tune_nemo.md

 
 * [Tune NEMO](#tune-nemo)
-    * [Vertical grid](#tune-nemo-vertical-grid)
+    * [Build grid](#tune-nemo-build-grid)
+    * [Time step](#tune-nemo-time-step)
+    * [Vertical coordinate](#tune-nemo-vertical-coord)
     * [Namelist key](#tune-nemo-namelist-key)
     * [Tuning config](#tune-nemo-tuning-config)
     * [Set diags](#tune-nemo-set-diags) 
@@ -9,20 +11,85 @@
 
 <a name="tune-nemo"></a>
 ===============================
-## Vertical grid
+## Tune Nemo
+
+<a name="tune-nemo-build-grid"></a>
+===============================
+#### Build the grid
 
 
-Here we show a view of ORCA2/ORCA025 vertical grid with depth* and vertical scale factor e3*
+Most of our configuration are designed using parameters from original ORCA configuration to build our grid.
+
+Here we show a view of ORCA2/ORCA025 vertical grid with depth and vertical scale factor e3
 
 ![Depth grid (NTATL025-SARG)](images/plot_depth_ORCA.png)
 
-Normally, vertical grid from ORCA family is used.  
 
 
+Partial step :
+when using z coordinate, we have a problem with depth, in contrast to the sigma coordinate which fit the change of bottom topography. 
+Here, we let the model to vary the scale factor e3t at the bottom so that it can see the variations of fine reliefs, we insert a ratio max, a threshold which gives the percentage of "relief" present in the last mesh.
 
-<a name="tune-nemo"></a>
+ln_zps      = .true.  
+rn_e3zps_min=      25.              !  partial step thickness is set larger than the minimum of
+rn_e3zps_rat=       0.2             !  rn_e3zps_min and rn_e3zps_rat * e3t, with 0 < rn_e3zps_rat < 1
+
+
+
+Min depth viewed by the model. 
+In case of Tidal cycles, it 's a key parameter to increase to prevent model blowup
+
+rn_hmin = -3  ! min depth of the ocean (>0) or min number of ocean level (<0)
+
+
+
+
+<a name="tune-nemo-time-step"></a>
+===============================
+#### Time step
+
+
+TODO
+nn_sbc issue
+rdt & nn_sbc
+
+
+
+<a name="tune-nemo-vertical-coord"></a>
 ===============================
-## Tune NEMO
+#### Vertical coordinate
+
+
+Vertical grid :
+
+![coordinate](images/zstar_coord.png) [ from Nemo book 4.2 Chapter1 Model basics ]
+a) Z coordinate with linear free surface
+ln_vvl_layer  = .true.  /  ln_linssh   = .true.
+b) Z coordinate with non linear free surface
+ln_vvl_layer  = .true.  /  ln_linssh   = .false.
+c) Zstar coordinate 
+ln_vvl_zstar  = .true.
+
+
+<a name="tune-nemo-advection-scheme"></a>
+===============================
+#### Advection scheme tracers
+
+
+
+
+###### aht/avt
+
+
+
+#### Advection scheme Momentum
+
+
+
+
+###### ahm/avm
+
+
 
 
 <a name="tune-nemo-namelist-key"></a>
@@ -31,6 +98,7 @@ Normally, vertical grid from ORCA family is used.
 
 | section available | some keys | Description / tips  | dependency |
 |:---:|:---:|:---:|:---:|
+| **  Domain & Run management namelists  ** | 
 | namrun | nn_rstctl | 2: read the date on restart file | |
 |         | ln_rstart | T / F |  |  
 | namdom | ln_linssh | linear free surface :  e3 before, now and after are set equal one for all, and we use exactly the same calculation as in non-linear case (except that update of e3 at each time-step is by-passed)  |  | 
@@ -42,11 +110,42 @@ Normally, vertical grid from ORCA family is used.
 | nambdy | ln_tra_dmp=.false. | | if condition "frs" on tracers  : cn_tra ='frs' the same  for "dyn3d" |
 
 
-rappel 
+
+bdy
+ * schema flather/ orlanski/ neumann / frs
+ * (2 facon)
 bdy avec marées
+
 bdy differentes facon de precrire
 
+
+
 runoff
+runoffs (modif a faire ds namelist ou code ?)
+  * mouth mixing
+  * fichier depths
+      attention qd on utilise depths.nc en entree, il doit etre generer avec le mm nombre de procs que la simu lancee 
+
+  * fichier tempe
+  * apply bdy
+
+
+MPI
+
+
+XIOS
+
+atmospheric pressure forcing
+traqsr
+
+
+ddm (Double diffusive Mixing)
+bbl (bottom boundary layer)
+drag (bottom/top drag coeficient)
+eos (equation of state)
+barotropic timestep
+
+
 
 
 <a name="tune-nemo-tuning-config"></a>
@@ -68,7 +167,11 @@ to process tides simulation on namelist_cfg:
   * variable vertical coordinate / &nam_vvl  / *zstar* ln_vvl_zstar = T 
   * Hydrostatic pressure gradient option / &namdyn_hpg / ln_hpg_sco  = .true.   !  s-coordinate (standard jacobian formulation)
   * The total volume correction is not working with tides.  ln_vol=.FALSE.
+  * volctl = 0 (no check volume correction)
   * rajout bdy line
+  * (25h mean daily)
+  * ln_bdytide_2ddta =T  if you  prescribe 2d file
+
 
 _Update bathy_ :
 
@@ -180,10 +283,6 @@ and then process your domaincfg binary
 
 
 
-_Miscellaneous_:
-
-TODO
-
 <a name="tune-nemo-set-diags"></a>    
 ========================  
 #### Set diagnostics 
@@ -207,6 +306,10 @@ _Trends 3D_:
 
 _Tides Diags_:
 
+
+   dia25h & diaharm si tide actif
+   diaharm nitend
+
    activation harmonic analysis of tidal constituents
 
      a) on namelist_cfg : &nam_diaharm section :