tune_nemo.md

 
 * [Tune NEMO](#tune-nemo)
     * [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) 
@@ -44,72 +42,71 @@ 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-namelist-key"></a>
+========================
+#### Some description of namelist keys
 
-<a name="tune-nemo-vertical-coord"></a>
-===============================
-#### Vertical coordinate
+=====================================
+| **Domain & Run management namelists** keys | Description | tips  | dependency |
+|:---:|:---:|:---:|:---:|
+| 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)  |  | 
+|  | rn_dt  | time step |  divisible by 86400s : .. 900/960/1080/1152/1200/1350/1440/1600/1800..  |
+|  | rn_hmin | -  | Minimum levels nemo could see (tricky for runoff to deal with high resolution config)  |
+| namtsd | ln_tsd_init | | if False,  it will wait for a restart file (if ln_restart T) |
 
 
-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.
 
+TODO
+nn_sbc issue
+rdt & nn_sbc
 
-<a name="tune-nemo-advection-scheme"></a>
-===============================
-#### Advection scheme tracers
 
 
 
 
-###### aht/avt
 
 
+===================================
+| **Surface Boundary Condition namelists** keys | Description | tips  | dependency |
+| namsbc | nn_fsbc | ( timestep * nn_fsbc )./60 = frequency in minutes you prescribed the 1h atmo field interpolated in time )   | for instance if you have 1h hour input frequency (ts=150s/nn_fsbc=8) => each 20 min, nemo will interpolate your input data / better if 15,20,30 ...  | 
 
-#### Advection scheme Momentum
+nn_fsbc
+ln_blk
+ln_traqsr
+ln_dm2dc
+ln_rnf
 
 
+ln_NCAR
+ln_ECMWF
 
+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 
 
-###### ahm/avm
+  * fichier tempe
+  * apply bdy
 
 
+atmospheric pressure forcing
 
 
-<a name="tune-nemo-namelist-key"></a>
-========================
-#### Some description of namelist keys
 
-| 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)  |  | 
-|  | rn_dt  | time step |  divisible by 86400s : .. 900/960/1080/1152/1200/1350/1440/1600/1800..  |
-|  | rn_hmin | -  | Minimum levels nemo could see (tricky for runoff to deal with high resolution config)  |
-| namtsd | ln_tsd_init | | if False,  it will wait for a restart file (if ln_restart T) |
-| namsbc | nn_fsbc | ( timestep * nn_fsbc )./60 = frequency in minutes you prescribed the 1h atmo field interpolated in time )   | for instance if you have 1h hour input frequency (ts=150s/nn_fsbc=8) => each 20 min, nemo will interpolate your input data / better if 15,20,30 ...  | 
+===================================
+| **Lateral boundary condition** keys | Description | tips  | dependency |
 | nambdy | ln_dm2dc    = .false. | | if shortwave inputs frequency <24h  then ln_dm2dc    = .false. |
 | nambdy | ln_tra_dmp=.false. | | if condition "frs" on tracers  : cn_tra ='frs' the same  for "dyn3d" |
 
 
+shlat
+
+ln_full_vel ?
 
 bdy
  * schema flather/ orlanski/ neumann / frs
@@ -118,32 +115,58 @@ bdy avec marées
 
 bdy differentes facon de precrire
 
+tides
 
+====================================
+| **Top/Bottom boundary condition** keys | Description | tips  | dependency |
+| ln_lin |  | | |
+| ln_trabbl | | | |
 
-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 
+====================================
+| **Tracer (T-S) namelists** keys | Description | tips  | dependency |
 
-  * fichier tempe
-  * apply bdy
+eos
 
+Advection scheme tracers
 
-MPI
+aht/avt
 
+ldf
+mle
 
-XIOS
+====================================
+| **Dynamics namelists** keys | Description | tips  | dependency |
 
-atmospheric pressure forcing
-traqsr
+Vertical coordinate :
+
+![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.
+
+Advection scheme momentum
+
+ahm/avm
+
+namdyn_hpg
+
+lateral diffusion 
+
+
+
+
+====================================
+| **Vertical physics** keys | Description | tips  | dependency |
+
+TKE/GLS
+double diffusive mixing
+
+vertical eddy viscosity avm0  / diffusivity avt0
 
 
-ddm (Double diffusive Mixing)
-bbl (bottom boundary layer)
-drag (bottom/top drag coeficient)
-eos (equation of state)
-barotropic timestep