# 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. Use when this capability is needed.

- Skill: `tomevault-io/glm-basics` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add tomevault-io/glm-basics`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/glm-basics/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: tomevault-io (https://skillmd.com/u/tomevault-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/tomevault-io/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

---
> Converted and distributed by [TomeVault](https://tomevault.io/claim/benchflow-ai) — claim your Tome and manage your conversions.
<!-- tomevault:4.0:skill_md:2026-04-11 -->