Create domain file

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.