Agent skill
glm-basics
Basic usage of the General Lake Model (GLM) for lake temperature simulation. Use when you need to run GLM, understand input files, or modify configuration parameters.
Install this agent skill to your Project
npx add-skill https://github.com/benchflow-ai/skillsbench/tree/main/tasks-no-skills/glm-lake-mendota/environment/skills/glm-basics
SKILL.md
GLM Basics Guide
Overview
GLM (General Lake Model) is a 1D hydrodynamic model that simulates vertical temperature and mixing dynamics in lakes. It reads configuration from a namelist file and produces NetCDF output.
Running GLM
cd /root
glm
GLM reads glm3.nml in the current directory and produces output in output/output.nc.
Input File Structure
| File | Description |
|---|---|
glm3.nml |
Main configuration file (Fortran namelist format) |
bcs/*.csv |
Boundary condition files (meteorology, inflows, outflows) |
Configuration File Format
glm3.nml uses Fortran namelist format with multiple sections:
&glm_setup
sim_name = 'LakeName'
max_layers = 500
/
&light
Kw = 0.3
/
&mixing
coef_mix_hyp = 0.5
/
&meteorology
meteo_fl = 'bcs/meteo.csv'
wind_factor = 1
lw_factor = 1
ch = 0.0013
/
&inflow
inflow_fl = 'bcs/inflow1.csv','bcs/inflow2.csv'
/
&outflow
outflow_fl = 'bcs/outflow.csv'
/
Modifying Parameters with Python
import re
def modify_nml(nml_path, params):
with open(nml_path, 'r') as f:
content = f.read()
for param, value in params.items():
pattern = rf"({param}\s*=\s*)[\d\.\-e]+"
replacement = rf"\g<1>{value}"
content = re.sub(pattern, replacement, content)
with open(nml_path, 'w') as f:
f.write(content)
# Example usage
modify_nml('glm3.nml', {'Kw': 0.25, 'wind_factor': 0.9})
Common Issues
| Issue | Cause | Solution |
|---|---|---|
| GLM fails to start | Missing input files | Check bcs/ directory |
| No output generated | Invalid nml syntax | Check namelist format |
| Simulation crashes | Unrealistic parameters | Use values within valid ranges |
Best Practices
- Always backup
glm3.nmlbefore modifying - Run GLM after each parameter change to verify it works
- Check
output/directory for results after each run
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