run_glm_simulation

Before processing, extract the lake_depth from the &init_profiles section of the namelist to correctly derive the depth of water layers (depth = lake_depth - z). Ensure the output at /root/output/output.nc is generated successfully.

import subprocess
import f90nml
import xarray as xr

def run_simulation():
    # Extract lake depth from nml for correct depth calculation
    nml = f90nml.read('/root/glm3.nml')
    lake_depth = nml['init_profiles']['lake_depth']
    
    # Run the model
    subprocess.run(['glm', 'x86_64', '--nml', '/root/glm3.nml'], check=True)
    return lake_depth