xushuwenn/redact/glm-basics

Name: glm-basics
Author: xushuwenn

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data/tasks/glm-lake-mendota/environment/skills/glm-basics/SKILL.md
Updated 9 Oct 2026
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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

npx vskill@latest install xushuwenn/redact/glm-basics

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SKILL.md

The same SKILL.md was published earlier as benchflow-ai/skillsbench/glm-basics.

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

bash

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:

fortran

&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

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.nml before modifying
Run GLM after each parameter change to verify it works
Check output/ directory for results after each run

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Source

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Extension points

configConfiguration overrides

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