Changeset 12377 for NEMO/trunk/src/OCE/step.F90

Timestamp:

2020-02-12T15:39:06+01:00 (4 years ago)

Author:

acc

Message:

The big one. Merging all 2019 developments from the option 1 branch back onto the trunk.

This changeset reproduces 2019/dev_r11943_MERGE_2019 on the trunk using a 2-URL merge
onto a working copy of the trunk. I.e.:

svn merge --ignore-ancestry \

​svn+ssh://acc@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/NEMO/trunk \
​svn+ssh://acc@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/NEMO/branches/2019/dev_r11943_MERGE_2019 ./

The --ignore-ancestry flag avoids problems that may otherwise arise from the fact that
the merge history been trunk and branch may have been applied in a different order but
care has been taken before this step to ensure that all applicable fixes and updates
are present in the merge branch.

The trunk state just before this step has been branched to releases/release-4.0-HEAD
and that branch has been immediately tagged as releases/release-4.0.2. Any fixes
or additions in response to tickets on 4.0, 4.0.1 or 4.0.2 should be done on
releases/release-4.0-HEAD. From now on future 'point' releases (e.g. 4.0.2) will
remain unchanged with periodic releases as needs demand. Note release-4.0-HEAD is a
transitional naming convention. Future full releases, say 4.2, will have a release-4.2
branch which fulfills this role and the first point release (e.g. 4.2.0) will be made
immediately following the release branch creation.

2020 developments can be started from any trunk revision later than this one.

Location:

NEMO/trunk

Files:

• . (modified) (1 prop)
• src/OCE/step.F90 (modified) (15 diffs)

NEMO/trunk

@@ -3 +3 @@
 ^/utils/build/mk@HEAD         mk
 ^/utils/tools@HEAD            tools
-^/vendors/AGRIF/dev@HEAD      ext/AGRIF
+^/vendors/AGRIF/dev_r11615_ENHANCE-04_namelists_as_internalfiles_agrif@HEAD      ext/AGRIF
 ^/vendors/FCM@HEAD            ext/FCM
 ^/vendors/IOIPSL@HEAD         ext/IOIPSL

@@ -3 +3 @@
 ^/utils/build/mk@HEAD         mk
 ^/utils/tools@HEAD            tools
-^/vendors/AGRIF/dev@HEAD      ext/AGRIF
+^/vendors/AGRIF/dev_r11615_ENHANCE-04_namelists_as_internalfiles_agrif@HEAD      ext/AGRIF
 ^/vendors/FCM@HEAD            ext/FCM
 ^/vendors/IOIPSL@HEAD         ext/IOIPSL

NEMO/trunk/src/OCE/step.F90

@@ -31 +31 @@
    !!             -   !  2015-11  (J. Chanut) free surface simplification (remove filtered free surface)
    !!            4.0  !  2017-05  (G. Madec)  introduction of the vertical physics manager (zdfphy)
+   !!            4.1  !  2019-08  (A. Coward, D. Storkey) rewrite in preparation for new timestepping scheme
    !!----------------------------------------------------------------------
 
@@ -44 +45 @@
 
    PUBLIC   stp   ! called by nemogcm.F90
+
+   !!----------------------------------------------------------------------
+   !! time level indices
+   !!----------------------------------------------------------------------
+   INTEGER, PUBLIC :: Nbb, Nnn, Naa, Nrhs          !! used by nemo_init
 
    !!----------------------------------------------------------------------
@@ -82 +88 @@
 #if defined key_agrif
       kstp = nit000 + Agrif_Nb_Step()
+      Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs   ! agrif_oce module copies of time level indices
       IF( lk_agrif_debug ) THEN
          IF( Agrif_Root() .and. lwp)   WRITE(*,*) '---'
@@ -100 +107 @@
                              
       IF( kstp == nit000 ) THEN                       ! initialize IOM context (must be done after nemo_init for AGRIF+XIOS+OASIS)
-                             CALL iom_init(      cxios_context          )  ! for model grid (including passible AGRIF zoom)
+                             CALL iom_init( cxios_context, ld_closedef=.FALSE. )   ! for model grid (including passible AGRIF zoom)
+         IF( lk_diamlr   )   CALL dia_mlr_iom_init    ! with additional setup for multiple-linear-regression analysis
+                             CALL iom_init_closedef
          IF( ln_crs      )   CALL iom_init( TRIM(cxios_context)//"_crs" )  ! for coarse grid
       ENDIF
@@ -108 +117 @@
 
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-      ! Update external forcing (tides, open boundaries, and surface boundary condition (including sea-ice)
-      !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-      IF( ln_tide    )   CALL sbc_tide( kstp )                   ! update tide potential
-      IF( ln_apr_dyn )   CALL sbc_apr ( kstp )                   ! atmospheric pressure (NB: call before bdy_dta which needs ssh_ib) 
-      IF( ln_bdy     )   CALL bdy_dta ( kstp, kt_offset = +1 )   ! update dynamic & tracer data at open boundaries
-                         CALL sbc     ( kstp )                   ! Sea Boundary Condition (including sea-ice)
+      ! Update external forcing (tides, open boundaries, ice shelf interaction and surface boundary condition (including sea-ice)
+      !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+      IF( ln_tide    )   CALL tide_update( kstp )                     ! update tide potential
+      IF( ln_apr_dyn )   CALL sbc_apr ( kstp )                        ! atmospheric pressure (NB: call before bdy_dta which needs ssh_ib) 
+      IF( ln_bdy     )   CALL bdy_dta ( kstp, Nnn )                   ! update dynamic & tracer data at open boundaries
+      IF( ln_isf     )   CALL isf_stp ( kstp, Nnn )
+                         CALL sbc     ( kstp, Nbb, Nnn )              ! Sea Boundary Condition (including sea-ice)
 
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -119 +129 @@
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
       IF( ln_sto_eos ) CALL sto_par( kstp )          ! Stochastic parameters
-      IF( ln_sto_eos ) CALL sto_pts( tsn  )          ! Random T/S fluctuations
+      IF( ln_sto_eos ) CALL sto_pts( ts(:,:,:,:,Nnn)  )          ! Random T/S fluctuations
 
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -125 +135 @@
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
       !  THERMODYNAMICS
-                         CALL eos_rab( tsb, rab_b )       ! before local thermal/haline expension ratio at T-points
-                         CALL eos_rab( tsn, rab_n )       ! now    local thermal/haline expension ratio at T-points
-                         CALL bn2    ( tsb, rab_b, rn2b ) ! before Brunt-Vaisala frequency
-                         CALL bn2    ( tsn, rab_n, rn2  ) ! now    Brunt-Vaisala frequency
+                         CALL eos_rab( ts(:,:,:,:,Nbb), rab_b, Nnn )       ! before local thermal/haline expension ratio at T-points
+                         CALL eos_rab( ts(:,:,:,:,Nnn), rab_n, Nnn )       ! now    local thermal/haline expension ratio at T-points
+                         CALL bn2    ( ts(:,:,:,:,Nbb), rab_b, rn2b, Nnn ) ! before Brunt-Vaisala frequency
+                         CALL bn2    ( ts(:,:,:,:,Nnn), rab_n, rn2, Nnn  ) ! now    Brunt-Vaisala frequency
 
       !  VERTICAL PHYSICS
-                         CALL zdf_phy( kstp )         ! vertical physics update (top/bot drag, avt, avs, avm + MLD)
+                         CALL zdf_phy( kstp, Nbb, Nnn, Nrhs )   ! vertical physics update (top/bot drag, avt, avs, avm + MLD)
 
       !  LATERAL  PHYSICS
       !
       IF( l_ldfslp ) THEN                             ! slope of lateral mixing
-                         CALL eos( tsb, rhd, gdept_0(:,:,:) )               ! before in situ density
-
-         IF( ln_zps .AND. .NOT. ln_isfcav)                               &
-            &            CALL zps_hde    ( kstp, jpts, tsb, gtsu, gtsv,  &  ! Partial steps: before horizontal gradient
-            &                                          rhd, gru , grv    )  ! of t, s, rd at the last ocean level
-
-         IF( ln_zps .AND.       ln_isfcav)                               &
-            &            CALL zps_hde_isf( kstp, jpts, tsb, gtsu, gtsv, gtui, gtvi,  &  ! Partial steps for top cell (ISF)
-            &                                          rhd, gru , grv , grui, grvi   )  ! of t, s, rd at the first ocean level
+                         CALL eos( ts(:,:,:,:,Nbb), rhd, gdept_0(:,:,:) )               ! before in situ density
+
+         IF( ln_zps .AND. .NOT. ln_isfcav)                                    &
+            &            CALL zps_hde    ( kstp, Nnn, jpts, ts(:,:,:,:,Nbb), gtsu, gtsv,  &  ! Partial steps: before horizontal gradient
+            &                                          rhd, gru , grv    )       ! of t, s, rd at the last ocean level
+
+         IF( ln_zps .AND.       ln_isfcav)                                                &
+            &            CALL zps_hde_isf( kstp, Nnn, jpts, ts(:,:,:,:,Nbb), gtsu, gtsv, gtui, gtvi,  &  ! Partial steps for top cell (ISF)
+            &                                          rhd, gru , grv , grui, grvi   )       ! of t, s, rd at the first ocean level
          IF( ln_traldf_triad ) THEN 
-                         CALL ldf_slp_triad( kstp )                       ! before slope for triad operator
+                         CALL ldf_slp_triad( kstp, Nbb, Nnn )             ! before slope for triad operator
          ELSE     
-                         CALL ldf_slp     ( kstp, rhd, rn2b )             ! before slope for standard operator
+                         CALL ldf_slp     ( kstp, rhd, rn2b, Nbb, Nnn )   ! before slope for standard operator
          ENDIF
       ENDIF
-      !                                                                   ! eddy diffusivity coeff.
-      IF( l_ldftra_time .OR. l_ldfeiv_time )   CALL ldf_tra( kstp )       !       and/or eiv coeff.
-      IF( l_ldfdyn_time                    )   CALL ldf_dyn( kstp )       ! eddy viscosity coeff. 
+      !                                                                        ! eddy diffusivity coeff.
+      IF( l_ldftra_time .OR. l_ldfeiv_time )   CALL ldf_tra( kstp, Nbb, Nnn )  !       and/or eiv coeff.
+      IF( l_ldfdyn_time                    )   CALL ldf_dyn( kstp, Nbb )       ! eddy viscosity coeff. 
+
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
       !  Ocean dynamics : hdiv, ssh, e3, u, v, w
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-                            CALL ssh_nxt       ( kstp )  ! after ssh (includes call to div_hor)
-      IF( .NOT.ln_linssh )  CALL dom_vvl_sf_nxt( kstp )  ! after vertical scale factors 
-                            CALL wzv           ( kstp )  ! now cross-level velocity 
-      IF( ln_zad_Aimp )     CALL wAimp         ( kstp )  ! Adaptive-implicit vertical advection partitioning
-                            CALL eos    ( tsn, rhd, rhop, gdept_n(:,:,:) )  ! now in situ density for hpg computation
+                            CALL ssh_nxt       ( kstp, Nbb, Nnn, ssh, Naa )    ! after ssh (includes call to div_hor)
+      IF( .NOT.ln_linssh )  CALL dom_vvl_sf_nxt( kstp, Nbb, Nnn,      Naa )    ! after vertical scale factors 
+                            CALL wzv           ( kstp, Nbb, Nnn, ww,  Naa )    ! now cross-level velocity 
+      IF( ln_zad_Aimp )     CALL wAimp         ( kstp,      Nnn           )  ! Adaptive-implicit vertical advection partitioning
+                            CALL eos    ( ts(:,:,:,:,Nnn), rhd, rhop, gdept(:,:,:,Nnn) )  ! now in situ density for hpg computation
                             
                             
-                         ua(:,:,:) = 0._wp            ! set dynamics trends to zero
-                         va(:,:,:) = 0._wp
+                         uu(:,:,:,Nrhs) = 0._wp            ! set dynamics trends to zero
+                         vv(:,:,:,Nrhs) = 0._wp
 
       IF(  lk_asminc .AND. ln_asmiau .AND. ln_dyninc )   &
-               &         CALL dyn_asm_inc   ( kstp )  ! apply dynamics assimilation increment
-      IF( ln_bdy     )   CALL bdy_dyn3d_dmp ( kstp )  ! bdy damping trends
+               &         CALL dyn_asm_inc   ( kstp, Nbb, Nnn, uu, vv, Nrhs )  ! apply dynamics assimilation increment
+      IF( ln_bdy     )   CALL bdy_dyn3d_dmp ( kstp, Nbb,      uu, vv, Nrhs )  ! bdy damping trends
 #if defined key_agrif
       IF(.NOT. Agrif_Root())  & 
                &         CALL Agrif_Sponge_dyn        ! momentum sponge
 #endif
-                         CALL dyn_adv       ( kstp )  ! advection (vector or flux form)
-                         CALL dyn_vor       ( kstp )  ! vorticity term including Coriolis
-                         CALL dyn_ldf       ( kstp )  ! lateral mixing
-      IF( ln_zdfosm  )   CALL dyn_osm       ( kstp )  ! OSMOSIS non-local velocity fluxes
-                         CALL dyn_hpg       ( kstp )  ! horizontal gradient of Hydrostatic pressure
-                         CALL dyn_spg       ( kstp )  ! surface pressure gradient
-
-                                                      ! With split-explicit free surface, since now transports have been updated and ssha as well
+                         CALL dyn_adv( kstp, Nbb, Nnn      , uu, vv, Nrhs )  ! advection (VF or FF)   ==> RHS
+                         CALL dyn_vor( kstp,      Nnn      , uu, vv, Nrhs )  ! vorticity              ==> RHS
+                         CALL dyn_ldf( kstp, Nbb, Nnn      , uu, vv, Nrhs )  ! lateral mixing
+      IF( ln_zdfosm  )   CALL dyn_osm( kstp,      Nnn      , uu, vv, Nrhs )  ! OSMOSIS non-local velocity fluxes ==> RHS
+                         CALL dyn_hpg( kstp,      Nnn      , uu, vv, Nrhs )  ! horizontal gradient of Hydrostatic pressure
+                         CALL dyn_spg( kstp, Nbb, Nnn, Nrhs, uu, vv, ssh, uu_b, vv_b, Naa )  ! surface pressure gradient
+
+                                                      ! With split-explicit free surface, since now transports have been updated and ssh(:,:,Nrhs) as well
       IF( ln_dynspg_ts ) THEN                         ! vertical scale factors and vertical velocity need to be updated
-                            CALL div_hor    ( kstp )              ! Horizontal divergence  (2nd call in time-split case)
-         IF(.NOT.ln_linssh) CALL dom_vvl_sf_nxt( kstp, kcall=2 )  ! after vertical scale factors (update depth average component)
-      ENDIF
-                            CALL dyn_zdf    ( kstp )  ! vertical diffusion
-      IF( ln_dynspg_ts ) THEN                         ! vertical scale factors and vertical velocity need to be updated
-                            CALL wzv        ( kstp )              ! now cross-level velocity 
-         IF( ln_zad_Aimp )  CALL wAimp      ( kstp )  ! Adaptive-implicit vertical advection partitioning
+                            CALL div_hor       ( kstp, Nbb, Nnn )                ! Horizontal divergence  (2nd call in time-split case)
+         IF(.NOT.ln_linssh) CALL dom_vvl_sf_nxt( kstp, Nbb, Nnn, Naa, kcall=2 )  ! after vertical scale factors (update depth average component)
+      ENDIF
+                            CALL dyn_zdf    ( kstp, Nbb, Nnn, Nrhs, uu, vv, Naa  )  ! vertical diffusion
+      IF( ln_dynspg_ts ) THEN                                                       ! vertical scale factors and vertical velocity need to be updated
+                            CALL wzv        ( kstp, Nbb, Nnn, ww, Naa )             ! now cross-level velocity 
+         IF( ln_zad_Aimp )  CALL wAimp      ( kstp,      Nnn )                      ! Adaptive-implicit vertical advection partitioning
       ENDIF
       
@@ -197 +208 @@
       ! cool skin
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<      
-      IF ( ln_diurnal )  CALL stp_diurnal( kstp )
+      IF ( ln_diurnal )  CALL diurnal_layers( kstp )
       
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
       ! diagnostics and outputs
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-      IF( ln_floats  )   CALL flo_stp ( kstp )        ! drifting Floats
-      IF( ln_diacfl  )   CALL dia_cfl ( kstp )        ! Courant number diagnostics
-                         CALL dia_hth ( kstp )        ! Thermocline depth (20 degres isotherm depth)
-      IF( ln_diadct  )   CALL dia_dct ( kstp )        ! Transports
-                         CALL dia_ar5 ( kstp )        ! ar5 diag
-      IF( ln_diaptr  )   CALL dia_ptr                 ! Poleward adv/ldf TRansports diagnostics
-      IF( ln_diaharm )   CALL dia_harm( kstp )        ! Tidal harmonic analysis
-                         CALL dia_wri ( kstp )        ! ocean model: outputs
-      !
-      IF( ln_crs     )   CALL crs_fld       ( kstp )  ! ocean model: online field coarsening & output
+      IF( ln_floats  )   CALL flo_stp   ( kstp, Nbb, Nnn )      ! drifting Floats
+      IF( ln_diacfl  )   CALL dia_cfl   ( kstp,      Nnn )      ! Courant number diagnostics
+                         CALL dia_hth   ( kstp,      Nnn )      ! Thermocline depth (20 degres isotherm depth)
+      IF( ln_diadct  )   CALL dia_dct   ( kstp,      Nnn )      ! Transports
+                         CALL dia_ar5   ( kstp,      Nnn )      ! ar5 diag
+                         CALL dia_ptr   ( kstp,      Nnn )      ! Poleward adv/ldf TRansports diagnostics
+                         CALL dia_wri   ( kstp,      Nnn )      ! ocean model: outputs
+      IF( ln_crs     )   CALL crs_fld   ( kstp,      Nnn )      ! ocean model: online field coarsening & output
+      IF( lk_diadetide ) CALL dia_detide( kstp )                ! Weights computation for daily detiding of model diagnostics
+      IF( lk_diamlr  )   CALL dia_mlr                           ! Update time used in multiple-linear-regression analysis
       
 #if defined key_top
@@ -217 +228 @@
       ! Passive Tracer Model
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-                         CALL trc_stp       ( kstp )  ! time-stepping
+                         CALL trc_stp       ( kstp, Nbb, Nnn, Nrhs, Naa )  ! time-stepping
 #endif
 
@@ -223 +234 @@
       ! Active tracers                              
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-                         tsa(:,:,:,:) = 0._wp         ! set tracer trends to zero
+                         ts(:,:,:,:,Nrhs) = 0._wp         ! set tracer trends to zero
 
       IF(  lk_asminc .AND. ln_asmiau .AND. &
-         & ln_trainc )   CALL tra_asm_inc   ( kstp )  ! apply tracer assimilation increment
-                         CALL tra_sbc       ( kstp )  ! surface boundary condition
-      IF( ln_traqsr  )   CALL tra_qsr       ( kstp )  ! penetrative solar radiation qsr
-      IF( ln_trabbc  )   CALL tra_bbc       ( kstp )  ! bottom heat flux
-      IF( ln_trabbl  )   CALL tra_bbl       ( kstp )  ! advective (and/or diffusive) bottom boundary layer scheme
-      IF( ln_tradmp  )   CALL tra_dmp       ( kstp )  ! internal damping trends
-      IF( ln_bdy     )   CALL bdy_tra_dmp   ( kstp )  ! bdy damping trends
+         & ln_trainc )   CALL tra_asm_inc( kstp, Nbb, Nnn, ts, Nrhs )  ! apply tracer assimilation increment
+                         CALL tra_sbc    ( kstp,      Nnn, ts, Nrhs )  ! surface boundary condition
+      IF( ln_traqsr  )   CALL tra_qsr    ( kstp,      Nnn, ts, Nrhs )  ! penetrative solar radiation qsr
+      IF( ln_isf     )   CALL tra_isf    ( kstp,      Nnn, ts, Nrhs )  ! ice shelf heat flux
+      IF( ln_trabbc  )   CALL tra_bbc    ( kstp,      Nnn, ts, Nrhs )  ! bottom heat flux
+      IF( ln_trabbl  )   CALL tra_bbl    ( kstp, Nbb, Nnn, ts, Nrhs )  ! advective (and/or diffusive) bottom boundary layer scheme
+      IF( ln_tradmp  )   CALL tra_dmp    ( kstp, Nbb, Nnn, ts, Nrhs )  ! internal damping trends
+      IF( ln_bdy     )   CALL bdy_tra_dmp( kstp, Nbb,      ts, Nrhs )  ! bdy damping trends
 #if defined key_agrif
       IF(.NOT. Agrif_Root())  & 
                &         CALL Agrif_Sponge_tra        ! tracers sponge
 #endif
-                         CALL tra_adv       ( kstp )  ! horizontal & vertical advection
-      IF( ln_zdfosm  )   CALL tra_osm       ( kstp )  ! OSMOSIS non-local tracer fluxes
+                         CALL tra_adv    ( kstp, Nbb, Nnn, ts, Nrhs )  ! hor. + vert. advection ==> RHS
+      IF( ln_zdfosm  )   CALL tra_osm    ( kstp,      Nnn, ts, Nrhs )  ! OSMOSIS non-local tracer fluxes ==> RHS
       IF( lrst_oce .AND. ln_zdfosm ) &
-           &             CALL osm_rst( kstp, 'WRITE' )! write OSMOSIS outputs + wn (so must do here) to restarts
-                         CALL tra_ldf       ( kstp )  ! lateral mixing
-
-                         CALL tra_zdf       ( kstp )  ! vertical mixing and after tracer fields
-      IF( ln_zdfnpc  )   CALL tra_npc       ( kstp )  ! update after fields by non-penetrative convection
-
-      !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-      ! Set boundary conditions and Swap
+           &             CALL osm_rst    ( kstp,      Nnn, 'WRITE'  )  ! write OSMOSIS outputs + ww (so must do here) to restarts
+                         CALL tra_ldf    ( kstp, Nbb, Nnn, ts, Nrhs )  ! lateral mixing
+
+                         CALL tra_zdf    ( kstp, Nbb, Nnn, Nrhs, ts, Naa  )  ! vertical mixing and after tracer fields
+      IF( ln_zdfnpc  )   CALL tra_npc    ( kstp,      Nnn, Nrhs, ts, Naa  )  ! update after fields by non-penetrative convection
+
+      !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+      ! Set boundary conditions, time filter and swap time levels
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 !!jc1: For agrif, it would be much better to finalize tracers/momentum here (e.g. bdy conditions) and move the swap 
@@ -262 +274 @@
 !!    place.
 !! 
-!!jc2: dynnxt must be the latest call. e3t_b are indeed updated in that routine
-                         CALL tra_nxt       ( kstp )  ! finalize (bcs) tracer fields at next time step and swap
-                         CALL dyn_nxt       ( kstp )  ! finalize (bcs) velocities at next time step and swap (always called after tra_nxt)
-                         CALL ssh_swp       ( kstp )  ! swap of sea surface height
-      IF(.NOT.ln_linssh) CALL dom_vvl_sf_swp( kstp )  ! swap of vertical scale factors
-      !
-      IF( ln_diahsb  )   CALL dia_hsb       ( kstp )  ! - ML - global conservation diagnostics
+!!jc2: dynnxt must be the latest call. e3t(:,:,:,Nbb) are indeed updated in that routine
+                         CALL tra_atf       ( kstp, Nbb, Nnn, Naa, ts )                      ! time filtering of "now" tracer arrays
+                         CALL dyn_atf       ( kstp, Nbb, Nnn, Naa, uu, vv, e3t, e3u, e3v  )  ! time filtering of "now" velocities and scale factors
+                         CALL ssh_atf       ( kstp, Nbb, Nnn, Naa, ssh )                     ! time filtering of "now" sea surface height
+      !
+      ! Swap time levels
+      Nrhs = Nbb
+      Nbb = Nnn
+      Nnn = Naa
+      Naa = Nrhs
+      !
+      IF(.NOT.ln_linssh) CALL dom_vvl_sf_update( kstp, Nbb, Nnn, Naa )  ! recompute vertical scale factors
+      !
+      IF( ln_diahsb  )   CALL dia_hsb       ( kstp, Nbb, Nnn )  ! - ML - global conservation diagnostics
 
 !!gm : This does not only concern the dynamics ==>>> add a new title
@@ -275 +294 @@
 !!jc: That would be better, but see comment above
 !!
-      IF( lrst_oce   )   CALL rst_write    ( kstp )   ! write output ocean restart file
+      IF( lrst_oce   )   CALL rst_write    ( kstp, Nbb, Nnn )   ! write output ocean restart file
       IF( ln_sto_eos )   CALL sto_rst_write( kstp )   ! write restart file for stochastic parameters
 
@@ -282 +301 @@
       ! AGRIF
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<      
-                         CALL Agrif_Integrate_ChildGrids( stp )  ! allows to finish all the Child Grids before updating
-
-                         IF( Agrif_NbStepint() == 0 ) CALL Agrif_update_all( ) ! Update all components
-#endif
-      IF( ln_diaobs  )   CALL dia_obs      ( kstp )      ! obs-minus-model (assimilation) diagnostics (call after dynamics update)
+                         Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs      ! agrif_oce module copies of time level indices
+                         CALL Agrif_Integrate_ChildGrids( stp )       ! allows to finish all the Child Grids before updating
+
+                         IF( Agrif_NbStepint() == 0 ) THEN
+                            CALL Agrif_update_all( )                  ! Update all components
+                         ENDIF
+#endif
+      IF( ln_diaobs  )   CALL dia_obs      ( kstp, Nnn )      ! obs-minus-model (assimilation) diagnostics (call after dynamics update)
 
       !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
       ! Control
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-                         CALL stp_ctl      ( kstp, indic )
+                         CALL stp_ctl      ( kstp, Nbb, Nnn, indic )
                          
       IF( kstp == nit000 ) THEN                          ! 1st time step only
@@ -303 +325 @@
       !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 !!gm why lk_oasis and not lk_cpl ????
-      IF( lk_oasis   )   CALL sbc_cpl_snd( kstp )     ! coupled mode : field exchanges
+      IF( lk_oasis   )   CALL sbc_cpl_snd( kstp, Nbb, Nnn )        ! coupled mode : field exchanges
       !
 #if defined key_iomput
@@ -316 +338 @@
       !
    END SUBROUTINE stp
-   
+   !
    !!======================================================================
 END MODULE step

@@ -3 +3 @@
 ^/utils/build/mk@HEAD         mk
 ^/utils/tools@HEAD            tools
-^/vendors/AGRIF/dev@HEAD      ext/AGRIF
+^/vendors/AGRIF/dev_r11615_ENHANCE-04_namelists_as_internalfiles_agrif@HEAD      ext/AGRIF
 ^/vendors/FCM@HEAD            ext/FCM
 ^/vendors/IOIPSL@HEAD         ext/IOIPSL