Index: branches/2012/dev_v3_4_STABLE_2012/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/1_namelist
===================================================================
--- branches/2012/dev_v3_4_STABLE_2012/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/1_namelist	(revision 3942)
+++ branches/2012/dev_v3_4_STABLE_2012/NEMOGCM/CONFIG/ORCA2_LIM/EXP00/1_namelist	(revision 3945)
@@ -27,5 +27,5 @@
    cn_exp      = "Agulhas" !  experience name 
    nn_it000    =       1   !  first time step
-   nn_itend    =   10950   !  last  time step
+   nn_itend    =     480   !  last  time step
    nn_date0    =  010101   !  date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
    nn_leapy    =       0   !  Leap year calendar (1) or not (0)
@@ -66,12 +66,25 @@
 &namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
 !-----------------------------------------------------------------------
-   rn_sbot_min =  300.     !  minimum depth of s-bottom surface (>0) (m)
-   rn_sbot_max = 5250.     !  maximum depth of s-bottom surface (= ocean depth) (>0) (m)
-   rn_theta    =    6.0    !  surface control parameter (0<=rn_theta<=20)
-   rn_thetb    =    0.75   !  bottom control parameter  (0<=rn_thetb<= 1)
-   rn_rmax     =    0.15   !  maximum cut-off r-value allowed (0<rn_max<1)
-   ln_s_sigma  = .false.   !  hybrid s-sigma coordinates
-   rn_bb       =    0.8    !  stretching with s-sigma
-   rn_hc       =  150.0    !  critical depth with s-sigma 
+   ln_s_sh94   = .true.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)|
+   ln_s_sf12   = .false.   !  Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the NEMO tanh stretching is applied
+   ln_sigcrit  = .false.   !  use sigma coordinates below critical depth (T) or Z coordinates (F) for Siddorn & Furner stretch
+                           !  stretching coefficients for all functions
+   rn_sbot_min =   10.0    !  minimum depth of s-bottom surface (>0) (m)
+   rn_sbot_max = 7000.0    !  maximum depth of s-bottom surface (= ocean depth) (>0) (m)
+   rn_hc       =  150.0    !  critical depth for transition to stretched coordinates
+                        !!!!!!!  Envelop bathymetry
+   rn_rmax     =    0.3    !  maximum cut-off r-value allowed (0<r_max<1)
+                        !!!!!!!  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   
+                        !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.)
+   rn_alpha    =    4.4    !  stretching with SF12 s-sigma
+   rn_efold    =    0.0    !  efold length scale for transition to stretched coord
+   rn_zs       =    1.0    !  depth of surface grid box
+                           !  bottom cell depth (Zb) is a linear function of water depth Zb = H*a + b
+   rn_zb_a     =    0.024  !  bathymetry scaling factor for calculating Zb
+   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) 
 /
 !-----------------------------------------------------------------------
@@ -101,4 +114,7 @@
    sn_tem  = 'data_1m_potential_temperature_nomask', -1,'votemper',  .true.  , .true., 'yearly'   , ' '      , ' '
    sn_sal  = 'data_1m_salinity_nomask'             , -1,'vosaline',  .true.  , .true., 'yearly'   , ''       , ' '
+   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)
 /
 !!======================================================================
@@ -296,4 +312,38 @@
    rn_alphc    =    0.65   !  compute albedo between two extremes values 
    rn_alphdi   =    0.72   !  (Pyane, 1972)
+/
+!-----------------------------------------------------------------------
+&namberg       !   iceberg parameters
+!-----------------------------------------------------------------------
+      ln_icebergs              = .false.
+      ln_bergdia               = .true.               ! Calculate budgets
+      nn_verbose_level         = 1                    ! Turn on more verbose output if level > 0
+      nn_verbose_write         = 15                   ! Timesteps between verbose messages
+      nn_sample_rate           = 1                    ! Timesteps between sampling for trajectory storage
+                                                      ! 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
+      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
+      rn_mass_scaling          = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1
+                                                      ! thickness of newly calved bergs (m)
+      rn_initial_thickness     = 40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
+      rn_rho_bergs             = 850.                 ! Density of icebergs
+      rn_LoW_ratio             = 1.5                  ! Initial ratio L/W for newly calved icebergs
+      ln_operator_splitting    = .true.               ! Use first order operator splitting for thermodynamics
+      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
+      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
+
+               ! filename ! freq (hours) ! variable ! time interp. ! clim  !'yearly' or ! weights  ! rotation !
+               !          ! (<0  months) !   name   !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing  !
+      sn_icb =  'calving' ,     -1       , 'calvingmask',  .true.      , .true., 'yearly'   , ' '      , ' '
+
+      cn_dir = './'
 /
 
@@ -493,4 +543,5 @@
    ln_traadv_ubs    =  .false.  !  UBS scheme                 
    ln_traadv_qck    =  .false.  !  QUCIKEST scheme                 
+   ln_traadv_msc_ups=  .false.  !  use upstream scheme within muscl
 /
 !-----------------------------------------------------------------------
@@ -884,5 +935,4 @@
 !-----------------------------------------------------------------------
     ln_bkgwri = .false.    !  Logical switch for writing out background state 
-    ln_trjwri = .false.    !  Logical switch for writing out state trajectory
     ln_trainc = .false.    !  Logical switch for applying tracer increments
     ln_dyninc = .false.    !  Logical switch for applying velocity increments
@@ -895,5 +945,4 @@
     nitiaufin = 15         !  Timestep of end of IAU interval in [0,nitend-nit000-1]
     niaufn    = 0          !  Type of IAU weighting function
-    nittrjfrq = 0          !  Frequency of trajectory output for 4D-VAR
     ln_salfix = .false.    !  Logical switch for ensuring that the sa > salfixmin
     salfixmin = -9999      !  Minimum salinity after applying the increments
@@ -923,10 +972,2 @@
    rn_htrmax         =  200.0   ! max. depth of transition range
 /
-!-----------------------------------------------------------------------
-&namtrj ! Handling non-linear trajectory for TAM (output for direct model, input for TAM)
-!-----------------------------------------------------------------------
-    cn_dirtrj   = 'tam_trajectory'   ! prefix for input/ouput files
-    ln_trjhand  = .false.            ! Handling non linear trajectory
-    nn_ittrjfrq = 20                 ! Output/input frequency
-    ln_trj_spl = .false.             ! Handling trajectory at simple precision
-/
