Index: branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/SHARED/1_namelist_ref
===================================================================
--- branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/SHARED/1_namelist_ref	(revision 4020)
+++ branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/SHARED/1_namelist_ref	(revision 4025)
@@ -64,4 +64,64 @@
                                        !  = 5 North fold F-point pivot
                                        !  = 6 cyclic East-West AND North fold F-point pivot
+/
+!!======================================================================
+!!                      ***  Domain namelists  ***
+!!======================================================================
+!!   namzgr       vertical coordinate
+!!   namzgr_sco   s-coordinate or hybrid z-s-coordinate
+!!   namdom       space and time domain (bathymetry, mesh, timestep)
+!!   namtsd       data: temperature & salinity
+!!======================================================================
+!
+!-----------------------------------------------------------------------
+&namzgr        !   vertical coordinate
+!-----------------------------------------------------------------------
+   ln_zco      = .false.   !  z-coordinate - full    steps   (T/F)      ("key_zco" may also be defined)
+   ln_zps      = .true.    !  z-coordinate - partial steps   (T/F)
+   ln_sco      = .false.   !  s- or hybrid z-s-coordinate    (T/F)
+/
+!-----------------------------------------------------------------------
+&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
+!-----------------------------------------------------------------------
+   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) 
+/
+!-----------------------------------------------------------------------
+&namdom        !   space and time domain (bathymetry, mesh, timestep)
+!-----------------------------------------------------------------------
+   nn_bathy    =    1      !  compute (=0) or read (=1) the bathymetry file
+   nn_closea    =   0      !  remove (=0) or keep (=1) closed seas and lakes (ORCA)
+   nn_msh      =    0      !  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
+   rn_e3zps_rat=    0.1    !  rn_e3zps_min and rn_e3zps_rat*e3t, with 0<rn_e3zps_rat<1
+                           !
+   rn_rdt      = 5760.     !  time step for the dynamics (and tracer if nn_acc=0)
+   nn_baro     =   64      !  number of barotropic time step            ("key_dynspg_ts")
+   rn_atfp     =    0.1    !  asselin time filter parameter
+   nn_acc      =    0      !  acceleration of convergence : =1      used, rdt < rdttra(k)
+                                 !                          =0, not used, rdt = rdttra
+   rn_rdtmin   = 28800.          !  minimum time step on tracers (used if nn_acc=1)
+   rn_rdtmax   = 28800.          !  maximum time step on tracers (used if nn_acc=1)
+   rn_rdth     =  800.           !  depth variation of tracer time step  (used if nn_acc=1)
    jphgr_msh   =       0               !  type of horizontal mesh
                                        !  = 0 curvilinear coordinate on the sphere read in coordinate.nc
@@ -87,64 +147,4 @@
    ppkth2      =       48.029893720000 !
    ppacr2      =       13.000000000000 !
-/
-!!======================================================================
-!!                      ***  Domain namelists  ***
-!!======================================================================
-!!   namzgr       vertical coordinate
-!!   namzgr_sco   s-coordinate or hybrid z-s-coordinate
-!!   namdom       space and time domain (bathymetry, mesh, timestep)
-!!   namtsd       data: temperature & salinity
-!!======================================================================
-!
-!-----------------------------------------------------------------------
-&namzgr        !   vertical coordinate
-!-----------------------------------------------------------------------
-   ln_zco      = .false.   !  z-coordinate - full    steps   (T/F)      ("key_zco" may also be defined)
-   ln_zps      = .true.    !  z-coordinate - partial steps   (T/F)
-   ln_sco      = .false.   !  s- or hybrid z-s-coordinate    (T/F)
-/
-!-----------------------------------------------------------------------
-&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate
-!-----------------------------------------------------------------------
-   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) 
-/
-!-----------------------------------------------------------------------
-&namdom        !   space and time domain (bathymetry, mesh, timestep)
-!-----------------------------------------------------------------------
-   nn_bathy    =    1      !  compute (=0) or read (=1) the bathymetry file
-   nn_closea    =   0      !  remove (=0) or keep (=1) closed seas and lakes (ORCA)
-   nn_msh      =    0      !  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
-   rn_e3zps_rat=    0.1    !  rn_e3zps_min and rn_e3zps_rat*e3t, with 0<rn_e3zps_rat<1
-                           !
-   rn_rdt      = 5760.     !  time step for the dynamics (and tracer if nn_acc=0)
-   nn_baro     =   64      !  number of barotropic time step            ("key_dynspg_ts")
-   rn_atfp     =    0.1    !  asselin time filter parameter
-   nn_acc      =    0      !  acceleration of convergence : =1      used, rdt < rdttra(k)
-                                 !                          =0, not used, rdt = rdttra
-   rn_rdtmin   = 28800.          !  minimum time step on tracers (used if nn_acc=1)
-   rn_rdtmax   = 28800.          !  maximum time step on tracers (used if nn_acc=1)
-   rn_rdth     =  800.           !  depth variation of tracer time step  (used if nn_acc=1)
 /
 !-----------------------------------------------------------------------
Index: branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/cfg.txt
===================================================================
--- branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/cfg.txt	(revision 4020)
+++ branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/cfg.txt	(revision 4025)
@@ -3,5 +3,4 @@
 GYRE_BFM OPA_SRC TOP_SRC
 GYRE OPA_SRC
-ORCA2_LIM OPA_SRC LIM_SRC_2 NST_SRC
 AMM12 OPA_SRC
 ORCA2_SAS_LIM OPA_SRC SAS_SRC LIM_SRC_2 NST_SRC
@@ -10,3 +9,4 @@
 GYRE_PISCES OPA_SRC TOP_SRC
 ORCA2_LIM_CFC_C14b OPA_SRC LIM_SRC_2 NST_SRC TOP_SRC
+ORCA2_LIM OPA_SRC LIM_SRC_2 NST_SRC
 AGRIF OPA_SRC LIM_SRC_2 NST_SRC
Index: branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/NST_SRC/agrif_user.F90
===================================================================
--- branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/NST_SRC/agrif_user.F90	(revision 4020)
+++ branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/NST_SRC/agrif_user.F90	(revision 4025)
@@ -31,4 +31,9 @@
       jpi     = ( jpiglo-2*jpreci + (jpni-1+0) ) / jpni + 2*jpreci
       jpj     = ( jpjglo-2*jprecj + (jpnj-1+0) ) / jpnj + 2*jprecj
+      jpk     = jpkdta 
+      jpim1   = jpi-1 
+      jpjm1   = jpj-1 
+      jpkm1   = jpk-1                                         
+      jpij    = jpi*jpj 
       jpidta  = jpiglo
       jpjdta  = jpjglo
@@ -67,4 +72,5 @@
       ENDIF
    ENDIF
+PRINT *, " cp_cfg = ",cp_cfg," jp_cfg= ", jp_cfg
    ! Specific fine grid Initializations
    ! no tracer damping on fine grids
Index: branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90
===================================================================
--- branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90	(revision 4020)
+++ branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90	(revision 4025)
@@ -504,22 +504,4 @@
          WRITE(numout,*) '      left bottom j index of the zoom (in data domain) jpizoom = ', jpjzoom
          WRITE(numout,*) '      lateral cond. type (between 0 and 6) jperio = ', jperio   
-         WRITE(numout,*) '      type of horizontal mesh jphgr_msh           = ', jphgr_msh
-         WRITE(numout,*) '      longitude of first raw and column T-point ppglam0 = ', ppglam0
-         WRITE(numout,*) '      latitude  of first raw and column T-point ppgphi0 = ', ppgphi0
-         WRITE(numout,*) '      zonal      grid-spacing (degrees) ppe1_deg        = ', ppe1_deg
-         WRITE(numout,*) '      meridional grid-spacing (degrees) ppe2_deg        = ', ppe2_deg
-         WRITE(numout,*) '      zonal      grid-spacing (degrees) ppe1_m          = ', ppe1_m
-         WRITE(numout,*) '      meridional grid-spacing (degrees) ppe2_m          = ', ppe2_m
-         WRITE(numout,*) '      ORCA r4, r2 and r05 coefficients  ppsur           = ', ppsur
-         WRITE(numout,*) '                                        ppa0            = ', ppa0
-         WRITE(numout,*) '                                        ppa1            = ', ppa1
-         WRITE(numout,*) '                                        ppkth           = ', ppkth
-         WRITE(numout,*) '                                        ppacr           = ', ppacr
-         WRITE(numout,*) '      Minimum vertical spacing ppdzmin                  = ', ppdzmin
-         WRITE(numout,*) '      Maximum depth pphmax                              = ', pphmax
-         WRITE(numout,*) '      Use double tanf function for vertical coordinates ldbletanh = ', ldbletanh
-         WRITE(numout,*) '      Double tanh function parameters ppa2              = ', ppa2
-         WRITE(numout,*) '                                      ppkth2            = ', ppkth2
-         WRITE(numout,*) '                                      ppacr2            = ', ppacr2
       ENDIF
       !                             ! Parameter control
