Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/AMM12/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/AMM12/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/AMM12/EXP00/namelist_cfg	(revision 9356)
@@ -18,21 +18,40 @@
 /
 !-----------------------------------------------------------------------
-&namcfg        !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.   !  (=T) read the domain configuration file
-      !                    !  (=F) user defined configuration  ==>>>  see usrdef(_...) modules
-      cn_domcfg = "AMM_R12_sco_domcfg"     ! domain configuration filename
-/
-
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+      !                   !  (=F) user defined configuration  ==>>>  see usrdef(_...) modules
+   cn_domcfg   = "AMM_R12_sco_domcfg"     ! domain configuration filename
+/
+!-----------------------------------------------------------------------
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    rn_rdt      =   600.    !  time step for the dynamics (and tracer if nn_acc=0)
 /
 !-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namtsd        !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -62,10 +81,26 @@
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
 !-----------------------------------------------------------------------
    nn_chldta   =      0    !  RGB : Chl data (=1) or cst value (=0)
 /
 !-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
 !-----------------------------------------------------------------------
 !          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
@@ -82,5 +117,13 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
 !-----------------------------------------------------------------------
 !          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
@@ -94,5 +137,5 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
 !-----------------------------------------------------------------------
 !          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
@@ -108,9 +151,9 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
 /
@@ -146,5 +189,6 @@
 /
 !-----------------------------------------------------------------------
-&nambdy        !  unstructured open boundaries
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
     ln_bdy         = .true.
     nb_bdy         =  1
@@ -155,5 +199,5 @@
 /
 !-----------------------------------------------------------------------
-&nambdy_dta      !  open boundaries - external data
+&nambdy_dta    !  open boundaries - external data                       
 !-----------------------------------------------------------------------
 !          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
@@ -170,11 +214,10 @@
 /
 !-----------------------------------------------------------------------
-&nambdy_tide     ! tidal forcing at open boundaries
+&nambdy_tide   !  tidal forcing at open boundaries
 !-----------------------------------------------------------------------
    filtide      = 'bdydta/amm12_bdytide_'         !  file name root of tidal forcing files
 /
-
-!-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_NONE    = .false.    !  free-slip       : Cd = 0                  (F => fill namdrg_bot
@@ -186,5 +229,9 @@
 /
 !-----------------------------------------------------------------------
-&namdrg_bot        !   BOTTOM friction                                  
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
 !-----------------------------------------------------------------------
    rn_Cd0     =  2.5e-3   !  drag coefficient [-]
@@ -194,5 +241,5 @@
    rn_z0      =  0.003    !  roughness [m]  (ln_loglayer=T)
    ln_boost   = .false.   !  =T regional boost of Cd0 ; =F constant
-      rn_boost=  50.         !  local boost factor  [-]
+   rn_boost   =  50.      !  local boost factor  [-]
 /
 !-----------------------------------------------------------------------
@@ -205,10 +252,10 @@
 /
 !-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10   = .true.         !  = Use TEOS-10 equation of state
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer                          (default: NO advection)
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_fct =  .true.   !  FCT scheme
@@ -217,10 +264,10 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)
-!-----------------------------------------------------------------------
-/
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    !                       !  Operator type:
    ln_traldf_NONE  = .false.   !           No operator (no explicit diffusion)
@@ -252,16 +299,20 @@
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.false.   ! use eddy induced velocity parameterization
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.  !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection                (default: None)
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .true.  !  vector form - 2nd centered scheme
@@ -269,5 +320,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -278,18 +329,18 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zps  = .false.   !  z-coordinate - partial steps (interpolation)
-   ln_hpg_prj  = .true.   !  s-coordinate (Pressure Jacobian scheme)
-/
-!-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient 
-!-----------------------------------------------------------------------
-   ln_dynspg_ts = .true.    ! split-explicit free surface
-      ln_bt_auto    = .false.  ! Number of sub-step defined from:
-         nn_baro       = 30       ! =F : the number of sub-step in rn_rdt seconds
-/
-!-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+   ln_hpg_prj  = .true.    !  s-coordinate (Pressure Jacobian scheme)
+/
+!-----------------------------------------------------------------------
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
+!-----------------------------------------------------------------------
+   ln_dynspg_ts = .true.   ! split-explicit free surface
+   ln_bt_auto   = .false.  ! Number of sub-step defined from:
+   nn_baro      = 30       ! =F : the number of sub-step in rn_rdt seconds
+/
+!-----------------------------------------------------------------------
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -357,5 +408,5 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_gls                !   GLS vertical diffusion                   (ln_zdfgls =T)
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
 !-----------------------------------------------------------------------
    rn_charn =  100000.     !  Charnock constant for wb induced roughness length
@@ -363,18 +414,60 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_osm                !   OSM vertical diffusion                   (ln_zdfosm =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_iwm    !   internal wave-driven mixing parameterization         (ln_zdfiwm =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+   ln_diatmb  = .true.    !  Choose Top Middle and Bottom output or not
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+   ln_dia25h  = .true.    ! Choose 25h mean output or not
 /
 !-----------------------------------------------------------------------
@@ -383,48 +476,13 @@
 /
 !-----------------------------------------------------------------------
-&namtrd        !   diagnostics on dynamics and/or tracer trends         ("key_trddyn" and/or "key_trdtra")
-!              !       or mixed-layer trends or barotropic vorticity    ("key_trdmld" or     "key_trdvor")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namflo       !   float parameters                                      ("key_float")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-&namhsb       !  Heat and salt budgets
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_diaharm   !   Harmonic analysis of tidal constituents ('key_diaharm')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdct        ! transports through sections
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namobs       !  observation usage switch                               ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_wave   ! External fields from wave model
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_diatmb  !  Top Middle Bottom Output
-!-----------------------------------------------------------------------
-   ln_diatmb  = .true.    !  Choose Top Middle and Bottom output or not
-/
-!-----------------------------------------------------------------------
-&nam_dia25h  !  25h Mean Output
-!-----------------------------------------------------------------------
-   ln_dia25h  = .true.    ! Choose 25h mean output or not
-/
-
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_BFM/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_BFM/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_BFM/EXP00/namelist_cfg	(revision 9356)
@@ -9,10 +9,4 @@
    jpkglo      =    31     !  number of model levels
 /
-!!======================================================================
-!!                   ***  Run management namelists  ***
-!!======================================================================
-!!   namrun        parameters of the run
-!!======================================================================
-!
 !-----------------------------------------------------------------------
 &namrun        !   parameters of the run
@@ -26,5 +20,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration   
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.   !  (=T) read the domain configuration file
@@ -34,22 +28,38 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
-!-----------------------------------------------------------------------
-   ln_linssh   = .true.    !  =T  linear free surface  ==>>  model level are fixed in time
-   !
-   rn_rdt      = 7200.     !  time step for the dynamics (and tracer if nn_acc=0)
-/
-!-----------------------------------------------------------------------
-&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
-!-----------------------------------------------------------------------
-!          ! file name ! frequency (hours)    ! variable ! time interp. ! clim  !'yearly' or ! weights  ! rotation !
-!          !           !  (if <0  months)     !   name   !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing
+&namdom        !   time and space domain
+!-----------------------------------------------------------------------
+     ln_linssh   = .true.    !  =T  linear free surface  ==>>  model level are fixed in time        |  -------------------------------------------------------------------------------------------------
+     !                                                                                              |  -------------------------------------------------------------------------------------------------
+     rn_rdt      = 7200.     !  time step for the dynamics (and tracer if nn_acc=0)
+/
+!-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+!              !  file name                 ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                            !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
    cn_dir        = './'      !  root directory for the location of the runoff files
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -66,5 +76,25 @@
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
 !-----------------------------------------------------------------------
    ln_qsr_rgb  = .false.   !  RGB (Red-Green-Blue) light penetration
@@ -73,22 +103,30 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
 !-----------------------------------------------------------------------
    ln_rnf_mouth = .false.   !  specific treatment at rivers mouths
 /
 !-----------------------------------------------------------------------
-&namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
 /
@@ -96,4 +134,5 @@
 &namlbc        !   lateral momentum boundary condition
 !-----------------------------------------------------------------------
+   !                       !  free slip  !   partial slip  !   no slip   ! strong slip
    rn_shlat    =    0.     !  shlat = 0  !  0 < shlat < 2  !  shlat = 2  !  2 < shlat
 /
@@ -103,5 +142,5 @@
 /
 !-----------------------------------------------------------------------
-&nam_tide      !    tide parameters
+&nam_tide      !   tide parameters
 !-----------------------------------------------------------------------
 /
@@ -111,31 +150,39 @@
 /
 !-----------------------------------------------------------------------
-&nambdy_dta      !  open boundaries - external data           
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nambdy_tide     ! tidal forcing at open boundaries
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_non_lin = .true.     !  non-linear  drag: Cd = Cd0 |U|
 /
 !-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_eos80    = .true.         !  = Use EOS80 equation of state
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer                          (default: No selection)
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_fct =  .true.   !  FCT scheme
@@ -144,12 +191,12 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)  (default: NO)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: No selection)
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Operator type:
-   ln_traldf_NONE  = .false.   !           No operator (no explicit advection)
+   ln_traldf_NONE  =  .false.  !  No explicit diffusion
    ln_traldf_lap   =  .true.   !    laplacian operator
    ln_traldf_blp   =  .false.  !  bilaplacian operator
@@ -185,10 +232,14 @@
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.  !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection                (default: No selection)
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .true.  !  vector form - 2nd centered scheme
@@ -196,5 +247,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .true.  !  enstrophy conserving scheme
@@ -205,5 +256,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zco  = .true.    !  z-coordinate - full steps
@@ -211,13 +262,13 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
-   ln_dynldf_NONE=  .false.    !           No operator (no explicit diffusion)
+   ln_dynldf_NONE=  .false.    !  No operator (i.e. no explicit diffusion)
    ln_dynldf_lap =  .true.     !    laplacian operator
    ln_dynldf_blp =  .false.    !  bilaplacian operator
@@ -276,14 +327,14 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke")
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
    nn_etau     =   0       !  penetration of tke below the mixed layer (ML) due to internal & intertial waves
 /
 !-----------------------------------------------------------------------
-&namzdf_gls                !   GLS vertical diffusion                   (ln_zdfgls =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_osm                !   OSM vertical diffusion                   (ln_zdfosm =T)
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
 !-----------------------------------------------------------------------
 /
@@ -293,34 +344,41 @@
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtrd        !   diagnostics on dynamics and/or tracer trends         ("key_trddyn" and/or "key_trdtra")
-!              !       or mixed-layer trends or barotropic vorticity    ("key_trdmld" or     "key_trdvor")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namflo       !   float parameters                                      ("key_float")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdct        ! transports through sections
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
 !-----------------------------------------------------------------------
     nn_dct      = 60       !  time step frequency for transports computing
@@ -329,13 +387,25 @@
 /
 !-----------------------------------------------------------------------
-&namobs       !  observation usage switch                               ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_wave   ! External fields from wave model
-!-----------------------------------------------------------------------
-/
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_BFM/EXP00/namelist_top_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_BFM/EXP00/namelist_top_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_BFM/EXP00/namelist_top_cfg	(revision 9356)
@@ -2,57 +2,57 @@
 !! NEMO-TOP : GYRE_BFM configuration namelist used to overwrite SHARED/namelist_top_ref
 !-----------------------------------------------------------------------
-&namtrc_run     !   run information
+&namtrc_run      !   run information
 !-----------------------------------------------------------------------
-   nn_writetrc   =  0        !  time step frequency for sn_tracer outputs
    ln_top_euler  = .true.    !  use Euler time-stepping for TOP
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&namtrc     !   tracers definition
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&namtrc          !   tracers definition
+!-----------------------------------------------------------------------
    ln_trcdta     =  .false.        !  Initialisation from data input file (T) or not (F)
 !
-!              !    name   !           title of the field              !   units    ! initial data ! save   !
-!              !           !                                           !            ! from file    ! or not !
-!              !           !                                           !            ! or not       !        !
-   sn_tracer(1)   = 'DUMMY   ' , 'Dummy tracer      '                 ,  'dummy-units' ,  .false.     ,  .true.
+!                !    name   !           title of the field            !   units    ! initial data from file or not ! 
+   sn_tracer(1)   = 'DUMMY   ' , 'Dummy tracer      '                 ,  'dummy-units' ,  .false.
 /
 !-----------------------------------------------------------------------
-&namtrc_dta    ! initial conditions
+&namage          !   AGE 
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc_adv    !   advection scheme for passive tracer                  (default: NO selection)
+&namtrc_dta      !    Initialisation from data input file
 !-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrc_adv      !   advection scheme for passive tracer                (default: NO selection)
    ln_trcadv_fct =  .true.   !  FCT scheme
       nn_fct_h   =  2               !  =2/4, horizontal 2nd / 4th order 
       nn_fct_v   =  2               !  =2/4, vertical   2nd / COMPACT 4th order 
-/
-!-----------------------------------------------------------------------
-&namtrc_ldf    !   lateral diffusion scheme for passive tracer 
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc_zdf        !   vertical physics
+&namtrc_ldf      !   lateral diffusion scheme for passive tracer 
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc_rad        !  treatment of negative concentrations 
+&namtrc_rad      !  treatment of negative concentrations 
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc_dmp    !   passive tracer newtonian damping
+&namtrc_dmp      !   passive tracer newtonian damping   
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc_bc     ! boundary conditions
+&namtrc_ice      !    Representation of sea ice growth & melt effects
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc_trd       !   diagnostics on tracer trends        ('key_trdtrc')
-!                          or mixed-layer trends          ('key_trdmld_trc')
+&namtrc_trd      !   diagnostics on tracer trends                       ('key_trdtrc')
 !----------------------------------------------------------------------
 /
+!----------------------------------------------------------------------
+&namtrc_bc       !   data for boundary conditions
 !-----------------------------------------------------------------------
-&namtrc_dia       !   parameters for passive tracer additional diagnostics
+/
 !----------------------------------------------------------------------
+&namtrc_bdy      !   Setup of tracer boundary conditions
+!-----------------------------------------------------------------------
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_cfg	(revision 9356)
@@ -26,13 +26,13 @@
 !!======================================================================
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration   
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.   !  (=T) read the domain configuration file
       !                    !  (=F) user defined configuration  ==>>>  see usrdef(_...) modules
    ln_write_cfg= .false.   !  (=T) create the domain configuration file
-!
-/
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+      !
+/
+!-----------------------------------------------------------------------
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .true.    !  =T  linear free surface  ==>>  model level are fixed in time
@@ -41,11 +41,31 @@
 /
 !-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
-!-----------------------------------------------------------------------
-!          ! file name ! frequency (hours)    ! variable ! time interp. ! clim  !'yearly' or ! weights  ! rotation !
-!          !           !  (if <0  months)     !   name   !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+!              !  file name                 ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                            !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
    cn_dir        = './'      !  root directory for the location of the runoff files
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 
@@ -66,5 +86,25 @@
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
 !-----------------------------------------------------------------------
    ln_qsr_rgb  = .false.   !  RGB (Red-Green-Blue) light penetration
@@ -73,4 +113,32 @@
 /
 !-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namlbc        !   lateral momentum boundary condition
 !-----------------------------------------------------------------------
@@ -78,19 +146,51 @@
 /
 !-----------------------------------------------------------------------
-&namdrg        !   top/bottom friction
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_non_lin = .true.     !  non-linear  drag: Cd = Cd0 |U|
 /
 !-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambbc        !   bottom temperature boundary condition                (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbl        !   bottom boundary layer scheme                         (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_eos80    = .true.         !  = Use EOS80 equation of state
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer                          (default: No selection)
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_fct =  .true.   !  FCT scheme
@@ -99,9 +199,9 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)  (default: NO)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: No selection)
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Operator type:
@@ -109,4 +209,5 @@
    ln_traldf_lap   =  .true.   !    laplacian operator
    ln_traldf_blp   =  .false.  !  bilaplacian operator
+   !
    !                       !  Direction of action:
    ln_traldf_lev   =  .false.  !  iso-level
@@ -129,21 +230,25 @@
    !                                !   = 20 F(i,j)    =ldf_c2d 
    !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation
-   !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d
-   !                                !   = 31 F(i,j,k,t)=F(local velocity)
+   !                                !   = 30 F(i,j,k)  =ldf_c2d * ldf_c1d
+   !                                !   = 31 F(i,j,k,t)=F(local velocity and grid-spacing)
    rn_aht_0        = 1000.     !  lateral eddy diffusivity   (lap. operator) [m2/s]
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.false.   ! use eddy induced velocity parameterization
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.  !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection                (default: No selection)
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .true.  !  vector form - 2nd centered scheme
@@ -151,5 +256,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm                          (default: No selection)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .true.  !  enstrophy conserving scheme
@@ -160,5 +265,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zco  = .true.    !  z-coordinate - full steps
@@ -166,10 +271,10 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum                        (default: No selection)
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -201,5 +306,5 @@
 &namzdf        !   vertical physics                                     (default: NO selection)
 !-----------------------------------------------------------------------
-   !                       ! type of vertical closure
+   !                       ! type of vertical closure (required)
    ln_zdfcst   = .false.      !  constant mixing
    ln_zdfric   = .false.      !  local Richardson dependent formulation (T =>   fill namzdf_ric)
@@ -229,55 +334,62 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric=T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke=T)
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
    nn_etau     =   0       !  penetration of tke below the mixed layer (ML) due to internal & intertial waves
 /
 !-----------------------------------------------------------------------
-&namzdf_gls                !   GLS vertical diffusion                   (ln_zdfgls=T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_osm                !   OSM vertical diffusion                   (ln_zdfosm =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_ddm    !   double diffusive mixing parameterization             (ln_zdfddm=T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtrd        !   diagnostics on dynamics and/or tracer trends         ("key_trddyn" and/or "key_trdtra")
-!              !       or mixed-layer trends or barotropic vorticity    ("key_trdmld" or     "key_trdvor")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namflo       !   float parameters                                      ("key_float")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdct        ! transports through sections
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
 !-----------------------------------------------------------------------
     nn_dct      = 60       !  time step frequency for transports computing
@@ -286,13 +398,25 @@
 /
 !-----------------------------------------------------------------------
-&namobs       !  observation usage switch                               ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_wave   ! External fields from wave model
-!-----------------------------------------------------------------------
-/
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_pisces_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_pisces_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_pisces_cfg	(revision 9356)
@@ -11,73 +11,105 @@
 !!              11 - Damping                                  (nampisdmp)
 !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &nampismod     !  Model used 
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
     ln_p4z = .false.
     ln_p2z = .true.
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &nampisext     !   air-sea exchange
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &nampisatm     !  Atmospheric prrssure 
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &nampisbio     !   biological parameters
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampislim     !   parameters for nutrient limitations
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&namp4zlim     !   parameters for nutrient limitations for PISCES std  - ln_p4z
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
+&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA    - ln_p5z
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namp5zquota   !   parameters for nutrient limitations PISCES quota    - ln_p5z
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nampisopt     !   parameters for optics
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 / 
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampisprod     !   parameters for phytoplankton growth
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&namp4zprod    !   parameters for phytoplankton growth for PISCES std  - ln_p4z
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampismort     !   parameters for phytoplankton sinks
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&namp5zprod    !   parameters for phytoplankton growth for PISCES quota- ln_p5z
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampismes     !   parameters for mesozooplankton
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&namp4zmort    !   parameters for phytoplankton sinks for PISCES std   - ln_p4z
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampiszoo     !   parameters for microzooplankton
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&namp5zmort    !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
+&namp4zmes     !   parameters for mesozooplankton for PISCES std       - ln_p4z
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namp5zmes     !   parameters for mesozooplankton
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namp4zzoo     !   parameters for microzooplankton for PISCES std      - ln_p4z
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namp5zzoo     !   parameters for microzooplankton
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nampisfer     !   parameters for iron chemistry
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-/  
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------  
 &nampisrem     !   parameters for remineralization
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
+&nampispoc     !   parameters for organic particles
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nampiscal     !   parameters for Calcite chemistry
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &nampissbc     !   parameters for inputs deposition
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampisice      !  Prescribed sea ice tracers
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&nampislig     !   Namelist parameters for ligands, nampislig
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampisdmp     !  Damping 
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&nampisice     !   Prescribed sea ice tracers
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
-&nampismass     !  Mass conservation
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
+&nampisdmp     !   Damping 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nampismass    !   Mass conservation
+!-----------------------------------------------------------------------
 /
 !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -92,34 +124,34 @@
 !!              8  - optical parameters                         (namlobopt)
 !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobphy     !   biological parameters for phytoplankton
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobnut     !   biological parameters for nutrients
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobzoo     !   biological parameters for zooplankton
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobdet     !   biological parameters for detritus
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobdom     !   biological parameters for DOM
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobsed     !   parameters from aphotic layers to sediment
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobrat     !   general coefficients
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
-!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+!-----------------------------------------------------------------------
 &namlobopt     !   optical parameters
-!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+!-----------------------------------------------------------------------
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_top_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_top_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/GYRE_PISCES/EXP00/namelist_top_cfg	(revision 9356)
@@ -3,9 +3,9 @@
 !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 !-----------------------------------------------------------------------
-&namtrc_run     !   run information
+&namtrc_run      !   run information
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtrc     !   tracers definition
+&namtrc          !   tracers definition
 !-----------------------------------------------------------------------
    jp_bgc        =  6
@@ -29,5 +29,13 @@
 /
 !-----------------------------------------------------------------------
-&namtrc_adv    !   advection scheme for passive tracer                  (default: NO selection)
+&namage          !   AGE 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrc_dta      !    Initialisation from data input file
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrc_adv      !   advection scheme for passive tracer                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_trcadv_fct =  .true.   !  FCT scheme
@@ -36,15 +44,15 @@
 /
 !-----------------------------------------------------------------------
-&namtrc_ldf    !   lateral diffusion scheme for passive tracer
+&namtrc_ldf      !   lateral diffusion scheme for passive tracer 
 !-----------------------------------------------------------------------
    rn_ahtrc_0       =  1000.    !  horizontal eddy diffusivity for tracers [m2/s]
 /
 !-----------------------------------------------------------------------
-&namtrc_rad        !  treatment of negative concentrations
+&namtrc_rad      !  treatment of negative concentrations 
 !-----------------------------------------------------------------------
    ln_trcrad   =  .false.  !  artificially correct negative concentrations (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namtrc_dmp      !   passive tracer newtonian damping
+&namtrc_dmp      !   passive tracer newtonian damping   
 !-----------------------------------------------------------------------
 /
@@ -55,5 +63,4 @@
 !-----------------------------------------------------------------------
 &namtrc_trd      !   diagnostics on tracer trends                       ('key_trdtrc')
-!                          or mixed-layer trends                        ('key_trdmld_trc')
 !----------------------------------------------------------------------
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/1_namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/1_namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/1_namelist_cfg	(revision 9356)
@@ -13,5 +13,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
@@ -20,9 +20,16 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
-!-----------------------------------------------------------------------  
+&namdom        !   time and space domain
+!-----------------------------------------------------------------------
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
    !
    rn_rdt      = 2880.     !  time step for the dynamics (and tracer if nn_acc=0)
+!-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -31,5 +38,13 @@
 /
 !-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
 !-----------------------------------------------------------------------
 /
@@ -49,5 +64,9 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_blk   !   namsbc_blk  Bulk formulae
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
 !-----------------------------------------------------------------------
 !              !  file name                   ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights                              ! rotation ! land/sea mask !
@@ -68,5 +87,17 @@
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
 !-----------------------------------------------------------------------
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
@@ -75,17 +106,29 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
       ln_icebergs              = .false.               ! iceberg floats or not
@@ -96,10 +139,34 @@
 /
 !-----------------------------------------------------------------------
-&namdrg        !   top/bottom friction
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_lin = .true.         !     linear  drag: Cd = Cd0 Uc0
 /
 !-----------------------------------------------------------------------
-&namagrif      !  AGRIF zoom                                            ("key_agrif")
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
 !-----------------------------------------------------------------------
 /
@@ -119,5 +186,5 @@
 /
 !-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10   = .false.         !  = Use TEOS-10 equation of state
@@ -126,5 +193,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer                          (default: NO advection)
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_fct = .true.     !  FCT scheme
@@ -133,10 +200,10 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param)
-!-----------------------------------------------------------------------
-/
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    !                       !  Operator type:
    ln_traldf_NONE  =  .false.  !           No operator (no explicit advection)
@@ -168,7 +235,7 @@
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.false.   ! use eddy induced velocity parameterization
 /
@@ -179,5 +246,9 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection                (default: No selection)
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_NONE= .false. !  linear dynamics (no momentum advection)
@@ -188,5 +259,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -197,15 +268,15 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_sco  = .true.   !  s-coordinate (standard jacobian formulation)
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -229,8 +300,7 @@
    rn_ahm_b      =      0.     !  background eddy viscosity for ldf_iso [m2/s]
    rn_bhm_0      = 8.5e+11     !  horizontal bilaplacian eddy viscosity [m4/s]
-/
-!!======================================================================
-!!                     vertical physics namelists                     !!
-!!======================================================================
+   !
+   ! Caution in 20 and 30 cases the coefficient have to be given for a 1 degree grid (~111km)
+/
 !-----------------------------------------------------------------------
 &namzdf        !   vertical physics                                     (default: NO selection)
@@ -241,4 +311,5 @@
    ln_zdftke   = .true.       !  Turbulent Kinetic Energy closure       (T =>   fill namzdf_tke)
    ln_zdfgls   = .false.      !  Generic Length Scale closure           (T =>   fill namzdf_gls)
+   ln_zdfosm   = .false.      !  OSMOSIS BL closure                     (T =>   fill namzdf_osm)
    !
    !                       ! convection
@@ -262,33 +333,85 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion 
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_iwm    !   tidal mixing parameterization                        (ln_zdfiwm =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets                                  (default F)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namobs       !  observation usage                                      ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/1_namelist_ice_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/1_namelist_ice_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/1_namelist_ice_cfg	(revision 9356)
@@ -1,49 +1,64 @@
-!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-!! NEMO/LIM3 configuration namelist: Overwrites 1_namelist_ice_ref
-!!              1 - Generic parameters                 (namicerun)
-!!              2 - Diagnostics                        (namicediag)
-!!              3 - Ice initialization                 (namiceini)
-!!              4 - Ice discretization                 (namiceitd)
-!!              5 - Ice dynamics and transport         (namicedyn)
-!!              6 - Ice diffusion                      (namicehdf)
-!!              7 - Ice thermodynamics                 (namicethd)
-!!              8 - Ice salinity                       (namicesal)
-!!              9 - Ice mechanical redistribution      (namiceitdme)
-!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 !------------------------------------------------------------------------------
-&namicerun     !   Generic parameters
+&nampar         !   Generic parameters
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namicediag    !   Diagnostics
+&namitd         !   Ice discretization
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namiceini     !   Ice initialization
+&namdyn         !   Ice dynamics
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namiceitd     !   Ice discretization
+&namdyn_rdgrft  !   Ice ridging/rafting
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namicedyn     !   Ice dynamics and transport
+&namdyn_rhg     !   Ice rheology
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namicehdf     !   Ice horizontal diffusion
+&namdyn_adv     !   Ice advection
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namicethd     !   Ice thermodynamics
+&namforcing     !   Ice surface forcing
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namicesal     !   Ice salinity
+&namthd         !   Ice thermodynamics
 !------------------------------------------------------------------------------
 /
 !------------------------------------------------------------------------------
-&namiceitdme   !   Ice mechanical redistribution (ridging and rafting)
+&namthd_zdf     !   Ice heat diffusion
 !------------------------------------------------------------------------------
 /
+!------------------------------------------------------------------------------
+&namthd_da      !   Ice lateral melting
+!------------------------------------------------------------------------------
+/
+!------------------------------------------------------------------------------
+&namthd_do      !   Ice growth in open water
+!------------------------------------------------------------------------------
+/
+!------------------------------------------------------------------------------
+&namthd_sal     !   Ice salinity
+!------------------------------------------------------------------------------
+/
+!------------------------------------------------------------------------------
+&namthd_pnd     !   Melt ponds
+!------------------------------------------------------------------------------
+/
+!------------------------------------------------------------------------------
+&namini         !   Ice initialization
+!------------------------------------------------------------------------------
+/
+!------------------------------------------------------------------------------
+&namalb         !   albedo parameters
+!------------------------------------------------------------------------------
+/
+!------------------------------------------------------------------------------
+&namdia         !   Diagnostics
+!------------------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg	(revision 9356)
@@ -11,5 +11,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
@@ -25,5 +25,5 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
@@ -32,9 +32,25 @@
 /
 !-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtsd        !   data : Temperature  & Salinity
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
 !-----------------------------------------------------------------------
 /
@@ -45,30 +61,54 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_blk    !   namsbc_blk  Bulk formulae
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
 !-----------------------------------------------------------------------
    ln_NCAR     = .true.   ! "NCAR"      algorithm   (Large and Yeager 2008)
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_cpl    !
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
       ln_icebergs              = .true.               ! iceberg floats or not
@@ -108,10 +148,34 @@
 /
 !-----------------------------------------------------------------------
-&namdrg        !   top/bottom friction
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_lin = .true.         !     linear  drag: Cd = Cd0 Uc0
 /
 !-----------------------------------------------------------------------
-&namagrif      !  AGRIF zoom                                            ("key_agrif")
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
 !-----------------------------------------------------------------------
 /
@@ -131,5 +195,5 @@
 /
 !-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10   = .false.         !  = Use TEOS-10 equation of state
@@ -138,5 +202,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer                          (default: NO advection)
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_fct = .true.     !  FCT scheme
@@ -145,11 +209,11 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param)
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
 !-----------------------------------------------------------------------
    ln_mle      = .true.   ! (T) use the Mixed Layer Eddy (MLE) parameterisation
 /
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    !                       !  Operator type:
    ln_traldf_NONE  =  .false.  !           No operator (no explicit advection)
@@ -181,7 +245,7 @@
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.true.   ! use eddy induced velocity parameterization
    ln_ldfeiv_dia =.true.   ! diagnose eiv stream function and velocities
@@ -200,5 +264,9 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection                (default: No selection)
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_NONE= .false. !  linear dynamics (no momentum advection)
@@ -209,5 +277,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -218,15 +286,15 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_sco  = .true.   !  s-coordinate (standard jacobian formulation)
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -253,7 +321,4 @@
    ! Caution in 20 and 30 cases the coefficient have to be given for a 1 degree grid (~111km)
 /
-!!======================================================================
-!!                     vertical physics namelists                     !!
-!!======================================================================
 !-----------------------------------------------------------------------
 &namzdf        !   vertical physics                                     (default: NO selection)
@@ -286,9 +351,21 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion 
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namzdf_iwm    !   tidal mixing parameterization                        (ln_zdfiwm =T)
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
 !-----------------------------------------------------------------------
    nn_zpyc     = 2         !  pycnocline-intensified dissipation scales as N (=1) or N^2 (=2)
@@ -297,5 +374,5 @@
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
 !-----------------------------------------------------------------------
 /
@@ -309,18 +386,58 @@
 /
 !-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets                                  (default F)
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
 !-----------------------------------------------------------------------
    ln_diahsb  = .true.    !  check the heat and salt budgets (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namobs       !  observation usage                                      ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_pisces_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_pisces_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_pisces_cfg	(revision 9356)
@@ -16,13 +16,13 @@
 /
 !-----------------------------------------------------------------------
-&namp4zlim     !   parameters for nutrient limitations for PISCES std - ln_p4z
+&namp4zlim     !   parameters for nutrient limitations for PISCES std  - ln_p4z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA - ln_p5z
+&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA    - ln_p5z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zquota    !   parameters for nutrient limitations PISCES quota - ln_p5z
+&namp5zquota   !   parameters for nutrient limitations PISCES quota    - ln_p5z
 !-----------------------------------------------------------------------
 /
@@ -32,21 +32,21 @@
 / 
 !-----------------------------------------------------------------------
-&namp4zprod     !   parameters for phytoplankton growth for PISCES std - ln_p4z
+&namp4zprod    !   parameters for phytoplankton growth for PISCES std  - ln_p4z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zprod     !   parameters for phytoplankton growth for PISCES quota - ln_p5z
+&namp5zprod    !   parameters for phytoplankton growth for PISCES quota- ln_p5z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp4zmort     !   parameters for phytoplankton sinks for PISCES std - ln_p4z
+&namp4zmort    !   parameters for phytoplankton sinks for PISCES std   - ln_p4z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zmort     !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
+&namp5zmort    !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp4zmes     !   parameters for mesozooplankton for PISCES std - ln_p4z
+&namp4zmes     !   parameters for mesozooplankton for PISCES std       - ln_p4z
 !-----------------------------------------------------------------------
 /
@@ -56,5 +56,5 @@
 /
 !-----------------------------------------------------------------------
-&namp4zzoo     !   parameters for microzooplankton for PISCES std - ln_p4z
+&namp4zzoo     !   parameters for microzooplankton for PISCES std      - ln_p4z
 !-----------------------------------------------------------------------
 /
@@ -84,17 +84,17 @@
 /
 !-----------------------------------------------------------------------
-&nampislig      !  Namelist parameters for ligands, nampislig
+&nampislig     !   Namelist parameters for ligands, nampislig
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nampisice      !  Prescribed sea ice tracers
+&nampisice     !   Prescribed sea ice tracers
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nampisdmp     !  Damping 
+&nampisdmp     !   Damping 
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nampismass     !  Mass conservation
+&nampismass    !   Mass conservation
 !-----------------------------------------------------------------------
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_top_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_top_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_top_cfg	(revision 9356)
@@ -9,5 +9,5 @@
 !-----------------------------------------------------------------------
 &namtrc          !   tracers definition
-!-----------------------------------------------------------------------a
+!-----------------------------------------------------------------------
    jp_bgc        =  24
 !
@@ -49,5 +49,5 @@
 /
 !-----------------------------------------------------------------------
-&namage         !   AGE 
+&namage          !   AGE 
 !-----------------------------------------------------------------------
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_cfg	(revision 9356)
@@ -11,5 +11,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg        !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
@@ -18,10 +18,5 @@
 /
 !-----------------------------------------------------------------------
-&namzgr        !   vertical coordinate
-!-----------------------------------------------------------------------
-   ln_zps      = .true.    !  z-coordinate - partial steps
-/
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .true.   !  =T  linear free surface  ==>>  model level are fixed in time
@@ -30,9 +25,26 @@
 /
 !-----------------------------------------------------------------------
-&namlbc        !   lateral momentum boundary condition
-!-----------------------------------------------------------------------
-   !                       !  free slip  !   partial slip  !   no slip   ! strong slip
-   rn_shlat    =    2.     !  shlat = 0  !  0 < shlat < 2  !  shlat = 2  !  2 < shlat
-   ln_vorlat   = .false.   !  consistency of vorticity boundary condition with analytical Eqs.
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -45,18 +57,101 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_blk   !   namsbc_blk  Bulk formulae
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
 !-----------------------------------------------------------------------
    ln_NCAR     = .true.   ! "NCAR"      algorithm   (Large and Yeager 2008)
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/      
-!-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namlbc        !   lateral momentum boundary condition
+!-----------------------------------------------------------------------
+   !                       !  free slip  !   partial slip  !   no slip   ! strong slip
+   rn_shlat    =    2.     !  shlat = 0  !  0 < shlat < 2  !  shlat = 2  !  2 < shlat
+   ln_vorlat   = .false.   !  consistency of vorticity boundary condition with analytical Eqs.
+/
+!-----------------------------------------------------------------------
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambbc        !   bottom temperature boundary condition                (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
 !-----------------------------------------------------------------------
    ln_trabbl   = .true.    !  Bottom Boundary Layer parameterisation flag
@@ -66,17 +161,24 @@
    rn_gambbl   =  10.      !  advective bbl coefficient                 [s]
 /
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
-!-----------------------------------------------------------------------
-   ln_teos10   = .false.        !  = Use TEOS-10 equation of state
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
+!-----------------------------------------------------------------------
+   ln_teos10   = .false.         !  = Use TEOS-10
    ln_eos80    = .true.         !  = Use EOS80
    ln_seos     = .false.        !  = Use S-EOS (simplified Eq.)
 /
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    !                       !  Operator type:
-   ln_traldf_NONE  =  .false.  !           No operator (no explicit advection)
+   ln_traldf_NONE  =  .false.  !  No explicit diffusion
    ln_traldf_lap   =  .true.   !    laplacian operator
    ln_traldf_blp   =  .false.  !  bilaplacian operator
@@ -85,15 +187,15 @@
    ln_traldf_hor   =  .false.  !  horizontal (geopotential)
    ln_traldf_iso   =  .true.   !  iso-neutral
-   ln_traldf_triad =  .false.  !  iso-neutral using Griffies triads
+   ln_traldf_triad =  .false.  !  iso-neutral (triad    operator)
    !
    !		       	         !  iso-neutral options:        
    ln_traldf_msc   =  .true.   !  Method of Stabilizing Correction (both operators)
    rn_slpmax       =   0.01    !  slope limit                      (both operators)
-   ln_triad_iso    =  .false.  !  pure horizontal mixing in ML     (triad only)
+   ln_triad_iso    =  .false.  !  pure horizontal mixing in ML              (triad only)
    rn_sw_triad     =  1        !  =1 switching triad ; =0 all 4 triads used (triad only)
-   ln_botmix_triad =  .false.  !  lateral mixing on bottom         (triad only)
+   ln_botmix_triad =  .false.  !  lateral mixing on bottom                  (triad only)
    !
    !                       !  Coefficients:
-   nn_aht_ijk_t    = 0        !  space/time variation of eddy coef
+   nn_aht_ijk_t    = 0         !  space/time variation of eddy coef
    !                                !   =-20 (=-30)    read in eddy_diffusivity_2D.nc (..._3D.nc) file
    !                                !   =  0           constant 
@@ -101,16 +203,15 @@
    !                                !   = 20 F(i,j)    =ldf_c2d 
    !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation
-   !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d
-   !                                !   = 31 F(i,j,k,t)=F(local velocity)
+   !                                !   = 30 F(i,j,k)  =ldf_c2d * ldf_c1d
+   !                                !   = 31 F(i,j,k,t)=F(local velocity and grid-spacing)
    rn_aht_0        = 2000.     !  lateral eddy diffusivity   (lap. operator) [m2/s]
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.true.   ! use eddy induced velocity parameterization
-   ln_ldfeiv_dia =.false.   ! diagnose eiv stream function and velocities
    rn_aeiv_0     = 2000.   ! eddy induced velocity coefficient   [m2/s]
-   nn_aei_ijk_t  = 0      ! space/time variation of the eiv coeficient
+   nn_aei_ijk_t  = 0       ! space/time variation of the eiv coeficient
    !                                !   =-20 (=-30)    read in eddy_induced_velocity_2D.nc (..._3D.nc) file
    !                                !   =  0           constant
@@ -119,10 +220,121 @@
    !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation
    !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d
-/
-!-----------------------------------------------------------------------
-&namdta_dyn        !   offline dynamics read in files                ("key_offline")
-!-----------------------------------------------------------------------
-!          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
-!          !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   ln_ldfeiv_dia =.false.  ! diagnose eiv stream function and velocities
+/
+!-----------------------------------------------------------------------
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf        !   vertical physics                                     (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
 !          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !          !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
@@ -147,10 +359,2 @@
 !   fwbcorr      = 3.786e-06    ! annual global mean of empmr for ssh correction
 /
-!-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_pisces_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_pisces_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_pisces_cfg	(revision 9356)
@@ -17,13 +17,13 @@
 /
 !-----------------------------------------------------------------------
-&namp4zlim     !   parameters for nutrient limitations for PISCES std - ln_p4z
+&namp4zlim     !   parameters for nutrient limitations for PISCES std  - ln_p4z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA - ln_p5z
+&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA    - ln_p5z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zquota    !   parameters for nutrient limitations PISCES quota - ln_p5z
+&namp5zquota   !   parameters for nutrient limitations PISCES quota    - ln_p5z
 !-----------------------------------------------------------------------
 /
@@ -33,21 +33,21 @@
 / 
 !-----------------------------------------------------------------------
-&namp4zprod     !   parameters for phytoplankton growth for PISCES std - ln_p4z
+&namp4zprod    !   parameters for phytoplankton growth for PISCES std  - ln_p4z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zprod     !   parameters for phytoplankton growth for PISCES quota - ln_p5z
+&namp5zprod    !   parameters for phytoplankton growth for PISCES quota- ln_p5z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp4zmort     !   parameters for phytoplankton sinks for PISCES std - ln_p4z
+&namp4zmort    !   parameters for phytoplankton sinks for PISCES std   - ln_p4z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp5zmort     !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
+&namp5zmort    !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namp4zmes     !   parameters for mesozooplankton for PISCES std - ln_p4z
+&namp4zmes     !   parameters for mesozooplankton for PISCES std       - ln_p4z
 !-----------------------------------------------------------------------
 /
@@ -57,5 +57,5 @@
 /
 !-----------------------------------------------------------------------
-&namp4zzoo     !   parameters for microzooplankton for PISCES std - ln_p4z
+&namp4zzoo     !   parameters for microzooplankton for PISCES std      - ln_p4z
 !-----------------------------------------------------------------------
 /
@@ -85,18 +85,18 @@
 /
 !-----------------------------------------------------------------------
-&nampislig      !  Namelist parameters for ligands, nampislig
+&nampislig     !   Namelist parameters for ligands, nampislig
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nampisice      !  Prescribed sea ice tracers
+&nampisice     !   Prescribed sea ice tracers
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nampisdmp     !  Damping 
+&nampisdmp     !   Damping 
 !-----------------------------------------------------------------------
    nn_pisdmp    =  1460       !  Frequency of Relaxation
 /
 !-----------------------------------------------------------------------
-&nampismass     !  Mass conservation
+&nampismass    !   Mass conservation
 !-----------------------------------------------------------------------
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_top_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_top_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_OFF_PISCES/EXP00/namelist_top_cfg	(revision 9356)
@@ -9,5 +9,5 @@
 !-----------------------------------------------------------------------
 &namtrc          !   tracers definition
-!-----------------------------------------------------------------------a
+!-----------------------------------------------------------------------
    jp_bgc        =  24
 !
@@ -20,7 +20,6 @@
 !
    ln_trcdta     =  .true.  !  Initialisation from data input file (T) or not (F)
-!                 !           !                                          !             !
-!                 !    name   !           title of the field             !   units     ! initial data from file or not !
-!                 !           !                                          !             !
+!                !           !                                         !            !                               !
+!                !    name   !           title of the field            !   units    ! initial data from file or not ! 
    sn_tracer(1)   = 'DIC     ' , 'Dissolved inorganic Concentration      ',  'mol-C/L' ,  .true.
    sn_tracer(2)   = 'Alkalini' , 'Total Alkalinity Concentration         ',  'eq/L '   ,  .true.
@@ -49,5 +48,5 @@
 /
 !-----------------------------------------------------------------------
-&namage         !   AGE 
+&namage          !   AGE 
 !-----------------------------------------------------------------------
 /
@@ -77,5 +76,5 @@
 &namtrc_adv      !   advection scheme for passive tracer                (default: NO selection)
 !-----------------------------------------------------------------------
-   ln_trcadv_mus =  .true.  !  MUSCL scheme
+   ln_trcadv_mus =  .true.   !  MUSCL scheme
       ln_mus_ups =  .false.         !  use upstream scheme near river mouths
 /
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_SAS_LIM3/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_SAS_LIM3/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/ORCA2_SAS_LIM3/EXP00/namelist_cfg	(revision 9356)
@@ -12,5 +12,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .true.    !  (=T) read the domain configuration file
@@ -19,14 +19,30 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .true.   !  =T  linear free surface  ==>>  model level are fixed in time
 /
 !-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
 !-----------------------------------------------------------------------
 /
@@ -37,26 +53,54 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_blk   !   namsbc_blk  Bulk formulae
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
 !-----------------------------------------------------------------------
    ln_NCAR     = .true.   ! "NCAR"      algorithm   (Large and Yeager 2008)
 /
 !-----------------------------------------------------------------------
-&namsbc_sas    !   Stand-Alone Surface module
-!-----------------------------------------------------------------------
-/      
-!-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
 /
@@ -66,5 +110,45 @@
 /
 !-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambbc        !   bottom temperature boundary condition                (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10    = .true.         !  = Use TEOS-10 equation of state
@@ -75,20 +159,132 @@
    ln_traadv_NONE =  .true.    !  No advection
 /
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    ln_traldf_lap  =  .NONE.   ! No explicit diffusion
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_NONE =  .true.    !  No advection
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf        !   vertical physics                                     (default: NO selection)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/README.namelists
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/README.namelists	(revision 9356)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/README.namelists	(revision 9356)
@@ -0,0 +1,110 @@
+Simple style rules for namelists
+--------------------------------
+
+NEMO reference namelists should adhere to the following simple style rules:
+
+1.	Comments outside a namelist block start with !! in column 1
+2.	Each namelist block starts with 3 lines of the form:
+
+!-----------------------------------------------------------------------
+&namblockname        !   short description of block
+!-----------------------------------------------------------------------
+
+        with all ! and & 's starting in column 1
+3.	The closing / for each namelist block is in column 1
+4.	Comments within namelist blocks never start with !- . Use ! followed
+        by space or != etc. 
+
+These conventions make it possible to construct empty configuration namelists.
+For example, a namelist_cfg template can be produced from namelist_ref with
+the following grep command; e.g.:
+
+grep -E  '^!-|^&|^/' namelist_ref > namelist_cfg.template
+
+head namelist_cfg.template
+  
+!-----------------------------------------------------------------------
+&namrun        !   parameters of the run
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcfg        !   parameters of the configuration                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdom        !   time and space domain
+!-----------------------------------------------------------------------
+/
+.
+.
+
+If all configuration namelists are produced and maintained using this
+strategy then standard, side-by-side comaparators, such as vimdiff or xxdiff,
+can be used to compare and transfer lines from the reference namelist to a
+configuration namelist when setting up a new configuration.
+
+Tips and tricks
+---------------
+
+1. The following bash function is useful when checking which namelist blocks
+are in active use in a configuration namelist:
+
+  function  list_used_nl(){ grep -n -E '^&|^/' "$1" | sed -e 's/:/ /' \
+    | awk ' BEGIN { x = 0 } \
+      {if ( NR % 2 == 0 && $1 - x > 2 ) printf("%3d  %s\n", $1 - x , n) ; \
+       else x = $1; n = $2}' \
+    | sort -k 2;}
+
+which (assuming the namelist adheres to the conventions) will list the number
+of entries in each non-empty namelist block. The list is sorted on the block
+name to ease comparisons. For example:
+
+  list_used_nl ORCA2_LIM3_PISCES/EXP00/namelist_cfg
+
+  1 &nambbc
+  5 &nambbl
+  30 &namberg
+  10 &namcfg
+  4 &namctl
+  3 &namdom
+  1 &namdrg
+  5 &namdyn_adv
+  1 &namdyn_hpg
+  22 &namdyn_ldf
+  1 &namdyn_spg
+  5 &namdyn_vor
+  3 &nameos
+  1 &namhsb
+  4 &namrun
+  1 &namsbc
+  1 &namsbc_blk
+  3 &namtra_adv
+  1 &namtra_adv_mle
+  28 &namtra_ldf
+  10 &namtra_ldfeiv
+  25 &namzdf
+  3 &namzdf_iwm
+
+2. vimdiff can give garish colours in some terminals. Usually this is because
+vim assumes, incorrectly, that the terminal only supports 8 colours. Try forcing
+256 colours with:
+
+  :set t_Co=256
+
+to produce more pastel shades (add this to ~/.vimrc if successful).
+
+3. Switching between vsplit panes in vim is a multi-key sequence. The tool is 
+much easier to use if the sequence is mapped to a spare key. Here I use the
+§ and ± key on my Mac keyboard (add to ~/.vimrc):
+
+  map § ^Wl
+  map ± ^Wh 
+
+4. With easy switching between panes, constructing namelists in vimdiff just
+requires the following commands in addition to normal editing:
+
+  ]c    - Go to next block of the diff
+  dp    - Push version of the block under cursor into the other pane
+  do    - Pull version of the block under cursor from the other pane
+
+
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_ice_lim3_ref
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_ice_lim3_ref	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_ice_lim3_ref	(revision 9356)
@@ -138,5 +138,5 @@
 /
 !------------------------------------------------------------------------------
-&namthd_da     !   Ice lateral melting
+&namthd_da      !   Ice lateral melting
 !------------------------------------------------------------------------------
    rn_beta          =   1.0           !  coef. beta for lateral melting param. Recommended range=[0.8-1.2]
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_pisces_ref
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_pisces_ref	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_pisces_ref	(revision 9356)
@@ -62,5 +62,5 @@
 /
 !-----------------------------------------------------------------------
-&namp4zlim     !   parameters for nutrient limitations for PISCES std - ln_p4z
+&namp4zlim     !   parameters for nutrient limitations for PISCES std  - ln_p4z
 !-----------------------------------------------------------------------
    concnno3   =  1.e-6    ! Nitrate half saturation of nanophytoplankton
@@ -86,5 +86,5 @@
 /
 !-----------------------------------------------------------------------
-&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA - ln_p5z
+&namp5zlim     !   parameters for nutrient limitations PISCES QUOTA    - ln_p5z
 !-----------------------------------------------------------------------
    concnno3   =  3e-6     ! Nitrate half saturation of nanophytoplankton
@@ -117,5 +117,5 @@
 /
 !-----------------------------------------------------------------------
-&namp5zquota    !   parameters for nutrient limitations PISCES quota - ln_p5z
+&namp5zquota   !   parameters for nutrient limitations PISCES quota    - ln_p5z
 !-----------------------------------------------------------------------
    qfnopt     =  7.E-6    ! Optimal Fe quota of nanophyto
@@ -149,5 +149,5 @@
 / 
 !-----------------------------------------------------------------------
-&namp4zprod     !   parameters for phytoplankton growth for PISCES std - ln_p4z
+&namp4zprod    !   parameters for phytoplankton growth for PISCES std  - ln_p4z
 !-----------------------------------------------------------------------
    pislopen   =  2.       ! P-I slope
@@ -166,5 +166,5 @@
 /
 !-----------------------------------------------------------------------
-&namp5zprod     !   parameters for phytoplankton growth for PISCES quota - ln_p5z
+&namp5zprod    !   parameters for phytoplankton growth for PISCES quota- ln_p5z
 !-----------------------------------------------------------------------
    pislopen   =  3.       ! P-I slope
@@ -183,5 +183,5 @@
 /
 !-----------------------------------------------------------------------
-&namp4zmort     !   parameters for phytoplankton sinks for PISCES std - ln_p4z
+&namp4zmort    !   parameters for phytoplankton sinks for PISCES std   - ln_p4z
 !-----------------------------------------------------------------------
    wchl       =  0.01     ! quadratic mortality of phytoplankton
@@ -192,5 +192,5 @@
 /
 !-----------------------------------------------------------------------
-&namp5zmort     !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
+&namp5zmort    !   parameters for phytoplankton sinks for PISCES quota - ln_p5z
 !-----------------------------------------------------------------------
    wchln      =  0.01     ! quadratic mortality of nanophytoplankton
@@ -203,5 +203,5 @@
 /
 !-----------------------------------------------------------------------
-&namp4zmes     !   parameters for mesozooplankton for PISCES std - ln_p4z
+&namp4zmes     !   parameters for mesozooplankton for PISCES std       - ln_p4z
 !-----------------------------------------------------------------------
    part2      =  0.75     ! part of calcite not dissolved in mesozoo guts
@@ -253,5 +253,5 @@
 /
 !-----------------------------------------------------------------------
-&namp4zzoo     !   parameters for microzooplankton for PISCES std - ln_p4z
+&namp4zzoo     !   parameters for microzooplankton for PISCES std      - ln_p4z
 !-----------------------------------------------------------------------
    part       =  0.5      ! part of calcite not dissolved in microzoo guts
@@ -384,5 +384,5 @@
 /
 !-----------------------------------------------------------------------
-&nampislig      !  Namelist parameters for ligands, nampislig
+&nampislig     !   Namelist parameters for ligands, nampislig
 !-----------------------------------------------------------------------
    rfep        =  0.001    ! Dissolution rate of FeP
@@ -393,17 +393,20 @@
 /
 !-----------------------------------------------------------------------
-&nampisice      !  Prescribed sea ice tracers
-!-----------------------------------------------------------------------
-!! constant ocean tracer concentrations are defined in trcice_pisces.F90 (Global, Arctic, Antarctic and Baltic)
-!! trc_ice_ratio     * betw 0 and 1: prescribed ice/ocean tracer concentration ratio
-!!                  * -1 => the ice-ocean tracer concentration ratio follows the 
-!!                           ice-ocean salinity ratio
-!!                   * -2 => tracer concentration in sea ice is prescribed and 
-!!                           trc_ice_prescr is used
-!! trc_ice_prescr    * prescribed tracer concentration. used only if 
-!!                     trc_ice_ratio = -2. equals -99 if not used.
-!! cn_trc_o          * 'GL' use global ocean values making the Baltic distinction only
-!!                     'AA' use specific Arctic/Antarctic/Baltic values
-!!-----------------------------------------------------------------------
+&nampisice     !   Prescribed sea ice tracers
+!-----------------------------------------------------------------------
+!========================================================================
+! constant ocean tracer concentrations are defined in trcice_pisces.F90 
+!                               (Global, Arctic, Antarctic and Baltic)
+! trc_ice_ratio  : >=0 & <=1 => prescribed ice/ocean tracer concentration ratio
+!                :  = -1     => the ice-ocean tracer concentration ratio
+!                               follows the ice-ocean salinity ratio
+!                :  = -2     => tracer concentration in sea ice is prescribed
+!                               and trc_ice_prescr is used
+! trc_ice_prescr : prescribed tracer concentration. used only if 
+!                  trc_ice_ratio = -2. equals -99 if not used.
+! cn_trc_o       :  = 'GL'   => use global ocean values making the Baltic 
+!                               distinction only
+!                :  = 'AA'   => use specific Arctic/Antarctic/Baltic values
+!========================================================================
 !    sn_tri_ ! trc_ice_ratio ! trc_ice_prescr !     cn_trc_o
    sn_tri_dic =           -1.,           -99.,          'AA'
@@ -434,11 +437,11 @@
 /
 !-----------------------------------------------------------------------
-&nampisdmp     !  Damping 
-!-----------------------------------------------------------------------
-   ln_pisdmp    =  .true.     !  Relaxation fo some tracers to a mean value
+&nampisdmp     !   Damping 
+!-----------------------------------------------------------------------
+   ln_pisdmp    =  .true.     !  Relaxation for some tracers to a mean value
    nn_pisdmp    =  5475       !  Frequency of Relaxation 
 /
 !-----------------------------------------------------------------------
-&nampismass     !  Mass conservation
+&nampismass    !   Mass conservation
 !-----------------------------------------------------------------------
    ln_check_mass =  .false.    !  Check mass conservation
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_ref
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_ref	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_ref	(revision 9356)
@@ -70,5 +70,5 @@
 !
 !-----------------------------------------------------------------------
-&namcfg        !   parameters of the configuration                     !   (default: user defined GYRE)
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.   !  (=T) read the domain configuration file
@@ -114,5 +114,5 @@
 /
 !-----------------------------------------------------------------------
-&namwad  !   Wetting and drying  default it no WAD
+&namwad        !   Wetting and drying  default is no WAD
 !-----------------------------------------------------------------------
    ln_wd_il          = .false   ! T/F activation of iterative limiter for  wetting and drying scheme
@@ -631,5 +631,5 @@
 !
 !-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_NONE    = .false.    !  free-slip       : Cd = 0                  (F => fill namdrg_bot
@@ -641,5 +641,5 @@
 /
 !-----------------------------------------------------------------------
-&namdrg_top        !   TOP friction                                     (ln_isfcav=T)
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
 !-----------------------------------------------------------------------
    rn_Cd0     =  1.e-3     !  drag coefficient [-]
@@ -652,5 +652,5 @@
 /
 !-----------------------------------------------------------------------
-&namdrg_bot        !   BOTTOM friction                                  
+&namdrg_bot    !   BOTTOM friction                                  
 !-----------------------------------------------------------------------
    rn_Cd0     =  1.e-3    !  drag coefficient [-]
@@ -812,5 +812,5 @@
 !
 !-----------------------------------------------------------------------
-&nam_vvl       !   vertical coordinate options                             (default: z-star)
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
 !-----------------------------------------------------------------------
    ln_vvl_zstar  = .true.           !  z-star vertical coordinate
@@ -1003,5 +1003,5 @@
 /
 !-----------------------------------------------------------------------
-&namzdf_osm                !   OSM vertical diffusion                   (ln_zdfosm =T)
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
 !-----------------------------------------------------------------------
    ln_use_osm_la = .false.      !  Use namelist  rn_osm_la
@@ -1115,5 +1115,5 @@
 !!gm
 !-----------------------------------------------------------------------
-&namptr        !   Poleward Transport Diagnostic                         (default F)
+&namptr        !   Poleward Transport Diagnostic                        (default F)
 !-----------------------------------------------------------------------
    ln_diaptr   = .false.   !  Poleward heat and salt transport (T) or not (F)
@@ -1121,10 +1121,10 @@
 /
 !-----------------------------------------------------------------------
-&namhsb        !  Heat and salt budgets                                  (default F)
+&namhsb        !  Heat and salt budgets                                 (default F)
 !-----------------------------------------------------------------------
    ln_diahsb   = .false.   !  check the heat and salt budgets (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdiu        !   Cool skin and warm layer models                       (default F)
+&namdiu        !   Cool skin and warm layer models                      (default F)
 !-----------------------------------------------------------------------
    ln_diurnal      = .false.   !
@@ -1132,5 +1132,5 @@
 /
 !-----------------------------------------------------------------------
-&namflo        !   float parameters                                      ("key_float")
+&namflo        !   float parameters                                     ("key_float")
 !-----------------------------------------------------------------------
    jpnfl       = 1         !  total number of floats during the run
@@ -1146,5 +1146,5 @@
 /
 !-----------------------------------------------------------------------
-&nam_diaharm   !   Harmonic analysis of tidal constituents               ("key_diaharm")
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
 !-----------------------------------------------------------------------
     nit000_han = 1         ! First time step used for harmonic analysis
@@ -1155,5 +1155,5 @@
 /
 !-----------------------------------------------------------------------
-&namdct        ! transports through some sections                        ("key_diadct")
+&namdct        ! transports through some sections                       ("key_diadct")
 !-----------------------------------------------------------------------
     nn_dct     = 15        !  time step frequency for transports computing
@@ -1164,15 +1164,15 @@
 /
 !-----------------------------------------------------------------------
-&nam_diatmb    !  Top Middle Bottom Output                               (default F)
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
 !-----------------------------------------------------------------------
    ln_diatmb   = .false.   !  Choose Top Middle and Bottom output or not
 /
 !-----------------------------------------------------------------------
-&nam_dia25h    !  25h Mean Output                                        (default F)
+&nam_dia25h    !  25h Mean Output                                       (default F)
 !-----------------------------------------------------------------------
    ln_dia25h   = .false.   ! Choose 25h mean output or not
 /
 !-----------------------------------------------------------------------
-&namnc4        !   netcdf4 chunking and compression settings             ("key_netcdf4")
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
 !-----------------------------------------------------------------------
    nn_nchunks_i=   4       !  number of chunks in i-dimension
@@ -1266,5 +1266,5 @@
 /
 !-----------------------------------------------------------------------
-&namdta_dyn        !   offline dynamics read in files                   ("key_offline")
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
 !-----------------------------------------------------------------------
 !          !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_top_ref
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_top_ref	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/SHARED/namelist_top_ref	(revision 9356)
@@ -47,5 +47,5 @@
 /
 !-----------------------------------------------------------------------
-&namage         !   AGE 
+&namage          !   AGE 
 !-----------------------------------------------------------------------
    rn_age_depth      = 10            ! depth over which age tracer reset to zero
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/CANAL/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/CANAL/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/CANAL/EXP00/namelist_cfg	(revision 9356)
@@ -38,9 +38,9 @@
 /
 !-----------------------------------------------------------------------
-&namcfg        !   parameters of the configuration
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   =  .true.  !  =T  linear free surface  ==>>  model level are fixed in time
@@ -49,17 +49,28 @@
 /
 !-----------------------------------------------------------------------
-&namagrif      !  AGRIF zoom                                            ("key_agrif")
-!-----------------------------------------------------------------------
-   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
-   rn_sponge_tra =  800.   !  coefficient for tracer   sponge layer [m2/s]
-   rn_sponge_dyn =  800.   !  coefficient for dynamics sponge layer [m2/s]
-   ln_chk_bathy  = .FALSE. !
-/
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namtsd        !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -77,19 +88,108 @@
 /
 !-----------------------------------------------------------------------
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namlbc        !   lateral momentum boundary condition
 !-----------------------------------------------------------------------
-!                         !  free slip  !   partial slip  !   no slip   ! strong slip
+   !                       !  free slip  !   partial slip  !   no slip   ! strong slip
   rn_shlat     =    0.    !  shlat = 0  !  0 < shlat < 2  !  shlat = 2  !  2 < shlat
 /
 !-----------------------------------------------------------------------
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
+   rn_sponge_tra =  800.   !  coefficient for tracer   sponge layer [m2/s]
+   rn_sponge_dyn =  800.   !  coefficient for dynamics sponge layer [m2/s]
+   ln_chk_bathy  = .FALSE. !
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
+!-----------------------------------------------------------------------
+   ln_NONE    = .true.    !  free-slip       : Cd = 0
+/
+!-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme                         ("key_trabbl")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_seos     = .true.         !  = Use simplified equation of state (S-EOS)
@@ -104,5 +204,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_cen = .false. !  2nd order centered scheme
@@ -123,5 +223,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
 !-----------------------------------------------------------------------
   !                       !  Operator type:
@@ -160,10 +260,15 @@
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping                       (default: YES)
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.   !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+   ln_vvl_zstar  = .false.           !  zstar vertical coordinate
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .false. !  vector form (T) or flux form (F)
@@ -173,10 +278,5 @@
 /
 !-----------------------------------------------------------------------
-&nam_vvl    !   vertical coordinate options                             (default: zstar)
-!-----------------------------------------------------------------------
-   ln_vvl_zstar  = .false.           !  zstar vertical coordinate
-/
-!-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -187,5 +287,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zps  = .true.  !  z-coordinate - partial steps (interpolation)
@@ -193,5 +293,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   Surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_exp  = .false. 
@@ -206,5 +306,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -236,9 +336,4 @@
 /
 !-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
-!-----------------------------------------------------------------------
-   ln_NONE    = .true.    !  free-slip       : Cd = 0
-/
-!-----------------------------------------------------------------------
 &namzdf        !   vertical physics                                     (default: NO selection)
 !-----------------------------------------------------------------------
@@ -257,9 +352,85 @@
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/ISOMIP/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/ISOMIP/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/ISOMIP/EXP00/namelist_cfg	(revision 9356)
@@ -26,5 +26,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration   
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.   !  (=T) read the domain configuration file
@@ -36,5 +36,5 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .false.    !  =T  linear free surface  ==>>  model level are fixed in time
@@ -45,14 +45,29 @@
 /
 !-----------------------------------------------------------------------
-&namcrs        !   Grid coarsening for dynamics output and/or
-!              !   passive tracer coarsened online simulations
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namtsd        !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
    cn_dir        = './'      !  root directory for the location of the runoff files
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -82,13 +97,5 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_clio   !   namsbc_clio  CLIO bulk formulae
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_core   !   namsbc_core  CORE bulk formulae
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_mfs   !   namsbc_mfs  MFS bulk formulae
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
 !-----------------------------------------------------------------------
 /
@@ -98,13 +105,21 @@
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_isf    !  Top boundary layer (ISF)
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
 !-----------------------------------------------------------------------
 !              ! file name ! frequency (hours) ! variable ! time interpol. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
@@ -138,17 +153,21 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
 /
@@ -165,21 +184,21 @@
 /
 !-----------------------------------------------------------------------
-&nam_tide      !    tide parameters (#ifdef key_tide)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nambdy        !  unstructured open boundaries                          ("key_bdy")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nambdy_dta      !  open boundaries - external data           ("key_bdy")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nambdy_tide     ! tidal forcing at open boundaries
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_NONE    = .false.    !  free-slip       : Cd = 0                  (F => fill namdrg_bot
@@ -191,5 +210,5 @@
 /
 !-----------------------------------------------------------------------
-&namdrg_top        !   TOP friction                                     (ln_isfcav=T)
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
 !-----------------------------------------------------------------------
    rn_Cd0     =  2.5e-3    !  drag coefficient [-]
@@ -202,5 +221,5 @@
 /
 !-----------------------------------------------------------------------
-&namdrg_bot        !   BOTTOM friction                                  
+&namdrg_bot    !   BOTTOM friction                                  
 !-----------------------------------------------------------------------
    rn_Cd0     =  1.e-3    !  drag coefficient [-]
@@ -213,10 +232,10 @@
 /
 !-----------------------------------------------------------------------
-&nambbc        !   bottom temperature boundary condition
+&nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
    ln_trabbc   = .false.   !  Apply a geothermal heating at the ocean bottom
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
 !-----------------------------------------------------------------------
    nn_bbl_ldf  =  0      !  diffusive bbl (=1)   or not (=0)
@@ -224,5 +243,5 @@
 /
 !-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10   = .false.         !  = Use TEOS-10 equation of state
@@ -230,5 +249,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_fct =  .true.   !  FCT scheme
@@ -237,10 +256,10 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)
-!-----------------------------------------------------------------------
-/
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    !                       !  Operator type:
    ln_traldf_lap   =  .true.   !    laplacian operator
@@ -271,16 +290,20 @@
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.false.   ! use eddy induced velocity parameterization
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.  !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .true.  !  vector form (T) or flux form (F)
@@ -290,7 +313,5 @@
 /
 !-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .true.  !  enstrophy conserving scheme
@@ -301,5 +322,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zps  = .false.   !  z-coordinate - partial steps (interpolation)
@@ -307,10 +328,10 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient 
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -368,9 +389,69 @@
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
 !-----------------------------------------------------------------------
 /
@@ -380,22 +461,13 @@
 /
 !-----------------------------------------------------------------------
-&namtrd        !   diagnostics on dynamics and/or tracer trends         ("key_trddyn" and/or "key_trdtra")
-!              !       or mixed-layer trends or barotropic vorticity    ("key_trdmld" or     "key_trdvor")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namobs       !  observation usage switch                               (ln_diaobs =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_wave   ! External fields from wave model
-!-----------------------------------------------------------------------
-/
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/SAS_BIPER/EXP00/1_namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/SAS_BIPER/EXP00/1_namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/SAS_BIPER/EXP00/1_namelist_cfg	(revision 9356)
@@ -18,5 +18,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.    !  (=T) read the domain configuration file
@@ -25,5 +25,5 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .true.   !  =T  linear free surface  ==>>  model level are fixed in time
@@ -34,9 +34,25 @@
 /
 !-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
 !-----------------------------------------------------------------------
 /
@@ -50,30 +66,54 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk = T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_sas    !   Stand Alone Surface boundary condition
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
 !-----------------------------------------------------------------------
    l_sasread   = .false.   ! Read fields in a file if .TRUE. , or initialize to 0. in sbcssm.F90 if .FALSE.
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
    ln_bergdia               = .false.               ! Calculate budgets
@@ -90,18 +130,42 @@
 /
 !-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_NONE    = .true.     !  free-slip       : Cd = 0                  
 /
 !-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10    = .true.         !  = Use TEOS-10 equation of state
@@ -115,5 +179,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
 !-----------------------------------------------------------------------
 /
@@ -165,4 +229,8 @@
 !-----------------------------------------------------------------------
 &namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
 !-----------------------------------------------------------------------
 /
@@ -228,9 +296,21 @@
 /
 !-----------------------------------------------------------------------
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namzdf_iwm    !   tidal mixing parameterization                        (ln_zdfiwm =T)
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
 !-----------------------------------------------------------------------
 /
@@ -240,21 +320,61 @@
 /
 !-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets                                  (default F)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namobs       !  observation usage                                      ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/SAS_BIPER/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/SAS_BIPER/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/SAS_BIPER/EXP00/namelist_cfg	(revision 9356)
@@ -18,5 +18,5 @@
 /
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.    !  (=T) read the domain configuration file
@@ -25,5 +25,5 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .true.    !  =T  linear free surface  ==>>  model level are fixed in time
@@ -34,9 +34,25 @@
 /
 !-----------------------------------------------------------------------
+&namtsd        !   data : Temperature  & Salinity
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
 !-----------------------------------------------------------------------
 /
@@ -50,30 +66,54 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk = T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_sas    !   Stand Alone Surface boundary condition
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
 !-----------------------------------------------------------------------
    l_sasread   = .false.   ! Read fields in a file if .TRUE. , or initialize to 0. in sbcssm.F90 if .FALSE.
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
    ln_bergdia               = .false.               ! Calculate budgets
@@ -91,18 +131,42 @@
 /
 !-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_NONE    = .true.     !  free-slip       : Cd = 0                  
 /
 !-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10    = .true.         !  = Use TEOS-10 equation of state
@@ -116,5 +180,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
 !-----------------------------------------------------------------------
 /
@@ -166,4 +230,8 @@
 !-----------------------------------------------------------------------
 &namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
 !-----------------------------------------------------------------------
 /
@@ -229,9 +297,21 @@
 /
 !-----------------------------------------------------------------------
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namzdf_iwm    !   tidal mixing parameterization                        (ln_zdfiwm =T)
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
 !-----------------------------------------------------------------------
 /
@@ -241,21 +321,61 @@
 /
 !-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namptr       !   Poleward Transport Diagnostic
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets                                  (default F)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namobs       !  observation usage                                      ('key_diaobs')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/VORTEX/EXP00/1_namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/VORTEX/EXP00/1_namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/VORTEX/EXP00/1_namelist_cfg	(revision 9356)
@@ -24,9 +24,9 @@
 /
 !-----------------------------------------------------------------------
-&namcfg        !   parameters of the configuration
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   =  .false.  !  =T  linear free surface  ==>>  model level are fixed in time
@@ -35,17 +35,28 @@
 /
 !-----------------------------------------------------------------------
-&namagrif      !  AGRIF zoom                                            ("key_agrif")
-!-----------------------------------------------------------------------
-   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
-   rn_sponge_tra =  800.   !  coefficient for tracer   sponge layer [m2/s]
-   rn_sponge_dyn =  800.   !  coefficient for dynamics sponge layer [m2/s]
-   ln_chk_bathy  = .FALSE. !
-/
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namtsd        !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -63,4 +74,56 @@
 /
 !-----------------------------------------------------------------------
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namlbc        !   lateral momentum boundary condition
 !-----------------------------------------------------------------------
@@ -69,13 +132,50 @@
 /
 !-----------------------------------------------------------------------
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
+   rn_sponge_tra =  800.   !  coefficient for tracer   sponge layer [m2/s]
+   rn_sponge_dyn =  800.   !  coefficient for dynamics sponge layer [m2/s]
+   ln_chk_bathy  = .FALSE. !
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
+!-----------------------------------------------------------------------
+   ln_NONE    = .true.    !  free-slip       : Cd = 0
+/
+!-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme                         ("key_trabbl")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_seos     = .true.         !  = Use simplified equation of state (S-EOS)
@@ -90,5 +190,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_cen = .false. !  2nd order centered scheme
@@ -109,5 +209,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
 !-----------------------------------------------------------------------
   !                       !  Operator type:
@@ -121,10 +221,15 @@
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping                       (default: YES)
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.   !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+   ln_vvl_zstar  = .true.           !  zstar vertical coordinate
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .false. !  vector form (T) or flux form (F)
@@ -134,10 +239,5 @@
 /
 !-----------------------------------------------------------------------
-&nam_vvl    !   vertical coordinate options                             (default: zstar)
-!-----------------------------------------------------------------------
-   ln_vvl_zstar  = .true.           !  zstar vertical coordinate
-/
-!-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -148,5 +248,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zps  = .false.  !  z-coordinate - partial steps (interpolation)
@@ -154,5 +254,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   Surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_exp  = .false. 
@@ -167,5 +267,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -197,9 +297,4 @@
 /
 !-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
-!-----------------------------------------------------------------------
-   ln_NONE    = .true.    !  free-slip       : Cd = 0
-/
-!-----------------------------------------------------------------------
 &namzdf        !   vertical physics                                     (default: NO selection)
 !-----------------------------------------------------------------------
@@ -218,9 +313,85 @@
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/VORTEX/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/VORTEX/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/VORTEX/EXP00/namelist_cfg	(revision 9356)
@@ -24,9 +24,9 @@
 /
 !-----------------------------------------------------------------------
-&namcfg        !   parameters of the configuration
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   =  .false.  !  =T  linear free surface  ==>>  model level are fixed in time
@@ -35,17 +35,28 @@
 /
 !-----------------------------------------------------------------------
-&namagrif      !  AGRIF zoom                                            ("key_agrif")
-!-----------------------------------------------------------------------
-   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
-   rn_sponge_tra =  800.   !  coefficient for tracer   sponge layer [m2/s]
-   rn_sponge_dyn =  800.   !  coefficient for dynamics sponge layer [m2/s]
-   ln_chk_bathy  = .FALSE. !
-/
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namtsd        !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -63,4 +74,56 @@
 /
 !-----------------------------------------------------------------------
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namlbc        !   lateral momentum boundary condition
 !-----------------------------------------------------------------------
@@ -69,13 +132,50 @@
 /
 !-----------------------------------------------------------------------
+&namagrif      !  AGRIF zoom                                            ("key_agrif")
+!-----------------------------------------------------------------------
+   ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
+   rn_sponge_tra =  800.   !  coefficient for tracer   sponge layer [m2/s]
+   rn_sponge_dyn =  800.   !  coefficient for dynamics sponge layer [m2/s]
+   ln_chk_bathy  = .FALSE. !
+/
+!-----------------------------------------------------------------------
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_dta    !  open boundaries - external data                       
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
+!-----------------------------------------------------------------------
+   ln_NONE    = .true.    !  free-slip       : Cd = 0
+/
+!-----------------------------------------------------------------------
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme                         ("key_trabbl")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_seos     = .true.         !  = Use simplified equation of state (S-EOS)
@@ -90,5 +190,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_cen = .false. !  2nd order centered scheme
@@ -109,5 +209,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
 !-----------------------------------------------------------------------
   !                       !  Operator type:
@@ -121,10 +221,15 @@
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping                       (default: YES)
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.   !  add a damping termn (T) or not (F)
 /
 !-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+   ln_vvl_zstar  = .true.           !  zstar vertical coordinate
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: NO selection)
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .false. !  vector form (T) or flux form (F)
@@ -134,10 +239,5 @@
 /
 !-----------------------------------------------------------------------
-&nam_vvl    !   vertical coordinate options                             (default: zstar)
-!-----------------------------------------------------------------------
-   ln_vvl_zstar  = .true.           !  zstar vertical coordinate
-/
-!-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -148,5 +248,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zps  = .false.  !  z-coordinate - partial steps (interpolation)
@@ -154,5 +254,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   Surface pressure gradient
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_exp  = .false. 
@@ -167,5 +267,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -197,9 +297,4 @@
 /
 !-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
-!-----------------------------------------------------------------------
-   ln_NONE    = .true.    !  free-slip       : Cd = 0
-/
-!-----------------------------------------------------------------------
 &namzdf        !   vertical physics                                     (default: NO selection)
 !-----------------------------------------------------------------------
@@ -218,9 +313,85 @@
 /
 !-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
Index: /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/WAD/EXP00/namelist_cfg
===================================================================
--- /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/WAD/EXP00/namelist_cfg	(revision 9355)
+++ /branches/2017/dev_merge_2017/NEMOGCM/CONFIG/TEST_CASES/WAD/EXP00/namelist_cfg	(revision 9356)
@@ -22,8 +22,7 @@
    ln_clobber  = .true.    !  clobber (overwrite) an existing file
    nn_istate   =       0   !  output the initial state (1) or not (0)
-
-/
-!-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration
+/
+!-----------------------------------------------------------------------
+&namcfg        !   parameters of the configuration                      (default: user defined GYRE)
 !-----------------------------------------------------------------------
    ln_read_cfg = .false.   !  (=T) read the domain configuration file
@@ -32,5 +31,5 @@
 /
 !-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
+&namdom        !   time and space domain
 !-----------------------------------------------------------------------
    ln_linssh   = .false.   !  =T  linear free surface  ==>>  model level are fixed in time
@@ -40,13 +39,38 @@
 /
 !-----------------------------------------------------------------------
-&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtsd    !   data : Temperature  & Salinity
+&namtsd        !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
    cn_dir        = './'      !  root directory for the location of the runoff files
    ln_tsd_init   = .false.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
    ln_tsd_tradmp = .false.   !  damping of ocean T & S toward T &S input data (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&namwad        !   Wetting and drying  default is no WAD
+!-----------------------------------------------------------------------
+   ln_wd_il          = .false   ! T/F activation of iterative limiter for  wetting and drying scheme
+   ln_wd_dl          = .true.   ! T/F activation of directional llimiter for wetting drying scheme
+   ln_wd_dl_bc       = .true.   ! T/F Directional limiteer Baroclinic option
+   ln_wd_dl_rmp      = .true.   ! T/F Turn on directional limiter ramp
+   rn_wdmin0         =  0.30    ! dpoth at which wetting/drying starts
+   rn_wdmin1         =  0.2     ! Minimum wet depth on dried cells
+   rn_wdmin2         =  0.0001  ! Tolerance of min wet depth on dried cells
+   rn_wdld           =  2.5     ! Land elevation below which wetting/drying is allowed
+   nn_wdit           =   20     ! Max iterations for W/D limiter
+/
+!-----------------------------------------------------------------------
+&namcrs        !   coarsened grid (for outputs and/or TOP)              (ln_crs =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -63,9 +87,25 @@
 /
 !-----------------------------------------------------------------------
+&namsbc_flx    !   surface boundary condition : flux formulation
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_blk   !   namsbc_blk  generic Bulk formula                      (ln_blk =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
 !-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
-&namtra_qsr    !   penetrative solar radiation
+&namsbc_sas    !   Stand-Alone Surface boundary condition
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iif    !   Ice-IF : use observed ice cover                      (nn_ice = 1)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_qsr    !   penetrative solar radiation                          (ln_traqsr =T)
 !-----------------------------------------------------------------------
    ln_qsr_rgb  = .false.   !  RGB (Red-Green-Blue) light penetration
@@ -74,14 +114,22 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_rnf    !   runoffs namelist surface boundary condition
+&namsbc_rnf    !   runoffs namelist surface boundary condition          (ln_rnf =T)
 !-----------------------------------------------------------------------
    ln_rnf_mouth = .false.   !  specific treatment at rivers mouths
 /
 !-----------------------------------------------------------------------
-&namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
+&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_iscpl  !   land ice / ocean coupling option                     
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_apr    !   Atmospheric pressure used as ocean forcing           (ln_apr_dyn =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr =T)
 !-----------------------------------------------------------------------
    nn_sssr     =     0     !  add a damping     term in the surface freshwater flux (=2)
@@ -90,9 +138,9 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namberg       !   iceberg parameters
+&namsbc_wave   ! External fields from wave model                        (ln_wave=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters                                   (default: No iceberg)
 !-----------------------------------------------------------------------
 /
@@ -107,9 +155,9 @@
 /
 !-----------------------------------------------------------------------
-&nam_tide      !    tide parameters (#ifdef key_tide)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nambdy        !  unstructured open boundaries
+&nam_tide      !   tide parameters
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nambdy        !  unstructured open boundaries                          
 !-----------------------------------------------------------------------
     ln_bdy         = .false.            
@@ -158,5 +206,5 @@
 /
 !-----------------------------------------------------------------------
-&nambdy_dta      !  open boundaries - external data
+&nambdy_dta    !  open boundaries - external data                       
 !-----------------------------------------------------------------------
 !              !  file name      ! frequency (hours) ! variable  ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
@@ -169,14 +217,18 @@
 /
 !-----------------------------------------------------------------------
-&nambdy_tide     ! tidal forcing at open boundaries
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdrg            !   top/bottom drag coefficient                      (default: NO selection)
+&nambdy_tide   !  tidal forcing at open boundaries
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg        !   top/bottom drag coefficient                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_loglayer= .false.    !  logarithmic drag: Cd = vkarmn/log(z/z0) |U|
 /
 !-----------------------------------------------------------------------
-&namdrg_bot        !   BOTTOM friction                                  
+&namdrg_top    !   TOP friction                                         (ln_isfcav=T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdrg_bot    !   BOTTOM friction                                  
 !-----------------------------------------------------------------------
    rn_Cd0     =  1.e-4    !  drag coefficient [-]
@@ -189,5 +241,5 @@
 /
 !-----------------------------------------------------------------------
-&nambbc        !   bottom temperature boundary condition
+&nambbc        !   bottom temperature boundary condition                (default: NO)
 !-----------------------------------------------------------------------
    ln_trabbc   = .false.   !  Apply a geothermal heating at the ocean bottom
@@ -195,9 +247,9 @@
 /
 !-----------------------------------------------------------------------
-&nambbl        !   bottom boundary layer scheme
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+&nambbl        !   bottom boundary layer scheme                         (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nameos        !   ocean Equation Of Seawater                           (default: NO)
 !-----------------------------------------------------------------------
    ln_teos10   = .false.         !  = Use TEOS-10 equation of state
@@ -219,5 +271,5 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer                          (default: No selection)
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_NONE=  .false.  !  No tracer advection
@@ -229,10 +281,10 @@
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)
-!-----------------------------------------------------------------------
-/
-!----------------------------------------------------------------------------------
-&namtra_ldf    !   lateral diffusion scheme for tracers
-!----------------------------------------------------------------------------------
+&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO selection)
+!-----------------------------------------------------------------------
    !                       !  Operator type:
    ln_traldf_lap   =  .true.   !    laplacian operator
@@ -263,13 +315,17 @@
    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
 /
-!----------------------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.
-!----------------------------------------------------------------------------------
+!-----------------------------------------------------------------------
+&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
+!-----------------------------------------------------------------------
    ln_ldfeiv     =.false.   ! use eddy induced velocity parameterization
 /
 !-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping
+&namtra_dmp    !   tracer: T & S newtonian damping                      (default: NO)
 !-----------------------------------------------------------------------
    ln_tradmp   =  .false.  !  add a damping termn (T) or not (F)
+/
+!-----------------------------------------------------------------------
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -281,8 +337,7 @@
    ln_dynadv_cen2= .false. !  flux form - 2nd order centered scheme
    ln_dynadv_ubs = .false. !  flux form - 3rd order UBS      scheme
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
+/
+!-----------------------------------------------------------------------
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO)
 !-----------------------------------------------------------------------
    ln_dynvor_ene = .false. !  enstrophy conserving scheme
@@ -293,5 +348,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_hpg    !   Hydrostatic pressure gradient option
+&namdyn_hpg    !   Hydrostatic pressure gradient option                 (default: NO selection)
 !-----------------------------------------------------------------------
    ln_hpg_zco  = .false.   !  z-coordinate - full steps
@@ -300,5 +355,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient 
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
    ln_dynspg_ts  = .true.  !  split-explicit free surface
@@ -307,5 +362,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_ldf    !   lateral diffusion on momentum
+&namdyn_ldf    !   lateral diffusion on momentum                        (default: NO selection)
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
@@ -372,27 +427,38 @@
 /
 !-----------------------------------------------------------------------
+&namzdf_ric    !   richardson number dependent vertical diffusion       (ln_zdfric =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
 &namzdf_tke    !   turbulent eddy kinetic dependent vertical diffusion  (ln_zdftke =T)
 !-----------------------------------------------------------------------
    nn_etau     =   0       !  penetration of tke below the mixed layer (ML) due to internal & intertial waves
 /
-
-!!======================================================================
-!!                  ***  Miscellaneous namelists  ***
-!!======================================================================
-!-----------------------------------------------------------------------
-&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtrd        !   diagnostics on dynamics and/or tracer trends         ("key_trddyn" and/or "key_trdtra")
-!              !       or mixed-layer trends or barotropic vorticity    ("key_trdmld" or     "key_trdvor")
+!-----------------------------------------------------------------------
+&namzdf_gls    !   GLS vertical diffusion                               (ln_zdfgls =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_osm    !   OSM vertical diffusion                               (ln_zdfosm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namzdf_iwm    !    internal wave-driven mixing parameterization        (ln_zdfiwm =T)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namctl        !   Control prints 
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namsto        ! Stochastic parametrization of EOS                      (default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtrd        !   trend diagnostics                                    (default F)
 !-----------------------------------------------------------------------
    ln_glo_trd  = .false.   ! (T) global domain averaged diag for T, T^2, KE, and PE
@@ -406,17 +472,26 @@
    nn_trd      = 365       !  print frequency (ln_glo_trd=T) (unit=time step)
 /
-!!gm   nn_ctls     =   0       !  control surface type in mixed-layer trends (0,1 or n<jpk)
-!!gm   rn_ucf      =   1.      !  unit conversion factor (=1 -> /seconds ; =86400. -> /day)
-!!gm   cn_trdrst_in      = "restart_mld"   ! suffix of ocean restart name (input)
-!!gm   cn_trdrst_out     = "restart_mld"   ! suffix of ocean restart name (output)
-!!gm   ln_trdmld_restart = .false.         !  restart for ML diagnostics
-!!gm   ln_trdmld_instant = .false.         !  flag to diagnose trends of instantantaneous or mean ML T/S
-!!gm
-!-----------------------------------------------------------------------
-&namhsb       !  Heat and salt budgets
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namdct        ! transports through sections
+!-----------------------------------------------------------------------
+&namptr        !   Poleward Transport Diagnostic                        (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namhsb        !  Heat and salt budgets                                 (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdiu        !   Cool skin and warm layer models                      (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namflo        !   float parameters                                     ("key_float")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_diaharm   !   Harmonic analysis of tidal constituents              ("key_diaharm")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdct        ! transports through some sections                       ("key_diadct")
 !-----------------------------------------------------------------------
     nn_dct      = 60       !  time step frequency for transports computing
@@ -425,26 +500,25 @@
 /
 !-----------------------------------------------------------------------
-&namobs       !  observation usage switch
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nam_asminc   !   assimilation increments                               ('key_asminc')
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_wave   ! External fields from wave model
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namwad  !   Wetting and drying
-!-----------------------------------------------------------------------
-   ln_wd_il          = .false   ! T/F activation of iterative limiter for  wetting and drying scheme
-   ln_wd_dl          = .true.   ! T/F activation of directional llimiter for wetting drying scheme
-   ln_wd_dl_bc       = .true.   ! T/F Directional limiteer Baroclinic option
-   ln_wd_dl_rmp      = .true.   ! T/F Turn on directional limiter ramp
-   rn_wdmin0         =  0.30    ! dpoth at which wetting/drying starts
-   rn_wdmin1         =  0.2     ! Minimum wet depth on dried cells
-   rn_wdmin2         =  0.0001  ! Tolerance of min wet depth on dried cells
-   rn_wdld           =  2.5     ! Land elevation below which wetting/drying is allowed
-   nn_wdit           =   20     ! Max iterations for W/D limiter
-/
+&nam_diatmb    !  Top Middle Bottom Output                              (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_dia25h    !  25h Mean Output                                       (default F)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4")
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namobs        !  observation usage switch
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&nam_asminc    !   assimilation increments                              ('key_asminc')
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdta_dyn    !   offline dynamics read in files                       ("key_offline")
+!-----------------------------------------------------------------------
+/
