Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/CANAL/MY_SRC/usrdef_nam.F90
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/CANAL/MY_SRC/usrdef_nam.F90	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/CANAL/MY_SRC/usrdef_nam.F90	(revision 11954)
@@ -85,5 +85,5 @@
       !
       READ  ( numnam_cfg, namusr_def, IOSTAT = ios, ERR = 902 )
-902   IF( ios /= 0 )   CALL ctl_nam ( ios , 'namusr_def in configuration namelist', cdtxt )
+902   IF( ios /= 0 )   CALL ctl_nam ( ios , 'namusr_def in configuration namelist' )
       !
       IF(lwm)   WRITE( numond, namusr_def )
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_cen-ahm1000_cfg
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_cen-ahm1000_cfg	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_cen-ahm1000_cfg	(revision 11954)
@@ -210,5 +210,5 @@
    !                       ! coefficients
    rn_avm0     =   1.e-4     !  vertical eddy viscosity   [m2/s]       (background Kz if ln_zdfcst=F)
-   rn_avt0     =   0.0e      !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
+   rn_avt0     =   0.0       !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
    nn_avb      =    0        !  profile for background avt & avm (=1) or not (=0)
    nn_havtb    =    0        !  horizontal shape for avtb (=1) or not (=0)
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_ubs_cfg
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_ubs_cfg	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT2_flux_ubs_cfg	(revision 11954)
@@ -210,5 +210,5 @@
    !                       ! coefficients
    rn_avm0     =   1.e-4     !  vertical eddy viscosity   [m2/s]       (background Kz if ln_zdfcst=F)
-   rn_avt0     =   0.0e      !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
+   rn_avt0     =   0.0       !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
    nn_avb      =    0        !  profile for background avt & avm (=1) or not (=0)
    nn_havtb    =    0        !  horizontal shape for avtb (=1) or not (=0)
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT4_flux_ubs_cfg
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT4_flux_ubs_cfg	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_sco_FCT4_flux_ubs_cfg	(revision 11954)
@@ -210,5 +210,5 @@
    !                       ! coefficients
    rn_avm0     =   1.e-4     !  vertical eddy viscosity   [m2/s]       (background Kz if ln_zdfcst=F)
-   rn_avt0     =   0.0e      !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
+   rn_avt0     =   0.0       !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
    nn_avb      =    0        !  profile for background avt & avm (=1) or not (=0)
    nn_havtb    =    0        !  horizontal shape for avtb (=1) or not (=0)
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT2_flux_ubs_cfg
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT2_flux_ubs_cfg	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT2_flux_ubs_cfg	(revision 11954)
@@ -211,5 +211,5 @@
    !                       ! coefficients
    rn_avm0     =   1.e-4     !  vertical eddy viscosity   [m2/s]       (background Kz if ln_zdfcst=F)
-   rn_avt0     =   0.0e      !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
+   rn_avt0     =   0.0       !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
    nn_avb      =    0        !  profile for background avt & avm (=1) or not (=0)
    nn_havtb    =    0        !  horizontal shape for avtb (=1) or not (=0)
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT4_flux_ubs_cfg
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT4_flux_ubs_cfg	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT4_flux_ubs_cfg	(revision 11954)
@@ -34,9 +34,8 @@
    cn_exp      =   "OVF_zps_FCT4_flux_ubs"  !  experience name
    nn_it000    =       1   !  first time step
-   !nn_itend    =    6120  ! here 17h of simulation  (=6120 time-step) 
-   nn_itend    =    5760   ! here 16h of simulation  (=5760 time-step) abort after 5802 for zps: pb of physics conditions
+   nn_itend    =    6120   ! here 17h of simulation  (=6120 time-step) 
    nn_istate   =       0   !  output the initial state (1) or not (0)
-   nn_stock    =    1080   !  frequency of creation of a restart file (modulo referenced to 1)
-   nn_write    =    1080   !  frequency of write in the output file   (modulo referenced to nn_it000)
+   nn_stock    =    6120   !  frequency of creation of a restart file (modulo referenced to 1)
+   nn_write    =    6120   !  frequency of write in the output file   (modulo referenced to nn_it000)
 /
 !-----------------------------------------------------------------------
@@ -255,4 +254,7 @@
 &namzdf        !   vertical physics manager                             (default: NO selection)
 !-----------------------------------------------------------------------
+   !                       ! adaptive-implicit vertical advection
+   ln_zad_Aimp = .true.       !  Courant number dependent scheme (Shchepetkin 2015)
+   !
    !                       ! type of vertical closure (required)
    ln_zdfcst   = .true.      !  constant mixing
@@ -279,5 +281,5 @@
    !                       ! coefficients
    rn_avm0     =   1.e-4     !  vertical eddy viscosity   [m2/s]       (background Kz if ln_zdfcst=F)
-   rn_avt0     =   0.0e      !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
+   rn_avt0     =   0.0       !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
    nn_avb      =    0        !  profile for background avt & avm (=1) or not (=0)
    nn_havtb    =    0        !  horizontal shape for avtb (=1) or not (=0)
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT4_vect_een_cfg
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT4_vect_een_cfg	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/OVERFLOW/EXPREF/namelist_zps_FCT4_vect_een_cfg	(revision 11954)
@@ -210,5 +210,5 @@
    !                       ! coefficients
    rn_avm0     =   1.e-4     !  vertical eddy viscosity   [m2/s]       (background Kz if ln_zdfcst=F)
-   rn_avt0     =   0.0e      !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
+   rn_avt0     =   0.0       !  vertical eddy diffusivity [m2/s]       (background Kz if ln_zdfcst=F)
    nn_avb      =    0        !  profile for background avt & avm (=1) or not (=0)
    nn_havtb    =    0        !  horizontal shape for avtb (=1) or not (=0)
Index: NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/README.rst
===================================================================
--- NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/README.rst	(revision 11671)
+++ NEMO/branches/2019/dev_r11613_ENHANCE-04_namelists_as_internalfiles/tests/README.rst	(revision 11954)
@@ -3,8 +3,21 @@
 **********************
 
-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
+.. todo::
+
+   CANAL animated gif is missing
+
+.. contents::
+   :local:
+   :depth: 1
+
+Installation
+============
+
+Download
+--------
+
+| The complete and up-to-date set of test cases is available on
+  :github:`NEMO test cases repository <NEMO-examples>`.
+| Download it directly into the :file:`./tests` root directory with
 
 .. code-block:: console
@@ -12,140 +25,182 @@
    $ git clone http://github.com/NEMO-ocean/NEMO-examples
 
-.. contents::
-	:local:
-
-Procedure
-=========
-
-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:
+Compilation
+-----------
+
+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>`.
+
+| As the reference configurations are compiled with ``-r`` option,
+  test cases can be compiled by the use of :file:`makenemo` with ``-a`` option.
+| Here an example to compile a copy named WAD2 of the wetting and drying test case (WAD):
 
 .. 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. 
+   $ ./makenemo -n 'WAD2' -a 'WAD' -m 'my_arch' -j '4'
+
+Run and analysis
+----------------
+
+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 :github:`NEMO test cases repository <NEMO-examples>`
 
 The description below is a brief advertisement of some test cases.
 
+List of test cases
+==================
+
 ICE_AGRIF
-=========
-  
-  This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel
-  over a slab ocean (i.e. one ocean layer), and with an AGRIF zoom (1:3) in the center
-  The purpose of this configuration is to test the advection of the ice patch in  
-  and across the AGRIF boundary
-  One can either impose ice velocities or ice-atm. stresses and let rheology define velocities
-  (see README for details)
-
-  .. image:: _static/ICE_AGRIF_UDIAG_43days_UM5.gif
+---------
+
+.. figure:: _static/ICE_AGRIF_UDIAG_43days_UM5.gif
+   :width: 200px
+   :align: left
+
+   ..
+
+| This test case illustrates the advection of an ice patch across
+  an East/West and North/South periodic channel over a slab ocean (i.e. one ocean layer),
+  and with an AGRIF zoom (1:3) in the center.
+| The purpose of this configuration is to
+  test the advection of the ice patch in and across the AGRIF boundary.
+  One can either impose ice velocities or ice-atm.
+  Stresses and let rheology define velocities (see :file:`README` for details)
 
 VORTEX
-======
-  
-  This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom.
-  It is implemented here with an online refined subdomain (1:3) out of which the vortex propagates.
-  It serves as a benchmark for quantitative estimates of nesting errors as in Debreu et al. (2012) :cite:`DEBREU2012`,
-  Penven et al. (2006) :cite:`PENVEN2006` or Spall and Holland (1991) :cite:`SPALL1991`.
-  
-  The animation below (sea level anomaly in meters) illustrates with two 1:2 successively nested grids how
-  the vortex smoothly propagates out of the refined grids.
-  
-  .. image:: _static/VORTEX_anim.gif
+------
+
+.. figure:: _static/VORTEX_anim.gif
+   :width: 200px
+   :align: right
+
+   ..
+
+This test case illustrates the propagation of an anticyclonic eddy over a Beta plan and a flat bottom.
+It is implemented here with an online refined subdomain (1:3) out of which the vortex propagates.
+It serves as a benchmark for quantitative estimates of nesting errors as in :cite:`DEBREU2012`,
+:cite:`PENVEN2006` or :cite:`SPALL1991`.
+
+The animation (sea level anomaly in meters) illustrates with
+two 1:2 successively nested grids how the vortex smoothly propagates out of the refined grids.
 
 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.
-  This configuration served as initial assesment of the ice shelf module in Losh et al. (2008) :cite:`LOSCH2008` and Mathiot et al. (2017) :cite:`MATHIOT2017`. 
-  The default setup is the one described `here <http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf>`_.
-  
-  The figure below (meridional overturning circulation) illustrates the circulation generated after 10000 days by the ice shelf melting (ice pump).
-
-  .. image:: _static/ISOMIP_moc.png
+------
+
+.. figure:: _static/ISOMIP_moc.png
+   :width: 200px
+   :align: left
+
+   ..
+
+| The purpose of this test case is to evaluate the impact of various schemes and new development with
+  the iceshelf cavities circulation and melt.
+  This configuration served as initial assesment of the ice shelf module in :cite:`LOSCH2008` and
+  :cite:`MATHIOT2017`.
+  The default setup is the one described |ISOMIP|_.
+| The figure (meridional overturning circulation) illustrates
+  the circulation generated after 10000 days by the ice shelf melting (ice pump).
+
+.. |ISOMIP| replace:: here
 
 LOCK_EXCHANGE
-=============
-
-  The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted
-  by Haidvogel and Beckmann (1999) :cite:`HAIDVOGEL1999` for testing advection schemes in ocean circulation models.
-  It has been used by several authors including Burchard and Bolding (2002) :cite:`BURCHARD2002` and Ilicak et al. (2012) :cite:`ILICAK2012`.
-  The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes 
-  and/or subgrid closures on spurious interior mixing.
-
-  Below the animation of the LOCK_EXCHANGE test case using the advection scheme FCT4 (forth order) for tracer and ubs for dynamics.
-
-  .. image:: _static/LOCK-FCT4_flux_ubs.gif
+-------------
+
+.. figure:: _static/LOCK-FCT4_flux_ubs.gif
+   :width: 200px
+   :align: right
+
+   ..
+
+| The LOCK EXCHANGE experiment is a classical fluid dynamics experiment that has been adapted
+  by :cite:`HAIDVOGEL1999` for testing advection schemes in ocean circulation models.
+  It has been used by several authors including :cite:`BURCHARD2002` and :cite:`ILICAK2012`.
+  The LOCK EXCHANGE experiment can in particular illustrate
+  the impact of different choices of numerical schemes and/or subgrid closures on
+  spurious interior mixing.
+| Here the animation of the LOCK_EXCHANGE test case using
+  the advection scheme FCT4 (forth order) for tracer and ubs for dynamics.
 
 OVERFLOW
-========
-
-  The OVERFLOW experiment illustrates the impact of different choices of numerical schemes 
-  and/or subgrid closures on spurious interior mixing close to bottom topography. 
-  The OVERFLOW experiment is adapted from the non-rotating overflow configuration described 
-  in Haidvogel and Beckmann (1999) :cite:`HAIDVOGEL1999` and further used by Ilicak et al. (2012) :cite:`ILICAK2012`.
-  Here we can assess the behaviour of the second-order tracer advection scheme FCT2 and fortht-order FCT4, z-coordinate and sigma coordinate (...).
-
-  Below the animation of the OVERFLOW test case in sigma coordinate with the forth-order advection scheme FCT4.
-
-  .. image:: _static/OVF-sco_FCT4_flux_cen-ahm1000.gif
+--------
+
+.. figure:: _static/OVF-sco_FCT4_flux_cen-ahm1000.gif
+   :width: 200px
+   :align: left
+
+   ..
+
+| The OVERFLOW experiment illustrates the impact of different choices of numerical schemes and/or
+  subgrid closures on spurious interior mixing close to bottom topography.
+  The OVERFLOW experiment is adapted from the non-rotating overflow configuration described in
+  :cite:`HAIDVOGEL1999` and further used by :cite:`ILICAK2012`.
+  Here we can assess the behaviour of the second-order tracer advection scheme FCT2 and
+  forth-order FCT4, z-coordinate and sigma coordinate (...).
+| Here the animation of the OVERFLOW test case in sigma coordinate with
+  the forth-order advection scheme FCT4.
 
 WAD
-===
-
-  A set of simple closed basin geometries for testing the Wetting and drying capabilities. 
-  Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.
-  
-  Below the animation of the test case 7. This test case is a simple linear slope with a mid-depth shelf with an open boundary forced with a sinusoidally varying ssh.
-  This test case has been introduced to emulate a typical coastal application with a tidally forced open boundary with an adverse SSH gradient that, when released, creates a surge up the slope.
-  The parameters are chosen such that the surge rises above sea-level before falling back and oscillating towards an equilibrium position
-
-  .. image:: _static/wad_testcase_7.gif
+---
+
+.. figure:: _static/wad_testcase_7.gif
+   :width: 200px
+   :align: right
+
+   ..
+
+| A set of simple closed basin geometries for testing the Wetting and drying capabilities.
+  Examples range from a closed channel with EW linear bottom slope to
+  a parabolic EW channel with a Gaussian ridge.
+| Here the animation of the test case 7.
+  This test case is a simple linear slope with a mid-depth shelf with
+  an open boundary forced with a sinusoidally varying ssh.
+  This test case has been introduced to emulate a typical coastal application with
+  a tidally forced open boundary with an adverse SSH gradient that,
+  when released, creates a surge up the slope.
+  The parameters are chosen such that
+  the surge rises above sea-level before falling back and oscillating towards an equilibrium position.
 
 CANAL
-=====
-
-  East-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex).
-
-  .. image::_static/CANAL_image.gif
+-----
+
+.. figure:: _static/CANAL_image.gif
+   :width: 200px
+   :align: left
+
+   ..
+
+East-west periodic canal of variable size with several initial states and
+associated geostrophic currents (zonal jets or vortex).
 
 ICE_ADV2D
-=========
-  
-  This test case illustrates the advection of an ice patch across an East/West and North/South periodic channel
-  over a slab ocean (i.e. one ocean layer).
+---------
+
+| This test case illustrates the advection of an ice patch across
+  an East/West and North/South periodic channel over a slab ocean (i.e. one ocean layer).
   The configuration is similar to ICE_AGRIF, except for the AGRIF zoom.
-  The purpose of this configuration is to test the advection schemes available in the sea-ice code
+| The purpose of this configuration is to test the advection schemes available in the sea-ice code
   (for now, Prather and Ultimate-Macho from 1st to 5th order),
   especially the occurence of overshoots in ice thickness
-  
 
 ICE_ADV1D
-=========
-  
-  This experiment is the classical Schar & Smolarkiewicz (1996) test case :cite:`SCHAR1996`,
-  which has been used in :cite:`LIPSCOMB2004`,
-  and in which very specific shapes of ice concentration, thickness and volume converge toward the center of a basin.
+---------
+
+| This experiment is the classical :cite:`SCHAR1996` test case ,
+  which has been used in :cite:`LIPSCOMB2004`, and in which very specific shapes of ice concentration,
+  thickness and volume converge toward the center of a basin.
   Convergence is unidirectional (in x) while fields are homogeneous in y.
-  The purpose of this configuration is to test the caracteristics of advection schemes available in the sea-ice code
+| 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.  
-
-References
-==========
-
-.. bibliography:: test_cases.bib
-	:all:
-	:style: unsrt
-	:labelprefix: T
+  especially the constitency between concentration, thickness and volume,
+  and the preservation of initial shapes.
+
+.. rubric:: References
+
+.. bibliography:: tests.bib
+   :all:
+   :style: unsrt
+   :labelprefix: T
