GLM Output Guide

Overview

GLM produces NetCDF output containing simulated water temperature profiles. Processing this output requires understanding the coordinate system and matching with observations.

Output File

After running GLM, results are in output/output.nc:

Variable	Description	Shape
time	Hours since simulation start	(n_times,)
z	Height from lake bottom (not depth!)	(n_times, n_layers, 1, 1)
temp	Water temperature (°C)	(n_times, n_layers, 1, 1)

Reading Output with Python

from netCDF4 import Dataset
import numpy as np
import pandas as pd
from datetime import datetime

nc = Dataset('output/output.nc', 'r')
time = nc.variables['time'][:]
z = nc.variables['z'][:]
temp = nc.variables['temp'][:]
nc.close()

Coordinate Conversion

Important: GLM z is height from lake bottom, not depth from surface.

# Convert to depth from surface
# Set LAKE_DEPTH based on lake_depth in &init_profiles section of glm3.nml
LAKE_DEPTH = <lake_depth_from_nml>
depth_from_surface = LAKE_DEPTH - z

Complete Output Processing

from netCDF4 import Dataset
import numpy as np
import pandas as pd
from datetime import datetime

def read_glm_output(nc_path, lake_depth):
    nc = Dataset(nc_path, 'r')
    time = nc.variables['time'][:]
    z = nc.variables['z'][:]
    temp = nc.variables['temp'][:]
    start_date = datetime(2009, 1, 1, 12, 0, 0)

    records = []
    for t_idx in range(len(time)):
        hours = float(time[t_idx])
        date = pd.Timestamp(start_date) + pd.Timedelta(hours=hours)
        heights = z[t_idx, :, 0, 0]
        temps = temp[t_idx, :, 0, 0]

        for d_idx in range(len(heights)):
            h_val = heights[d_idx]
            t_val = temps[d_idx]
            if not np.ma.is_masked(h_val) and not np.ma.is_masked(t_val):
                depth = lake_depth - float(h_val)
                if 0 <= depth <= lake_depth:
                    records.append({
                        'datetime': date,
                        'depth': round(depth),
                        'temp_sim': float(t_val)
                    })
    nc.close()

    df = pd.DataFrame(records)
    df = df.groupby(['datetime', 'depth']).agg({'temp_sim': 'mean'}).reset_index()
    return df