tune_nemo.md

@@ -39,7 +39,8 @@ Normally, common vertical grid is used , if not (for one another config..)
 |  | rn_hmin | -  | tricky for runoff for high resolution config  |
 | namtsd | ln_tsd_init | | if F can be read  reatrt 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 1h hour data input (ts=150s/nn_fsbc=8) => each 20 min,  use of data interpolated / better if 15,20,30 ...  | 
-
+| 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" |
 
 
 <a name="tune-nemo-tuning-config"></a>
@@ -63,13 +64,116 @@ to process tides simulation on namelist_cfg:
   * The total volume correction is not working with tides.  ln_vol=.FALSE.
 
  
+_Update bathy_ :
+
+You will need to update the domain_cfg.nc file.
+2 cases :
+ * if you made a nesting you need to reprocess the NESTING tools first and then DOMAINcfg tools 
+ * if you only create a domain_cfg file from the DOMAINcfg tools (go directly to step 4')
+
+In both cases, you need to need to change the bathymetry file
+
+1 ) From NESTING, update normal zoom from global orca files and a bathy (Here Gebco)
+```console
+&coarse_grid_files
+    parent_coordinate_file = 'coordinates_ORCA12.nc'
+    parent_bathy_level     = ''
+    parent_level_name      = 'mbathy'
+    parent_bathy_meter     = 'bathy_meter_ORCA12.nc'
+    parent_meter_name      = 'Bathymetry'
+    parent_domcfg_out      = 'domain_cfg.nc'
+    parent_jperio          = 4
+/
+
+&bathymetry
+    new_topo = .false.
+    elevation_database = 'GEBCO_2019_2D.nc' !
+    elevation_name     = 'elevation'
+    smoothing          = .true.
+    smoothing_factor   = 0.6
+    ln_agrif_domain    = .false.
+    npt_connect        = 2      ! default = 3
+    npt_copy           = 2      ! default = 2
+    removeclosedseas   = .true.
+    type_bathy_interp  = 1
+    rn_hmin            = -1
+/
+```
+
+then process your nesting, you will have : 
+
+ * 1_coordinates_ORCA12.nc
+ * 1_bathy_meter_ORCA12.nc
+
+2)
+Change values on Bathymetry variable from your bathy_meter file (here : 1_bathy_meter_ORCA12.nc) and rename it on __1_bathy_meter_ORCA12_retoque.nc__ with nco or python scripts
+
+
+3)
+Again on NESTING, 
+```console
+&coarse_grid_files
+    parent_coordinate_file = 'coordinates_ORCA12.nc'
+    parent_bathy_level     = ''
+    parent_level_name      = 'mbathy'
+    parent_bathy_meter     = 'bathy_meter_ORCA12.nc'
+    parent_meter_name      = 'Bathymetry'
+    parent_domcfg_out      = 'domain_cfg.nc'
+    parent_jperio          = 4
+/
+
+&bathymetry
+    new_topo = .true.
+    elevation_database = '1_bathy_meter_ORCA12_retoque.nc' !
+    elevation_name     = 'Bathymetry'
+    smoothing          = .true.
+    smoothing_factor   = 0.6
+    ln_agrif_domain    = .false.
+    npt_connect        = 2      ! default = 3
+    npt_copy           = 2      ! default = 2
+    removeclosedseas   = .true.
+    type_bathy_interp  = 1
+    rn_hmin            = -5
+/
+```
+
+then process your nesting, you will have : 
+
+ * 1_coordinates_ORCA12.nc
+ * 1_bathy_meter_ORCA12.nc
+
+
+4)
+On Domaincfg tools, we use the new bathymetry file, here we can change the rnhmin variable:
+```
+ln -s ../NESTING/1_coordinates_ORCA12.nc coordinates.nc
+ln -s ../NESTING/1_bathy_meter_ORCA12.nc bathy_meter.nc
+```
+```
+!-----------------------------------------------------------------------
+&namdom        !   space and time domain (bathymetry, mesh, timestep)
+!-----------------------------------------------------------------------
+   jphgr_msh   =       0               !  type of horizontal mesh
+   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
+   nn_msh      =       7               !  create (=1) a mesh file or not (=0)
+   rn_hmin     =      -5.              !  min depth of the ocean (>0) or min number of ocean level (<0)
+```
+then process it ./make_domain_cfg.exe 
+you will have the domain_cfg.nc file ....
+
+ 
+4')
+Change the original bathymetry like on step 2) 
+
+
+> **Note** : On DOMAINcfg step, you can modify the rnhmin value, to find which level you need to write (if rnhmin have negative value) look on the meshmask file you have and just search on the gdept_1d or gdept_0.
+
+
+
+
 _Miscellaneous_:
 
-on namelist_cfg:
-  * &nambdy  if condition "frs" on tracers  : cn_tra ='frs'  then  ln_tra_dmp=False   the same  for "dyn3d"
-  * &nambdy  if shortwave inputs frequency <24h  then  &namsbc /   ln_dm2dc    = .false.
-  * &namsbc section / nn_fsbc     = 5         !  frequency of SBC module call  ... to develop ...
-  * time interpolation ... 
 
 
 <a name="tune-nemo-set-diags"></a>