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 9217)
+++ 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")
+!-----------------------------------------------------------------------
+/
