Skillsbench 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

source · Clone the upstream repo

git clone https://github.com/benchflow-ai/skillsbench

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/benchflow-ai/skillsbench "$T" && mkdir -p ~/.claude/skills && cp -r "$T/tasks/glm-lake-mendota/environment/skills/glm-basics" ~/.claude/skills/benchflow-ai-skillsbench-glm-basics && rm -rf "$T"

manifest: tasks/glm-lake-mendota/environment/skills/glm-basics/SKILL.md

source content

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