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tbrivoal edited this page Oct 25, 2022 · 25 revisions

HOW TO CREATE A NESTED CONFIGURATION (eNEATL36 + BIZoo case)

This wiki is a guide to create a nested configuration with one nest. This is complementary to the IMMERSE deliverable 6.1 (available here : https://github.com/immerse-project/eNEATL36-BIzoo_Demonstator/blob/main/DOC/PDFs/RAPPORT_IMMERSE_D6p1.pdf), which contains many additional informations. In particular, we recommend to read the part 'II.C : Setup of the nested configuration' of the deliverable.

See also the AGRIF user guide for NEMO4.X versions: https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/guide/html/zooms.html

1. Create the NEMO4.X coordinate files for both parent and child grid with emodnet

A. Retrieve emodnet bathymetry

Step 1 : interpolate tiles on the full emodnet grid with 1_interp_tiles_on_full_emodnet.sh

Step 2 : merge tiles with 2_merge_tiles_2018.py

  • At this point, you should have a netcdf file with the emodnet bathymetry bathy_emodnet_on_EMODNET_2018.nc

B. Create the parent domain_cfg.nc file

NEMO4.X versions now need a file domain_cfg.nc that contains the coordinates of the configuration. The first step is to create it for the parent configuration only (e.g: eNEATL36)

  • use the DOMAINCFG tool in NEMODIR/tools/DOMAINcfg, compiled without key_agrif

C. Create AGRIF_FixedGrids.in file

The AGRIF_FixedGrids.in file contains the information about the position of the nest in the parent grid. The file should contain at least three lines (for 1 zoom, and more if there is several nests) such as (for the BIZoo nest) :

1
220 1073 350 1245 3 3 3
0

The first line indicates the number of zooms (1). The second line contains the starting and ending indices in both directions on the root grid (imin=220 imax=1073 jmin=350 jmax=1245) followed by the space and time refinement factors (3 3 3). The last line is the number of child grid nested in the refined region (0). A more complex example with telescoping grids can be found below and in the AGRIF_DEMO reference configuration directory.

D. First creation of the domain_cfg.nc files for both parent and child grids

  • First, Compile the DOMAINCFG tool with the cpp key 'key_agrif' added in cpp_DOMAINcfg.fcm file
  • Then, run the DOMAINCFG tool

To run the tool with agrif, you should have one namelist per grid: in our case, one namelist 'namelist_cfg' for the parent grid, and another one 1_namelist_cfg for the child grid

  • To do this, a tool is available "SHOW WHERE" : make_namelist.py, the tool creates both namelists.

  • Then, you need to update some parameters of the namelist. One of the most important is nn_bathy=2 if you want the bathymetry to be generated from an external bathymetry dataset such as emodnet, nn_bathy=1 if you already have the bathymetry file on the nest grid and nn_bathy=3 otherwise. In our case, with emodnet:

    ln_read_cfg = .false. ! Read from a domain_cfg file nn_bathy = 2 ! = 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 = 'emodNET_2018.nc' ! Name of the bathymetry file cn_bath = 'bathymetry' ! Name of the bathymetry variable in cn_topo cn_lon = 'lon' ! Name of longitude in cn_topo cn_lat = 'lat' ! Name of latitude in cn_topo

  • finally, run the domain cfg tool (a script is available here :https://github.com/immerse-project/eNEATL36-BIzoo_Demonstator/blob/main/SCRIPTS/DOMAINcfg/run_domain_cfg_eNEATL36_AGRIF_emodNET2018_finaldomain_corrected_with_FES2014.sub)

E. Update the bathymetry with the BMG TOOL

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.

  • Download bmg tool, or load bmg module on mercator px:

module load bmg/bmg-5.0

  • 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 .line coastline file, you can find the GSHHG coastline file here : =======PATH_COASTLINES=======

  • Then run CheckBMG

CheckBMG

  • 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.

  • Then, 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)

F. Run domain_cfg a second time with the new updated bathymetry

  • Run the domaincfg tool once again while reading the new bathymetry file created at last step, 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 = 'emodNET_2018.nc' ! Name of the bathymetry file 
    cn_bath = 'bathymetry' ! Name of the bathymetry variable in cn_topo
    cn_lon = 'lon' ! Name of longitude in cn_topo
    cn_lat = 'lat' ! Name of latitude in cn_topo

At this step, you will have created both parent and child coordinate files domain_cfg.nc and 1_domain_cfg.nc respectively.

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