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2. Correct the nest bathymetry and update 1_domain_cfg.nc
External dataset bathymetry is interpolated on the nest grid with a classic bilinear interpolation. Thus, mismatches with the coastlines can occur. In order to refine the coaslines, you can download the BMG tool from IFREMER (https://mars3d.ifremer.fr/Les-outils/BathyMeshGridTOOLS) which is very useful to refine the bathymetry.
*Bathymetry in the bay of mont Saint Michel, before (top) and after (bottom) update*
- Follow the steps
1: *Download bmg tool, or load bmg module on mercator px:
module load bmg/bmg-5.0
2: The tool is not maintained anymore but remains useful. It requires the data to be formatted a certain way to work. The script SCRIPT HERE is meant to create the coordinate file and the bathymetry file which are needed by BMG from the DOMAINCFG
./make_domaincfg_compatible_BMG.sh DOMAIN_CFG_FILE_NAME OUT_COORD_FILE_NAME OUT_BATHY_FILE_NAME
- Download a coastline file, of untar the GSHHG coastline file here.
3: Run CheckBMG:
CheckBMG
4: *Go to 'files', then 'open files'. Select 'NEMO' as 'grid file format'. Then select the file OUT_COORD_FILE_NAME for the NEMO coordinates files, and OUT_BATHY_FILE_NAME for the bathymetry, and the .line file as coastline file.
5: have fun updating the bathymetry!
Nb: depending on the bathymetry source, one might want to also add the tidal amplitude to the bathymetry (see IMMERSE Deliverable 6.1)
- Run the domaincfg tool once again while reading the new bathymetry file created at last step, so with the following parameters:
ln_read_cfg = .false. ! Read from a domain_cfg file
nn_bathy = 1 ! = 0 compute analyticaly
! = 1 read the bathymetry file
! = 2 compute from external bathymetry (should be on a regular grid)
! = 3 compute from parent (if "key_agrif")
cn_topo = 'OUT_BATHY_FILE_NAME' ! Name of the bathymetry file
cn_bath = 'Bathymetry'
cn_lon = 'glamt'
cn_lat = 'gphit'
- At this step, you will have created both parent and child coordinate files domain_cfg.nc and 1_domain_cfg.nc respectively.