glm-fundamentals

name	glm-fundamentals
description	How to run the General Lake Model (GLM) for lake water temperature simulation. Use this skill whenever you need to execute GLM simulations, understand GLM configuration files (*.nml), interpret GLM output (NetCDF), or troubleshoot GLM execution. Essential for lake modeling and water temperature prediction tasks.

GLM Fundamentals

Overview

The General Lake Model (GLM) is a one-dimensional hydrodynamic and biogeochemical model for lakes. It simulates vertical water temperature, stratification, and mixing driven by meteorological forcing data.

Running GLM

Prerequisites

• GLM executable (typically glm or glm.exe in PATH)
• Configuration file: glm3.nml (Fortran namelist format)
• Forcing data: meteorological, inflow, outflow files referenced in config
• Output directory exists

Basic Execution

cd /root
glm

GLM reads the configuration from glm3.nml in the current directory and produces output according to the &output section.

Expected Output

• NetCDF output file (typically output/output.nc)
• CSV outputs if enabled (csv_lake_fname, csv_point_nlevs, etc.)

GLM Configuration (glm3.nml)

The configuration is a Fortran namelist file with sections:

Key Sections for Temperature Simulation

&light - Solar radiation and light extinction

• Kw: Light extinction coefficient (higher = more light absorbed)
• Default range: 0.1 to 0.5

&mixing - Turbulent mixing parameterization

• coef_mix_hyp: Hypolimnion mixing coefficient (higher = more mixing in deep water)
• Default range: 0.3 to 0.7

&meteorology - Atmospheric forcing and bulk transfer coefficients

• wind_factor: Wind speed multiplier (scales wind-driven mixing)
• lw_factor: Longwave radiation multiplier
• ch: Sensible heat transfer coefficient
• Default ranges: wind_factor [0.7, 1.3], lw_factor [0.7, 1.3], ch [0.0005, 0.002]

&init_profiles - Initial temperature and salinity

• the_depths, the_temps, the_sals: Initial conditions at start time

&time - Simulation period

• start, stop: Simulation dates in format 'YYYY-MM-DD HH:MM:SS'
• dt: Timestep in seconds (typically 3600 for hourly)

&output - Output configuration

• out_dir, out_fn: Output directory and filename
• nsave: Number of timesteps between outputs (24 = daily output for hourly timestep)

GLM Output (NetCDF)

The NetCDF output file contains:

• Time dimension: Simulation timesteps
• Depth dimension: Lake depth layers (adaptive, varies through simulation)
• Variables:
  • temp: Water temperature (°C) at each depth and time
  • z: Depth of each layer
  • Other biogeochemical variables if enabled

Reading NetCDF in Python

import xarray as xr
ds = xr.open_dataset('output/output.nc')
print(ds.data_vars)  # List available variables
print(ds.temp)        # Temperature array

Common Issues

GLM doesn't run: Verify glm3.nml exists in current directory and config is syntactically valid (check for missing commas, mismatched quotes).

Output file not created: Check the &output section exists and out_dir directory is writable.

Unrealistic temperatures: Usually indicates poor parameter choices. Start with defaults and adjust systematically.

Integration with Calibration

For calibration workflows:

1. Modify only allowed parameters in &light, &mixing, &meteorology
2. Keep &init_profiles, &time, inflow/outflow data unchanged
3. Run GLM: glm
4. Extract simulated temperatures at matched observation times/depths
5. Compute RMSE against field observations
6. Adjust parameters and repeat until RMSE threshold met