Index: branches/2017/dev_merge_2017/NEMOGCM/CONFIG/C1D_PAPA/EXP00/namelist_cfg
===================================================================
--- branches/2017/dev_merge_2017/NEMOGCM/CONFIG/C1D_PAPA/EXP00/namelist_cfg	(revision 9169)
+++ branches/2017/dev_merge_2017/NEMOGCM/CONFIG/C1D_PAPA/EXP00/namelist_cfg	(revision 9490)
@@ -2,4 +2,19 @@
 !! NEMO/OPA  : 1D configuration based on Kato-Philipps () exp.
 !!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+
+!!======================================================================
+!!              ***  Domain & Run management namelists  ***           !!
+!!                                                                    !!
+!!   namrun       parameters of the run
+!!   namdom       space and time domain
+!!   namcfg       parameters of the configuration                       (default: user defined GYRE)
+!!   namwad       Wetting and drying                                    (default NO)
+!!   namtsd       data: temperature & salinity                          (default NO)
+!!   namcrs       coarsened grid (for outputs and/or TOP)               (ln_crs =T)
+!!   namc1d       1D configuration options                              ("key_c1d")
+!!   namc1d_dyndmp 1D newtonian damping applied on currents             ("key_c1d")
+!!   namc1d_uvd   1D data (currents)                                    ("key_c1d")
+!!======================================================================
+!
 !-----------------------------------------------------------------------
 &namrun        !   parameters of the run
@@ -12,25 +27,4 @@
    nn_stock    =   87600   !  frequency of creation of a restart file (modulo referenced to 1)
    nn_write    =     240   !  frequency of write in the output file   (modulo referenced to nn_it000)
-/
-!-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration   
-!-----------------------------------------------------------------------
-   cp_cfg      =  "papa"                 !  name of the configuration
-   jp_cfg      =       1                 !  resolution of the configuration
-!   jpidta      =       3                 !  1st lateral dimension ( >= jpi ) = 30*jp_cfg+2
-!   jpjdta      =       3                 !  2nd    "         "    ( >= jpj ) = 20*jp_cfg+2 
-!   jpkdta      =      75                 !  number of levels      ( >= jpk )
-!   jpiglo      =       3                 !  1st dimension of global domain --> i  = jpidta
-!   jpjglo      =       3                 !  2nd    -                  -    --> j  = jpjdta
-   jperio      =       0                 !  lateral cond. type (between 0 and 6)
-/
-!-----------------------------------------------------------------------
-&namzgr        !   vertical coordinate
-!-----------------------------------------------------------------------
-   ln_zps      = .true.    !  z-coordinate - partial steps
-/
-!-----------------------------------------------------------------------
-&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
-!-----------------------------------------------------------------------
 /
 !-----------------------------------------------------------------------
@@ -60,29 +54,64 @@
 /
 !-----------------------------------------------------------------------
-&namc1d        !   1D configuration options                             ("key_c1d")
-!-----------------------------------------------------------------------
-   ln_c1d_locpt= .false.   ! Localization of 1D config in a grid (T) or independant point (F)
-/
-!-----------------------------------------------------------------------
-&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      !
-   sn_tem  = 'init_PAPASTATION',   24        ,'votemper' ,  .false.     , .true.,  'daily'  , ''       , ' '        , ''
-   sn_sal  = 'init_PAPASTATION',   24        ,'vosaline' ,  .false.     , .true.,  'daily'  , ''       , ' '        , ''
-   !
-   cn_dir        = './'     !  root directory for the location of the runoff files
-   ln_tsd_init   = .true.   !  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)
-/
-!-----------------------------------------------------------------------
-&namsbc        !   Surface Boundary Condition (surface module)
-!-----------------------------------------------------------------------
-   nn_fsbc     = 1         !  frequency of surface boundary condition computation
-                           !     (also = the frequency of sea-ice model call)
-   nn_ice      = 0         !  =0 no ice boundary condition   ,
-   ln_rnf      = .false.   !  runoffs                                   (T => fill namsbc_rnf)
-   ln_ssr      = .false.   !  Sea Surface Restoring on T and/or S       (T => fill namsbc_ssr)
-   nn_fwb      = 0         !  FreshWater Budget: =0 unchecked
+&namcfg     !   parameters of the configuration   
+!-----------------------------------------------------------------------
+   cp_cfg      =  "papa"                 !  name of the configuration
+   jp_cfg      =       1                 !  resolution of the configuration
+!   jpidta      =       3                 !  1st lateral dimension ( >= jpi ) = 30*jp_cfg+2
+!   jpjdta      =       3                 !  2nd    "         "    ( >= jpj ) = 20*jp_cfg+2 
+!   jpkdta      =      75                 !  number of levels      ( >= jpk )
+!   jpiglo      =       3                 !  1st dimension of global domain --> i  = jpidta
+!   jpjglo      =       3                 !  2nd    -                  -    --> j  = jpjdta
+   jperio      =       0                 !  lateral cond. type (between 0 and 6)
+/
+!-----------------------------------------------------------------------
+&namzgr        !   vertical coordinate
+!-----------------------------------------------------------------------
+   ln_zps      = .true.    !  z-coordinate - partial steps
+/
+!-----------------------------------------------------------------------
+&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d        !   1D configuration options                             ("key_c1d" default: PAPA station)
+!-----------------------------------------------------------------------
+   rn_lat1d    =      50.  !  Column latitude (default at PAPA station)
+   rn_lon1d    =    -145.  !  Column longitude (default at PAPA station)
+   ln_c1d_locpt=  .true.   ! Localization of 1D config in a grid (T) or independant point (F)
+/
+!-----------------------------------------------------------------------
+&namc1d_uvd    !   data: U & V currents                                 ("key_c1d" default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d" default: NO)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namtsd        !    Temperature & Salinity Data                         (default: NO)
+!-----------------------------------------------------------------------
+   !           !  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      !
+   sn_tem      = 'init_PAPASTATION'         ,         24        ,'votemper',  .false.     , .true.,  'daily'  , ''       , ' '      , ''
+   sn_sal      = 'init_PAPASTATION'         ,         24        ,'vosaline',  .false.     , .true.,  'daily'  , ''       , ' '      , ''
+   !
+   ln_tsd_init = .true.   !  Initialisation of ocean T & S with T &S input data (T) or not (F)
+   ln_tsd_dmp  = .false.  !  damping of ocean T & S toward T &S input data (T) or not (F)
+      cn_dir   = './'        !  root directory for the location of the runoff files
+/
+
+!!======================================================================
+!!            ***  Surface Boundary Condition namelists  ***          !!
+!!======================================================================
+!
+!-----------------------------------------------------------------------
+&namsbc        !   Surface Boundary Condition manager
+!-----------------------------------------------------------------------
+   nn_fsbc     = 1   !  frequency of the calling of SBC module
+                     ! Type of air-sea fluxes 
+   ln_blk      = .false.   !  Bulk formulation                          (T => fill namsbc_blk )
+                     ! Misc. options of sbc : 
+   ln_traqsr   = .false.   !  Light penetration in the ocean            (T => fill namtra_qsr)
 /
 !-----------------------------------------------------------------------
@@ -111,9 +140,5 @@
    ln_ECMWF    = .false.   ! "ECMWF"     algorithm   (IFS cycle 31)
 
-   rn_zqt      =  2.       !  Air temperature and humidity reference height (m)
-/
-!-----------------------------------------------------------------------
-&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
-!-----------------------------------------------------------------------
+   rn_zqt      =  2.       !  Air temperature & humidity reference height (m)
 /
 !-----------------------------------------------------------------------
@@ -123,19 +148,9 @@
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
    sn_chl      ='chlorophyll_PAPASTATION', -1    , 'CHLA'    ,   .true.     , .true. , 'yearly'  , ''       , ''       , ''
-/
-!-----------------------------------------------------------------------
-&namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namsbc_ssr    !   surface boundary condition : sea surface restoring
-!-----------------------------------------------------------------------
-   nn_sssr     =     0     !  add a damping     term in the surface freshwater flux (=2)
-   rn_deds     =   -27.7   !  magnitude of the damping on salinity   [mm/day]
-   ln_sssr_bnd =   .false. !  flag to bound erp term (associated with nn_sssr=2)
-/
-!-----------------------------------------------------------------------
-&namsbc_alb    !   albedo parameters
-!-----------------------------------------------------------------------
+
+   ln_qsr_rgb  = .true.    !  RGB (Red-Green-Blue) light penetration
+
+   nn_chldta   =      1    !  RGB : Chl data (=1) or cst value (=0)
+      cn_dir   = './'         !  root directory for the location of the runoff files
 /
 !-----------------------------------------------------------------------
@@ -144,52 +159,42 @@
    ln_non_lin = .true.     !  non-linear  drag: Cd = Cd0 |U|
 /
-!-----------------------------------------------------------------------
-&nambbc        !   bottom temperature boundary condition                (default: NO)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&nameos        !   ocean physical parameters
+
+!!======================================================================
+!!                        Tracer (T & S) namelists
+!!======================================================================
+!
+!-----------------------------------------------------------------------
+&nameos        !   ocean physical parameters                            (default: NO selection)
 !-----------------------------------------------------------------------
    ln_eos80    = .true.         !  = Use EOS80 equation of state
 /
 !-----------------------------------------------------------------------
-&namtra_adv    !   advection scheme for tracer
+&namtra_adv    !   advection scheme for tracer                          (default: NO selection)
 !-----------------------------------------------------------------------
    ln_traadv_NONE= .true.  !  No tracer advection
 /
 !-----------------------------------------------------------------------
-&namtra_adv_mle !  mixed layer eddy parametrisation (Fox-Kemper param)  (default: NO)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
 &namtra_ldf    !   lateral diffusion scheme for tracers
 !-----------------------------------------------------------------------
    ln_traldf_NONE= .true.  ! No operator (no explicit diffusion)
 /
-!-----------------------------------------------------------------------
-&namtra_ldfeiv !   eddy induced velocity param.                         (default: NO)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namtra_dmp    !   tracer: T & S newtonian damping
-!-----------------------------------------------------------------------
-   ln_tradmp   =  .false.  !  add a damping termn (T) or not (F)
-/
-!-----------------------------------------------------------------------
-&namdyn_adv    !   formulation of the momentum advection                (default: None)
+
+!!======================================================================
+!!                      ***  Dynamics namelists  ***                  !!
+!!======================================================================
+!
+!-----------------------------------------------------------------------
+&nam_vvl       !   vertical coordinate options                          (default: z-star)
+!-----------------------------------------------------------------------
+/
+!-----------------------------------------------------------------------
+&namdyn_adv    !   formulation of the momentum advection                (default: selection)
 !-----------------------------------------------------------------------
    ln_dynadv_NONE= .true.  !  linear dynamics (no momentum advection)
 /
 !-----------------------------------------------------------------------
-&namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namc1d_uvd    !   data: U & V currents                                 ("key_c1d")
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&namc1d_dyndmp !   U & V newtonian damping                              ("key_c1d")
-!-----------------------------------------------------------------------
+&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO selection)
+!-----------------------------------------------------------------------
+   ln_dynvor_ene = .true.  !  energy    conserving scheme
 /
 !-----------------------------------------------------------------------
@@ -198,5 +203,5 @@
 /
 !-----------------------------------------------------------------------
-&namdyn_spg    !   surface pressure gradient                            (default: NO spg)
+&namdyn_spg    !   surface pressure gradient                            (default: NO)
 !-----------------------------------------------------------------------
 /
@@ -206,4 +211,9 @@
    ln_dynldf_NONE= .true.     ! No operator (no explicit diffusion)
 /
+
+!!======================================================================
+!!                     vertical physics namelists                     !!
+!!======================================================================
+!
 !-----------------------------------------------------------------------
 &namzdf        !   vertical physics                                     (default: NO selection)
@@ -258,19 +268,2 @@
 !-----------------------------------------------------------------------
 /
-!-----------------------------------------------------------------------
-&namctl        !   Control prints & Benchmark
-!-----------------------------------------------------------------------
-/
-!-----------------------------------------------------------------------
-&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                               ('key_diaobs')
-!-----------------------------------------------------------------------
-/
