Index: branches/2015/dev_r5072_UKMO2_OBS_simplification/NEMOGCM/CONFIG/SHARED/namelist_ref
===================================================================
--- branches/2015/dev_r5072_UKMO2_OBS_simplification/NEMOGCM/CONFIG/SHARED/namelist_ref	(revision 5082)
+++ branches/2015/dev_r5072_UKMO2_OBS_simplification/NEMOGCM/CONFIG/SHARED/namelist_ref	(revision 5682)
@@ -10,5 +10,5 @@
 !!              7 - dynamics         (namdyn_adv, namdyn_vor, namdyn_hpg, namdyn_spg, namdyn_ldf)
 !!              8 - Verical physics  (namzdf, namzdf_ric, namzdf_tke, namzdf_kpp, namzdf_ddm, namzdf_tmx)
-!!              9 - diagnostics      (namnc4, namtrd, namspr, namflo, namptr, namhsb)
+!!              9 - diagnostics      (namnc4, namtrd, namspr, namflo, namhsb, namsto)
 !!             10 - miscellaneous    (namsol, nammpp, namctl)
 !!             11 - Obs & Assim      (namobs, nam_asminc)
@@ -37,11 +37,16 @@
                            !    = 2 nn_date0 read in restart  ; nn_it000 : check consistancy between namelist and restart
    cn_ocerst_in  = "restart"   !  suffix of ocean restart name (input)
+   cn_ocerst_indir = "."       !  directory from which to read input ocean restarts
    cn_ocerst_out = "restart"   !  suffix of ocean restart name (output)
+   cn_ocerst_outdir = "."      !  directory in which to write output ocean restarts
    nn_istate   =       0   !  output the initial state (1) or not (0)
+   ln_rst_list = .false.   !  output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F)
    nn_stock    =    5475   !  frequency of creation of a restart file (modulo referenced to 1)
+   nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written
    nn_write    =    5475   !  frequency of write in the output file   (modulo referenced to nn_it000)
    ln_dimgnnn  = .false.   !  DIMG file format: 1 file for all processors (F) or by processor (T)
    ln_mskland  = .false.   !  mask land points in NetCDF outputs (costly: + ~15%)
-   ln_clobber  = .false.   !  clobber (overwrite) an existing file
+   ln_cfmeta   = .false.   !  output additional data to netCDF files required for compliance with the CF metadata standard
+   ln_clobber  = .true.   !  clobber (overwrite) an existing file
    nn_chunksz  =       0   !  chunksize (bytes) for NetCDF file (works only with iom_nf90 routines)
 /
@@ -50,5 +55,5 @@
 !!                      ***  Domain namelists  ***
 !!======================================================================
-!!   namcfg       parameters of the configuration      
+!!   namcfg       parameters of the configuration
 !!   namzgr       vertical coordinate
 !!   namzgr_sco   s-coordinate or hybrid z-s-coordinate
@@ -58,5 +63,5 @@
 !
 !-----------------------------------------------------------------------
-&namcfg     !   parameters of the configuration      
+&namcfg     !   parameters of the configuration
 !-----------------------------------------------------------------------
    cp_cfg      =  "default"            !  name of the configuration
@@ -72,8 +77,10 @@
    jperio      =       0               !  lateral cond. type (between 0 and 6)
                                        !  = 0 closed                 ;   = 1 cyclic East-West
-                                       !  = 2 equatorial symmetric   ;   = 3 North fold T-point pivot 
+                                       !  = 2 equatorial symmetric   ;   = 3 North fold T-point pivot
                                        !  = 4 cyclic East-West AND North fold T-point pivot
                                        !  = 5 North fold F-point pivot
                                        !  = 6 cyclic East-West AND North fold F-point pivot
+   ln_use_jattr = .false.              !  use (T) the file attribute: open_ocean_jstart, if present
+                                       !  in netcdf input files, as the start j-row for reading
 /
 !-----------------------------------------------------------------------
@@ -83,5 +90,5 @@
    ln_zps      = .true.    !  z-coordinate - partial steps   (T/F)
    ln_sco      = .false.   !  s- or hybrid z-s-coordinate    (T/F)
-   ln_isfcav   = .false.   !  ice shelf cavity
+   ln_isfcav   = .false.   !  ice shelf cavity               (T/F)
 /
 !-----------------------------------------------------------------------
@@ -99,5 +106,5 @@
                         !!!!!!!  SH94 stretching coefficients  (ln_s_sh94 = .true.)
    rn_theta    =    6.0    !  surface control parameter (0<=theta<=20)
-   rn_bb       =    0.8    !  stretching with SH94 s-sigma   
+   rn_bb       =    0.8    !  stretching with SH94 s-sigma
                         !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.)
    rn_alpha    =    4.4    !  stretching with SF12 s-sigma
@@ -108,5 +115,5 @@
    rn_zb_b     =   -0.2    !  offset for calculating Zb
                         !!!!!!!! Other stretching (not SH94 or SF12) [also uses rn_theta above]
-   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1) 
+   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1)
 /
 !-----------------------------------------------------------------------
@@ -116,5 +123,5 @@
    rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1
    nn_closea   =    0      !  remove (=0) or keep (=1) closed seas and lakes (ORCA)
-   nn_msh      =    0      !  create (=1) a mesh file or not (=0)
+   nn_msh      =    1      !  create (=1) a mesh file or not (=0)
    rn_hmin     =   -3.     !  min depth of the ocean (>0) or min number of ocean level (<0)
    rn_e3zps_min=   20.     !  partial step thickness is set larger than the minimum of
@@ -162,9 +169,9 @@
    nn_baro       =    30               !  Number of iterations of barotropic mode
                                        !  during rn_rdt seconds. Only used if ln_bt_nn_auto=F
-   rn_bt_cmax    =    0.8              !  Maximum courant number allowed if ln_bt_nn_auto=T 
+   rn_bt_cmax    =    0.8              !  Maximum courant number allowed if ln_bt_nn_auto=T
    nn_bt_flt     =    1                !  Time filter choice
                                        !  = 0 None
                                        !  = 1 Boxcar over   nn_baro barotropic steps
-                                       !  = 2 Boxcar over 2*nn_baro     "        "  
+                                       !  = 2 Boxcar over 2*nn_baro     "        "
 /
 !-----------------------------------------------------------------------
@@ -213,5 +220,5 @@
 !!   namsbc_core     CORE bulk formulae formulation
 !!   namsbc_mfs      MFS  bulk formulae formulation
-!!   namsbc_cpl      CouPLed            formulation                     ("key_coupled")
+!!   namsbc_cpl      CouPLed            formulation                     ("key_oasis3")
 !!   namsbc_sas      StAndalone Surface module
 !!   namtra_qsr      penetrative solar radiation
@@ -233,4 +240,10 @@
    ln_blk_core = .true.    !  CORE bulk formulation                     (T => fill namsbc_core)
    ln_blk_mfs  = .false.   !  MFS bulk formulation                      (T => fill namsbc_mfs )
+   ln_cpl      = .false.   !  atmosphere coupled   formulation          ( requires key_oasis3 )
+   ln_mixcpl   = .false.   !  forced-coupled mixed formulation          ( requires key_oasis3 )
+   nn_components = 0       !  configuration of the opa-sas OASIS coupling
+                           !  =0 no opa-sas OASIS coupling: default single executable configuration
+                           !  =1 opa-sas OASIS coupling: multi executable configuration, OPA component
+                           !  =2 opa-sas OASIS coupling: multi executable configuration, SAS component 
    ln_apr_dyn  = .false.   !  Patm gradient added in ocean & ice Eqs.   (T => fill namsbc_apr )
    nn_ice      = 2         !  =0 no ice boundary condition   ,
@@ -243,6 +256,6 @@
    ln_rnf      = .true.    !  runoffs                                   (T   => fill namsbc_rnf)
    nn_isf      = 0         !  ice shelf melting/freezing                (/=0 => fill namsbc_isf)
-                           !  0 =no isf                  1 = presence of ISF 
-                           !  2 = bg03 parametrisation   3 = rnf file for isf   
+                           !  0 =no isf                  1 = presence of ISF
+                           !  2 = bg03 parametrisation   3 = rnf file for isf
                            !  4 = ISF fwf specified
                            !  option 1 and 4 need ln_isfcav = .true. (domzgr)
@@ -275,5 +288,5 @@
 &namsbc_flx    !   surface boundary condition : flux formulation
 !-----------------------------------------------------------------------
-!              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
+!              !  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_utau     = 'utau'      ,        24         , 'utau'    , .false.      , .false., 'yearly'  , ''       , ''       , ''
@@ -318,8 +331,8 @@
    ln_taudif   = .false.   !  HF tau contribution: use "mean of stress module - module of the mean stress" data
    rn_zqt      = 10.        !  Air temperature and humidity reference height (m)
-   rn_zu       = 10.        !  Wind vector reference height (m)                 
+   rn_zu       = 10.        !  Wind vector reference height (m)
    rn_pfac     = 1.        !  multiplicative factor for precipitation (total & snow)
    rn_efac     = 1.        !  multiplicative factor for evaporation (0. or 1.)
-   rn_vfac     = 0.        !  multiplicative factor for ocean/ice velocity 
+   rn_vfac     = 0.        !  multiplicative factor for ocean/ice velocity
                            !  in the calculation of the wind stress (0.=absolute winds or 1.=relative winds)
 /
@@ -340,5 +353,5 @@
 /
 !-----------------------------------------------------------------------
-&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_coupled")
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
 !-----------------------------------------------------------------------
 !                    !     description       !  multiple  !    vector   !      vector          ! vector !
@@ -371,11 +384,14 @@
 !              !  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_usp      = 'sas_grid_U' ,    120           , 'vozocrtx' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''      
+   sn_usp      = 'sas_grid_U' ,    120           , 'vozocrtx' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
    sn_vsp      = 'sas_grid_V' ,    120           , 'vomecrty' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
    sn_tem      = 'sas_grid_T' ,    120           , 'sosstsst' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
    sn_sal      = 'sas_grid_T' ,    120           , 'sosaline' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
    sn_ssh      = 'sas_grid_T' ,    120           , 'sossheig' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
-
-   ln_3d_uv    = .true.    !  specify whether we are supplying a 3D u,v field
+   sn_e3t      = 'sas_grid_T' ,    120           , 'e3t_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_frq      = 'sas_grid_T' ,    120           , 'frq_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+
+   ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field
+   ln_read_frq = .false.    !  specify whether we must read frq or not
    cn_dir      = './'      !  root directory for the location of the bulk files are
 /
@@ -410,5 +426,4 @@
 
    cn_dir       = './'      !  root directory for the location of the runoff files
-   ln_rnf_emp   = .false.   !  runoffs included into precipitation field (T) or into a file (F)
    ln_rnf_mouth = .true.    !  specific treatment at rivers mouths
    rn_hrnf      =  15.e0    !  depth over which enhanced vertical mixing is used
@@ -418,7 +433,11 @@
    ln_rnf_tem   = .false.   !  read in temperature information for runoff
    ln_rnf_sal   = .false.   !  read in salinity information for runoff
-/
-!-----------------------------------------------------------------------
-&namsbc_isf    !  Top boundary layer (ISF) 
+   ln_rnf_depth_ini = .false.  ! compute depth at initialisation from runoff file
+   rn_rnf_max   = 5.735e-4  !  max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true )
+   rn_dep_max   = 150.      !  depth over which runoffs is spread ( ln_rnf_depth_ini = .true )
+   nn_rnf_depth_file = 0    !  create (=1) a runoff depth file or not (=0)
+/
+!-----------------------------------------------------------------------
+&namsbc_isf    !  Top boundary layer (ISF)
 !-----------------------------------------------------------------------
 !              ! file name ! frequency (hours) ! variable ! time interpol. !  clim   ! 'yearly'/ ! weights  ! rotation !
@@ -457,5 +476,5 @@
 
    cn_dir      = './'       !  root directory for the location of the bulk files
-   rn_pref     = 101000._wp !  reference atmospheric pressure   [N/m2]/
+   rn_pref     = 101000.    !  reference atmospheric pressure   [N/m2]/
    ln_ref_apr  = .false.    !  ref. pressure: global mean Patm (T) or a constant (F)
    ln_apr_obc  = .false.    !  inverse barometer added to OBC ssh data
@@ -497,8 +516,8 @@
                                                       ! Initial mass required for an iceberg of each class
       rn_initial_mass          = 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-                                                      ! Proportion of calving mass to apportion to each class  
+                                                      ! Proportion of calving mass to apportion to each class
       rn_distribution          = 0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02
                                                       ! Ratio between effective and real iceberg mass (non-dim)
-                                                      ! i.e. number of icebergs represented at a point         
+                                                      ! i.e. number of icebergs represented at a point
       rn_mass_scaling          = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1
                                                       ! thickness of newly calved bergs (m)
@@ -509,15 +528,15 @@
       rn_bits_erosion_fraction = 0.                   ! Fraction of erosion melt flux to divert to bergy bits
       rn_sicn_shift            = 0.                   ! Shift of sea-ice concn in erosion flux (0<sicn_shift<1)
-      ln_passive_mode          = .false.              ! iceberg - ocean decoupling   
+      ln_passive_mode          = .false.              ! iceberg - ocean decoupling
       nn_test_icebergs         =  10                  ! Create test icebergs of this class (-1 = no)
                                                       ! Put a test iceberg at each gridpoint in box (lon1,lon2,lat1,lat2)
       rn_test_box              = 108.0,  116.0, -66.0, -58.0
-      rn_speed_limit           = 0.                   ! CFL speed limit for a berg   
+      rn_speed_limit           = 0.                   ! CFL speed limit for a berg
 
 !              ! 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_icb =  'calving' ,       -1           , 'calvingmask',  .true.        , .true.  , 'yearly'  , ''       , ''       , ''
-   
-      cn_dir = './' 
+
+      cn_dir = './'
 /
 
@@ -573,4 +592,5 @@
    rn_sponge_tra = 2880.   !  coefficient for tracer   sponge layer [m2/s]
    rn_sponge_dyn = 2880.   !  coefficient for dynamics sponge layer [m2/s]
+   ln_chk_bathy  = .FALSE. !
 /
 !-----------------------------------------------------------------------
@@ -580,15 +600,5 @@
    ln_tide_ramp  = .false.  !
    rdttideramp   =    0.    !
-   clname(1)     =   'M2'   !  name of constituent
-   clname(2)     =   'S2'
-   clname(3)     =   'N2'
-   clname(4)     =   'K1'
-   clname(5)     =   'O1'
-   clname(6)     =   'Q1'
-   clname(7)     =   'M4'
-   clname(8)     =   'K2'
-   clname(9)     =   'P1'
-   clname(10)    =   'Mf'
-   clname(11)    =   'Mm'
+   clname(1)     = 'DUMMY'  !  name of constituent - all tidal components must be set in namelist_cfg
 /
 !-----------------------------------------------------------------------
@@ -605,11 +615,11 @@
                                           !  = 2, use tidal harmonic forcing data from files
                                           !  = 3, use external data AND tidal harmonic forcing
-    cn_dyn3d      =  'none'               !  
+    cn_dyn3d      =  'none'               !
     nn_dyn3d_dta  =  0                    !  = 0, bdy data are equal to the initial state
                                           !  = 1, bdy data are read in 'bdydata   .nc' files
-    cn_tra        =  'none'               ! 
+    cn_tra        =  'none'               !
     nn_tra_dta    =  0                    !  = 0, bdy data are equal to the initial state
                                           !  = 1, bdy data are read in 'bdydata   .nc' files
-    cn_ice_lim      =  'none'             !  
+    cn_ice_lim      =  'none'             !
     nn_ice_lim_dta  =  0                  !  = 0, bdy data are equal to the initial state
                                           !  = 1, bdy data are read in 'bdydata   .nc' files
@@ -620,5 +630,5 @@
     ln_tra_dmp    =.false.                !  open boudaries conditions for tracers
     ln_dyn3d_dmp  =.false.                !  open boundary condition for baroclinic velocities
-    rn_time_dmp   =  1.                   ! Damping time scale in days 
+    rn_time_dmp   =  1.                   ! Damping time scale in days
     rn_time_dmp_out =  1.                 ! Outflow damping time scale
     nn_rimwidth   = 10                    !  width of the relaxation zone
@@ -673,5 +683,5 @@
    rn_bfri2_max =   1.e-1  !  max. bottom drag coefficient (non linear case and ln_loglayer=T)
    rn_bfeb2    =    2.5e-3 !  bottom turbulent kinetic energy background  (m2/s2)
-   rn_bfrz0    =    3.e-3  !  bottom roughness [m] if ln_loglayer=T 
+   rn_bfrz0    =    3.e-3  !  bottom roughness [m] if ln_loglayer=T
    ln_bfr2d    = .false.   !  horizontal variation of the bottom friction coef (read a 2D mask file )
    rn_bfrien   =    50.    !  local multiplying factor of bfr (ln_bfr2d=T)
@@ -690,4 +700,10 @@
 &nambbc        !   bottom temperature boundary condition
 !-----------------------------------------------------------------------
+!              !                              !  (if <0  months)  !  
+!              !  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_qgh      ='geothermal_heating.nc',  -12.  , 'heatflow'      ,   .false.      , .true.  , 'yearly'  , ''       , ''       , ''
+   !
+   cn_dir      = './'      !  root directory for the location of the runoff files
    ln_trabbc   = .true.    !  Apply a geothermal heating at the ocean bottom
    nn_geoflx   =    2      !  geothermal heat flux: = 0 no flux
@@ -695,4 +711,5 @@
                            !     = 2 variable flux (read in geothermal_heating.nc in mW/m2)
    rn_geoflx_cst = 86.4e-3 !  Constant value of geothermal heat flux [W/m2]
+
 /
 !-----------------------------------------------------------------------
@@ -719,6 +736,6 @@
 !-----------------------------------------------------------------------
    nn_eos      =  -1     !  type of equation of state and Brunt-Vaisala frequency
-                                 !  =-1, TEOS-10 
-                                 !  = 0, EOS-80 
+                                 !  =-1, TEOS-10
+                                 !  = 0, EOS-80
                                  !  = 1, S-EOS   (simplified eos)
    ln_useCT    = .true.  ! use of Conservative Temp. ==> surface CT converted in Pot. Temp. in sbcssm
@@ -791,14 +808,8 @@
 !-----------------------------------------------------------------------
    ln_tradmp   =  .true.   !  add a damping termn (T) or not (F)
-   nn_hdmp     =   -1      !  horizontal shape =-1, damping in Med and Red Seas only
-                           !                   =XX, damping poleward of XX degrees (XX>0)
-                           !                      + F(distance-to-coast) + Red and Med Seas
    nn_zdmp     =    0      !  vertical   shape =0    damping throughout the water column
                            !                   =1 no damping in the mixing layer (kz  criteria)
                            !                   =2 no damping in the mixed  layer (rho crieria)
-   rn_surf     =   50.     !  surface time scale of damping   [days]
-   rn_bot      =  360.     !  bottom  time scale of damping   [days]
-   rn_dep      =  800.     !  depth of transition between rn_surf and rn_bot [meters]
-   nn_file     =    0      !  create a damping.coeff NetCDF file (=1) or not (=0)
+   cn_resto    = 'resto.nc' ! Name of file containing restoration coefficient field (use dmp_tools to create this)
 /
 
@@ -817,4 +828,5 @@
 !-----------------------------------------------------------------------
    ln_dynadv_vec = .true.  !  vector form (T) or flux form (F)
+   nn_dynkeg     = 0       ! scheme for grad(KE): =0   C2  ;  =1   Hollingsworth correction
    ln_dynadv_cen2= .false. !  flux form - 2nd order centered scheme
    ln_dynadv_ubs = .false. !  flux form - 3rd order UBS      scheme
@@ -824,5 +836,5 @@
 &nam_vvl    !   vertical coordinate options
 !-----------------------------------------------------------------------
-   ln_vvl_zstar  = .true.           !  zstar vertical coordinate                   
+   ln_vvl_zstar  = .true.           !  zstar vertical coordinate
    ln_vvl_ztilde = .false.          !  ztilde vertical coordinate: only high frequency variations
    ln_vvl_layer  = .false.          !  full layer vertical coordinate
@@ -850,4 +862,5 @@
    ln_hpg_zps  = .true.    !  z-coordinate - partial steps (interpolation)
    ln_hpg_sco  = .false.   !  s-coordinate (standard jacobian formulation)
+   ln_hpg_isf  = .false.   !  s-coordinate (sco ) adapted to isf
    ln_hpg_djc  = .false.   !  s-coordinate (Density Jacobian with Cubic polynomial)
    ln_hpg_prj  = .false.   !  s-coordinate (Pressure Jacobian scheme)
@@ -945,5 +958,5 @@
                            !        = 1 add a tke source below the ML
                            !        = 2 add a tke source just at the base of the ML
-                           !        = 3 as = 1 applied on HF part of the stress    ("key_coupled")
+                           !        = 3 as = 1 applied on HF part of the stress    ("key_oasis3")
    rn_efr      =   0.05    !  fraction of surface tke value which penetrates below the ML (nn_etau=1 or 2)
    nn_htau     =   1       !  type of exponential decrease of tke penetration below the ML
@@ -967,18 +980,18 @@
 &namzdf_gls                !   GLS vertical diffusion                   ("key_zdfgls")
 !-----------------------------------------------------------------------
-   rn_emin       = 1.e-6   !  minimum value of e   [m2/s2]
+   rn_emin       = 1.e-7   !  minimum value of e   [m2/s2]
    rn_epsmin     = 1.e-12  !  minimum value of eps [m2/s3]
    ln_length_lim = .true.  !  limit on the dissipation rate under stable stratification (Galperin et al., 1988)
-   rn_clim_galp  = 0.53    !  galperin limit
-   ln_crban      = .true.  !  Use Craig & Banner (1994) surface wave mixing parametrisation
+   rn_clim_galp  = 0.267   !  galperin limit
    ln_sigpsi     = .true.  !  Activate or not Burchard 2001 mods on psi schmidt number in the wb case
    rn_crban      = 100.    !  Craig and Banner 1994 constant for wb tke flux
    rn_charn      = 70000.  !  Charnock constant for wb induced roughness length
-   nn_tkebc_surf =   1     !  surface tke condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
-   nn_tkebc_bot  =   1     !  bottom tke condition (0/1=Dir/Neum)
-   nn_psibc_surf =   1     !  surface psi condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
-   nn_psibc_bot  =   1     !  bottom psi condition (0/1=Dir/Neum)
-   nn_stab_func  =   2     !  stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB)
-   nn_clos       =   1     !  predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen)
+   rn_hsro       =  0.02   !  Minimum surface roughness
+   rn_frac_hs    =   1.3   !  Fraction of wave height as roughness (if nn_z0_met=2)
+   nn_z0_met     =     2   !  Method for surface roughness computation (0/1/2)
+   nn_bc_surf    =     1   !  surface condition (0/1=Dir/Neum)
+   nn_bc_bot     =     1   !  bottom condition (0/1=Dir/Neum)
+   nn_stab_func  =     2   !  stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB)
+   nn_clos       =     1   !  predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen)
 /
 !-----------------------------------------------------------------------
@@ -1008,4 +1021,5 @@
 !!   namc1d_uvd        data: U & V currents                             ("key_c1d")
 !!   namc1d_dyndmp     U & V newtonian damping                          ("key_c1d")
+!!   namsto            Stochastic parametrization of EOS
 !!======================================================================
 !
@@ -1066,4 +1080,21 @@
    ln_dyndmp   =  .false.  !  add a damping term (T) or not (F)
 /
+!-----------------------------------------------------------------------
+&namsto       ! Stochastic parametrization of EOS
+!-----------------------------------------------------------------------
+   ln_rststo = .false.           ! start from mean parameter (F) or from restart file (T)
+   ln_rstseed = .true.           ! read seed of RNG from restart file
+   cn_storst_in  = "restart_sto" !  suffix of stochastic parameter restart file (input)
+   cn_storst_out = "restart_sto" !  suffix of stochastic parameter restart file (output)
+
+   ln_sto_eos = .false.          ! stochastic equation of state
+   nn_sto_eos = 1                ! number of independent random walks
+   rn_eos_stdxy = 1.4            ! random walk horz. standard deviation (in grid points)
+   rn_eos_stdz  = 0.7            ! random walk vert. standard deviation (in grid points)
+   rn_eos_tcor  = 1440.0         ! random walk time correlation (in timesteps)
+   nn_eos_ord  = 1               ! order of autoregressive processes
+   nn_eos_flt  = 0               ! passes of Laplacian filter
+   rn_eos_lim  = 2.0             ! limitation factor (default = 3.0)
+/
 
 !!======================================================================
@@ -1072,6 +1103,6 @@
 !!   namnc4       netcdf4 chunking and compression settings             ("key_netcdf4")
 !!   namtrd       dynamics and/or tracer trends
+!!   namptr       Poleward Transport Diagnostics
 !!   namflo       float parameters                                      ("key_float")
-!!   namptr       Poleward Transport Diagnostics
 !!   namhsb       Heat and salt budgets
 !!======================================================================
@@ -1127,10 +1158,5 @@
 !-----------------------------------------------------------------------
    ln_diaptr  = .false.    !  Poleward heat and salt transport (T) or not (F)
-   ln_diaznl  = .true.     !  Add zonal means and meridional stream functions
-   ln_subbas  = .true.     !  Atlantic/Pacific/Indian basins computation (T) or not
-                           !  (orca configuration only, need input basins mask file named "subbasins.nc"
-   ln_ptrcomp = .true.     !  Add decomposition : overturning
-   nn_fptr    =  1         !  Frequency of ptr computation [time step]
-   nn_fwri    =  15        !  Frequency of ptr outputs [time step]
+   ln_subbas  = .false.     !  Atlantic/Pacific/Indian basins computation (T) or not
 /
 !-----------------------------------------------------------------------
@@ -1161,71 +1187,42 @@
 !!            ***  Observation & Assimilation namelists ***
 !!======================================================================
-!!   namobs       observation and model comparison                      ('key_diaobs')
+!!   namobs       observation and model comparison
 !!   nam_asminc   assimilation increments                               ('key_asminc')
 !!======================================================================
 !
 !-----------------------------------------------------------------------
-&namobs       !  observation usage switch                               ('key_diaobs')
-!-----------------------------------------------------------------------
-   ln_t3d     = .false.    ! Logical switch for T profile observations
-   ln_s3d     = .false.    ! Logical switch for S profile observations
-   ln_ena     = .false.    ! Logical switch for ENACT insitu data set
-   !                       !     ln_cor                  Logical switch for Coriolis insitu data set
-   ln_profb   = .false.    ! Logical switch for feedback insitu data set
-   ln_sla     = .false.    ! Logical switch for SLA observations
-
-   ln_sladt   = .false.    ! Logical switch for AVISO SLA data
-
-   ln_slafb   = .false.    ! Logical switch for feedback SLA data
-                           !     ln_ssh                  Logical switch for SSH observations
-
-   ln_sst     = .false.     ! Logical switch for SST observations
-   ln_reysst  = .false.     !     ln_reysst               Logical switch for Reynolds observations
-   ln_ghrsst  = .false.    !     ln_ghrsst               Logical switch for GHRSST observations      
-
-   ln_sstfb   = .false.    ! Logical switch for feedback SST data
-                           !     ln_sss                  Logical switch for SSS observations
-   ln_seaice  = .false.    ! Logical switch for Sea Ice observations
-                           !     ln_vel3d                Logical switch for velocity observations
-                           !     ln_velavcur             Logical switch for velocity daily av. cur.
-                           !     ln_velhrcur             Logical switch for velocity high freq. cur.
-                           !     ln_velavadcp            Logical switch for velocity daily av. ADCP
-                           !     ln_velhradcp            Logical switch for velocity high freq. ADCP
-                           !     ln_velfb                Logical switch for feedback velocity data
-                           !     ln_grid_global          Global distribtion of observations
-                           !     ln_grid_search_lookup   Logical switch for obs grid search w/lookup table
-                           !     grid_search_file        Grid search lookup file header
-                           !     enactfiles              ENACT input observation file names
-                           !     coriofiles              Coriolis input observation file name
-   !                       ! profbfiles: Profile feedback input observation file name
-   profbfiles = 'profiles_01.nc'
-                           !     ln_profb_enatim         Enact feedback input time setting switch
-                           !     slafilesact             Active SLA input observation file name
-                           !     slafilespas             Passive SLA input observation file name
-   !                       ! slafbfiles: Feedback SLA input observation file name
-   slafbfiles = 'sla_01.nc'
-                           !     sstfiles                GHRSST input observation file name
-   !                       ! sstfbfiles: Feedback SST input observation file name
-   sstfbfiles = 'sst_01.nc'
-                           !     seaicefiles             Sea Ice input observation file names
-   seaicefiles = 'seaice_01.nc'  
-                           !     velavcurfiles           Vel. cur. daily av. input file name
-                           !     velhvcurfiles           Vel. cur. high freq. input file name
-                           !     velavadcpfiles          Vel. ADCP daily av. input file name
-                           !     velhvadcpfiles          Vel. ADCP high freq. input file name
-                           !     velfbfiles              Vel. feedback input observation file name
-                           !     dobsini                 Initial date in window YYYYMMDD.HHMMSS
-                           !     dobsend                 Final date in window YYYYMMDD.HHMMSS
-                           !     n1dint                  Type of vertical interpolation method
-                           !     n2dint                  Type of horizontal interpolation method
-                           !     ln_nea                  Rejection of observations near land switch
-   nmsshc     = 0          ! MSSH correction scheme
-                           !     mdtcorr                 MDT  correction
-                           !     mdtcutoff               MDT cutoff for computed correction
-   ln_altbias = .false.    ! Logical switch for alt bias
-   ln_ignmis  = .true.     ! Logical switch for ignoring missing files
-                           !     endailyavtypes   ENACT daily average types
-   ln_grid_global = .true.
-   ln_grid_search_lookup = .false.
+&namobs       !  observation usage switch
+!-----------------------------------------------------------------------
+   ln_diaobs  = .false.             ! Logical switch for the observation operator
+   ln_t3d     = .false.             ! Logical switch for T profile observations
+   ln_s3d     = .false.             ! Logical switch for S profile observations
+   ln_sla     = .false.             ! Logical switch for SLA observations
+   ln_sst     = .false.             ! Logical switch for SST observations
+   ln_sic     = .false.             ! Logical switch for Sea Ice observations
+   ln_vel3d   = .false.             ! Logical switch for velocity observations
+   ln_altbias = .false.             ! Logical switch for altimeter bias correction
+   ln_nea     = .false.             ! Logical switch for rejection of observations near land
+   ln_grid_global = .true.          ! Logical switch for global distribution of observations
+   ln_grid_search_lookup = .false.  ! Logical switch for obs grid search w/lookup table
+   ln_ignmis  = .true.              ! Logical switch for ignoring missing files
+   ln_s_at_t  = .false.             ! Logical switch for computing model S at T obs if not there
+   ln_sstnight = .false.            ! Logical switch for calculating night-time average for SST obs
+! All of the *files* variables below are arrays. Use namelist_cfg to add more files
+   cn_profbfiles = 'profiles_01.nc'    ! Profile feedback input observation file names
+   cn_slafbfiles = 'sla_01.nc'         ! SLA feedback input observation file names
+   cn_sstfbfiles = 'sst_01.nc'         ! SST feedback input observation file names
+   cn_sicfbfiles = 'sic_01.nc'         ! SIC feedback input observation file names
+   cn_velfbfiles = 'vel_01.nc'         ! Velocity feedback input observation file names
+   cn_altbiasfile = 'altbias.nc'       ! Altimeter bias input file name
+   cn_gridsearchfile = 'gridsearch.nc' ! Grid search file name
+   rn_gridsearchres = 0.5              ! Grid search resolution
+   rn_dobsini = 00010101.000000        ! Initial date in window YYYYMMDD.HHMMSS
+   rn_dobsend = 00010102.000000        ! Final date in window YYYYMMDD.HHMMSS
+   nn_1dint = 0                        ! Type of vertical interpolation method
+   nn_2dint = 0                        ! Type of horizontal interpolation method
+   nn_msshc = 0                        ! MSSH correction scheme
+   rn_mdtcorr = 1.61                   ! MDT  correction
+   rn_mdtcutoff = 65.0                 ! MDT cutoff for computed correction
+   nn_profdavtypes = -1                ! Profile daily average types - array
 /
 !-----------------------------------------------------------------------
