refinement factors and area, a ``NESTING`` pre-processing tool may help to create needed input files
+Knowing the refinement factors and area,
+a ``NESTING`` pre-processing tool may help to create needed input files
 (mesh file, restart, climatological and forcing files).
 The key is to ensure volume matching near the child grid interface,
-a step done by invoking the ``Agrif_create_bathy.exe`` program.
-You may use the namelists provided in the ``NESTING`` directory as a guide.
+a step done by invoking the :file:`Agrif_create_bathy.exe` program.
+You may use the namelists provided in the :file:`NESTING` directory as a guide.
 These correspond to the namelists used to create ``AGRIF_DEMO`` inputs.
 
@@ -82,23 +86,15 @@
 
 Each child grid expects to read its own namelist so that different numerical choices can be made
-(these should be stored in the form ``1_namelist_cfg``, ``2_namelist_cfg``, etc... according to their rank in
-the grid hierarchy).
+(these should be stored in the form :file:`1_namelist_cfg`, :file:`2_namelist_cfg`, etc...
+according to their rank in the grid hierarchy).
 Consistent time steps and number of steps with the chosen time refinement have to be provided.
 Specific to AGRIF is the following block:
 
-.. code-block:: fortran
-
-	!-----------------------------------------------------------------------
-	&namagrif      !  AGRIF zoom                                            ("key_agrif")
-	!-----------------------------------------------------------------------
-	   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
-	   rn_sponge_tra = 2880.   !  coefficient for tracer   sponge layer [m2/s]
-	   rn_sponge_dyn = 2880.   !  coefficient for dynamics sponge layer [m2/s]
-	   ln_chk_bathy  = .false. !  =T  check the parent bathymetry
-	/
+.. literalinclude:: ../../namelists/namagrif
+   :language: fortran
 
 where sponge layer coefficients have to be chosen according to the child grid mesh size.
 The sponge area is hard coded in NEMO and applies on the following grid points:
-2 x refinement factor (from i=1+nbghostcells+1 to i=1+nbghostcells+sponge_area)
+2 x refinement factor (from ``i=1+nbghostcells+1`` to ``i=1+nbghostcells+sponge_area``)
 
 .. rubric:: References
Index: NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/README.rst
===================================================================
--- NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/README.rst	(revision 11777)
+++ NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/README.rst	(revision 11836)
@@ -29,5 +29,5 @@
 ===========================================================
 
-To compile the ORCA2_ICE_PISCES_ reference configuration using ``makenemo``,
+To compile the ORCA2_ICE_PISCES_ reference configuration using :file:`makenemo`,
 one should use the following, by selecting among available architecture file or
 providing a user defined one:
Index: NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/SHARED/README.rst
===================================================================
--- NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/SHARED/README.rst	(revision 11777)
+++ NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/SHARED/README.rst	(revision 11836)
@@ -11,35 +11,50 @@
 
 Output of diagnostics in NEMO is usually done using XIOS.
-This is an efficient way of writing diagnostics because the time averaging, file writing and even some simple arithmetic or regridding is carried out in parallel to the NEMO model run.
+This is an efficient way of writing diagnostics because
+the time averaging, file writing and even some simple arithmetic or regridding is carried out in
+parallel to the NEMO model run.
 This page gives a basic introduction to using XIOS with NEMO.
-Much more information is available from the XIOS homepage above and from the NEMO manual.
+Much more information is available from the :xios:`XIOS homepage<>` above and from the NEMO manual.
 
 Use of XIOS for diagnostics is activated using the pre-compiler key ``key_iomput``.
 
 Extracting and installing XIOS
-------------------------------
+==============================
 
 1. Install the NetCDF4 library.
-   If you want to use single file output you will need to compile the HDF & NetCDF libraries to allow parallel IO.
-2. Download the version of XIOS that you wish to use. The recommended version is now XIOS 2.5:
+   If you want to use single file output you will need to compile the HDF & NetCDF libraries to
+   allow parallel IO.
+2. Download the version of XIOS that you wish to use.
+   The recommended version is now XIOS 2.5:
 
-.. code-block:: console
+   .. code-block:: console
 
-	$ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 xios-2.5
+      $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5
 
-and follow the instructions in `XIOS documentation <http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation>`_ to compile it.
-   If you find problems at this stage, support can be found by subscribing to the `XIOS mailing list <http://forge.ipsl.jussieu.fr/mailman/listinfo.cgi/xios-users>`_ and sending a mail message to it.
+and follow the instructions in :xios:`XIOS documentation <wiki/documentation>` to compile it.
+If you find problems at this stage, support can be found by subscribing to
+the :xios:`XIOS mailing list <../mailman/listinfo.cgi/xios-users>` and sending a mail message to it.
 
 XIOS Configuration files
 ------------------------
 
-XIOS is controlled using xml input files that should be copied to your model run directory before running the model.
-Examples of these files can be found in the reference configurations (``cfgs``). The XIOS executable expects to find a file called ``iodef.xml`` in the model run directory.
-In NEMO we have made the decision to use include statements in the ``iodef.xml`` file to include ``field_def_nemo-oce.xml`` (for physics), ``field_def_nemo-ice.xml`` (for ice), ``field_def_nemo-pisces.xml`` (for biogeochemistry) and ``domain_def.xml`` from the /cfgs/SHARED directory.
-Most users will not need to modify ``domain_def.xml`` or ``field_def_nemo-???.xml`` unless they want to add new diagnostics to the NEMO code.
-The definition of the output files is organized into separate ``file_definition.xml`` files which are included in the ``iodef.xml`` file.
+XIOS is controlled using XML input files that should be copied to
+your model run directory before running the model.
+Examples of these files can be found in the reference configurations (:file:`./cfgs`).
+The XIOS executable expects to find a file called :file:`iodef.xml` in the model run directory.
+In NEMO we have made the decision to use include statements in the :file:`iodef.xml` file to include:
+
+- :file:`field_def_nemo-oce.xml` (for physics),
+- :file:`field_def_nemo-ice.xml` (for ice),
+- :file:`field_def_nemo-pisces.xml` (for biogeochemistry) and
+- :file:`domain_def.xml` from the :file:`./cfgs/SHARED` directory.
+
+Most users will not need to modify :file:`domain_def.xml` or :file:`field_def_nemo-???.xml` unless
+they want to add new diagnostics to the NEMO code.
+The definition of the output files is organized into separate :file:`file_definition.xml` files which
+are included in the :file:`iodef.xml` file.
 
 Modes
------
+=====
 
 Detached Mode
@@ -48,11 +63,12 @@
 In detached mode the XIOS executable is executed on separate cores from the NEMO model.
 This is the recommended method for using XIOS for realistic model runs.
-To use this mode set ``using_server`` to ``true`` at the bottom of the ``iodef.xml`` file:
+To use this mode set ``using_server`` to ``true`` at the bottom of the :file:`iodef.xml` file:
 
 .. code-block:: xml
 
-	<variable id="using_server" type="boolean">true</variable>
+   <variable id="using_server" type="boolean">true</variable>
 
-Make sure there is a copy (or link to) your XIOS executable in the working directory and in your job submission script allocate processors to XIOS.
+Make sure there is a copy (or link to) your XIOS executable in the working directory and
+in your job submission script allocate processors to XIOS.
 
 Attached Mode
@@ -60,33 +76,44 @@
 
 In attached mode XIOS runs on each of the cores used by NEMO.
-This method is less efficient than the detached mode but can be more convenient for testing or with small configurations.
-To activate this mode simply set ``using_server`` to false in the ``iodef.xml`` file
+This method is less efficient than the detached mode but can be more convenient for testing or
+with small configurations.
+To activate this mode simply set ``using_server`` to false in the :file:`iodef.xml` file
 
 .. code-block:: xml
 
-	<variable id="using_server" type="boolean">false</variable>
+   <variable id="using_server" type="boolean">false</variable>
 
 and don't allocate any cores to XIOS.
-Note that due to the different domain decompositions between XIOS and NEMO if the total number of cores is larger than the number of grid points in the j direction then the model run will fail.
+
+.. note::
+
+   Due to the different domain decompositions between XIOS and NEMO,
+   if the total number of cores is larger than the number of grid points in the ``j`` direction then
+   the model run will fail.
 
 Adding new diagnostics
-----------------------
+======================
 
 If you want to add a NEMO diagnostic to the NEMO code you will need to do the following:
 
 1. Add any necessary code to calculate you new diagnostic in NEMO
-2. Send the field to XIOS using ``CALL iom_put( 'field_id', variable )`` where ``field_id`` is a unique id for your new diagnostics and variable is the fortran variable containing the data.
-   This should be called at every model timestep regardless of how often you want to output the field. No time averaging should be done in the model code.
-3. If it is computationally expensive to calculate your new diagnostic you should also use "iom_use" to determine if it is requested in the current model run. For example,
+2. Send the field to XIOS using ``CALL iom_put( 'field_id', variable )`` where
+   ``field_id`` is a unique id for your new diagnostics and
+   variable is the fortran variable containing the data.
+   This should be called at every model timestep regardless of how often you want to output the field.
+   No time averaging should be done in the model code.
+3. If it is computationally expensive to calculate your new diagnostic
+   you should also use "iom_use" to determine if it is requested in the current model run.
+   For example,
 
-.. code-block:: fortran
+   .. code-block:: fortran
 
-		IF iom_use('field_id') THEN
-		   !Some expensive computation
-	   	!...
-		   !...
-	   	iom_put('field_id', variable)
-		ENDIF
+      IF iom_use('field_id') THEN
+         !Some expensive computation
+         !...
+         !...
+	 iom_put('field_id', variable)
+      ENDIF
 
-4. Add a variable definition to the ``field_def_nemo-???.xml`` file.
-5. Add the variable to the ``iodef.xml`` or ``file_definition.xml`` file.
+4. Add a variable definition to the :file:`field_def_nemo-???.xml` file.
+5. Add the variable to the :file:`iodef.xml` or :file:`file_definition.xml` file.
Index: NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/SHARED/namelist_ref
===================================================================
--- NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/SHARED/namelist_ref	(revision 11777)
+++ NEMO/branches/2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps/cfgs/SHARED/namelist_ref	(revision 11836)
@@ -290,5 +290,4 @@
    !                       !   -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel)
    nn_cats_cpl   =     5   !  Number of sea ice categories over which coupling is to be carried out (if not 1)
-
    !_____________!__________________________!____________!_____________!______________________!________!
    !             !        description       !  multiple  !    vector   !       vector         ! vector !
@@ -327,5 +326,5 @@
    sn_rcv_wper   =   'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
    sn_rcv_wnum   =   'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
-   sn_rcv_wstrf  =   'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
+   sn_rcv_wfreq  =   'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
    sn_rcv_wdrag  =   'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
    sn_rcv_ts_ice =   'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
