Domain Creation

Abstract

In this second tutorial of the NEMO SURGE demonstrator, we cover the creation of a single active layer domain_cfg.nc input file for the AMM12_SURGE configuration.

Bathymetry Creation

Before running the DOMAINcfg tool, we first need to create a file containing the bathymetry of the AMM12 reference configuration domain.

We do this by running the create_AMM12_SURGE_bathymetry.py Python script in the src/scripts/ directory using our env_surge_demo virtual environment as follows:

conda activate env_surge_demo

cd SURGE_demo/src/scripts

python3 create_AMM12_SURGE_bathymetry.py

The script calculates the Bathymetry (m) using the AMM_R12_sco_domcfg.nc stored in the AMM12_SURGE/EXP00 run directory and writes this to a new file bathy_meter_AMM12.nc in this directory.

DOMAINcfg Input File Preparation

Next we need to prepare the namelists and input files for the DOMAINcfg tool.

We start by creating a DOMAIN_AMM12_SURGE directory in our AMM12_SURGE/EXP00 run directory and adding a link to our newly created bathymetry input file:

cd .../SURGE_demo/nemo_5.0.1/cfgs/AMM12_SURGE
mkdir DOMAIN_AMM12_SURGE

cd DOMAIN_AMM12_SURGE
ln -s ../bathy_meter_AMM12.nc .

Then, we need to add links to the make_domain_cfg executable and namelist_ref files. We also include a link to the modified namelist_cfg file prepared for this demonstrator in the SURGE_demo/namelists/domain/ directory:

ln -s ../AMM_R12_sco_domcfg.nc .
ln -s .../SURGE_demo/nemo_5.0.1/tools/DOMAINcfg/BLD/bin/make_domain_cfg.exe .
ln -s .../SURGE_demo/nemo_5.0.1/tools/DOMAINcfg/namelist_ref .
ln -s .../SURGE_demo/namelists/domain/namelist_cfg .

Finally, we can run the DOMAINcfg tool using the following command:

./make_domain_cfg.exe

This will produce domain_cfg.nc and mesh_mask.nc files in the current directory, so we add links to these in the run directory.

cd ..

ln -s DOMAIN_AMM12_SURGE/domain_cfg.nc AMM12_SURGE_domcfg.nc .
ln -s DOMAIN_AMM12_SURGE/mesh_mask.nc AMM12_SURGE_mesh_mask.nc .

Success

You have now created the domain_cfg.nc file for our 1-layer barotropic AMM12_SURGE configuration.

Next, continue to the third tutorial Atmospheric Forcing Creation to generate idealised atmospheric forcing using a synthetic storm system.