Creation of domain files

The CIME submodule under ./gen_domain_files/ generates the domain files for CLM. This repository contains a simplified version of gen_domain which is easier to compile on JSC machines and you do not need the CIME repository. Required modules are imkl, netCDF and netCDF-Fortran (all provided by jsc.2024_Intel.sh). Then compile src/gen_domain.F90 with

gfortran -o gen_domain src/gen_domain.F90 -mkl -I${INC_NETCDF} -lnetcdff -lnetcdf

If the Intel Math Kernel Library (MKL) is not available on your system, you can remove the -mkl flag without consequences for the output. After the compilation you can execute gen_domain with \(MAPFILE being one of the mapping files created in the step before (in `mkmapdata/`) and \)GRIDNAME being a string with the name of your grid, e.g. EUR-R13B05 for the ~12-km icosahedral grid. The choice of $MAPFILE does not influence the lat- and longitude values in the domain file but can influence the land/sea mask.

Hint: For better reproducibility, specify the absolute path of $MAPFILE. The absolute path to the file can be printed using realpath $MAPFILE.

./gen_domain -m $MAPFILE -o $GRIDNAME -l $GRIDNAME -u $USER

The created domain file will later be modified.

Create domain file (old) - Click to expand

In this step you will create the domain file for your case using gen_domain. First, you need to navigate into the gen_domain_files/src/ directory and compile it with the loaded modules ifort, imkl, netCDF and netCDF-Fortran.

cd ../gen_domain_files/src/

# Compile the script
ifort -o ../gen_domain gen_domain.F90 -mkl -lnetcdff -lnetcdf

Attention

If you get a message saying “ifort: command line remark #10412: option ‘-mkl’ is deprecated and will be removed in a future release. Please use the replacement option ‘-qmkl’” or the compiling fails, replace -mkl with -qmkl.

Before running the script you need to export the environment variable GRIDNAME (same as what you used for the SCRIP grid file and in the runscript_mkmapdata.sh script).

export GRIDNAME="your gridname"

Then you can run the script:

cd ../
./gen_domain -m $MAPFILE -o $GRIDNAME -l $GRIDNAME

The output of this will be two netCDF files domain.lnd.*.nc and domain.ocn.*.nc that define the land and ocean mask respectively. The land mask will inform the atmosphere and land inputs of eCLM when running a case.

However, gen_domain defaults the use of the variables mask and frac on these files to be for ocean models, i.e. 0 for land and 1 for ocean. So to use them you have to either manipulate the domain.lnd.*.nc file to have mask and frac set to 1 instead of 0 (WARNING: some netCDF script languages have mask as a reserved keyword e.g. NCO, use single quotation marks as workaround). Or simply swap/rename the domain.lnd.*.nc and domain.ocn.*.nc file:

mv domain.lnd."your gridname"_"your gridname"."yymmdd".nc temp.nc
mv domain.ocn."your gridname"_"your gridname"."yymmdd".nc domain.lnd."your gridname"_"your gridname"."yymmdd".nc
mv temp.nc domain.ocn."your gridname"_"your gridname"."yymmdd".nc

Congratulations! You successfully created your domain files and can now move on to the final next step to create your surface data.