glm-output

•

9382423 months ago

Read and process GLM output files. Use when you need to extract temperature data from NetCDF output, convert depth coordinates, or calculate RMSE against observations.

Quick Install

npxskills add benchflow-ai/skillsbench--skill glm-output

Instructions

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

Reading Observations

def read_observations(obs_path):
    df = pd.read_csv(obs_path)
    df['datetime'] = pd.to_datetime(df['datetime'])
    df['depth'] = df['depth'].round().astype(int)
    df = df.rename(columns={'temp': 'temp_obs'})
    return df[['datetime', 'depth', 'temp_obs']]

Calculating RMSE

def calculate_rmse(sim_df, obs_df):
    merged = pd.merge(obs_df, sim_df, on=['datetime', 'depth'], how='inner')
    if len(merged) == 0:
        return 999.0
    rmse = np.sqrt(np.mean((merged['temp_sim'] - merged['temp_obs'])**2))
    return rmse

# Usage: get lake_depth from glm3.nml &init_profiles section
sim_df = read_glm_output('output/output.nc', lake_depth=25)
obs_df = read_observations('field_temp_oxy.csv')
rmse = calculate_rmse(sim_df, obs_df)
print(f"RMSE: {rmse:.2f}C")

Common Issues

Issue	Cause	Solution
RMSE very high	Wrong depth conversion	Use `lake_depth - z`, not `z` directly
No matched observations	Datetime mismatch	Check datetime format consistency
Empty merged dataframe	Depth rounding issues	Round depths to integers

Best Practices

Check lake_depth in &init_profiles section of glm3.nml
Always convert z to depth from surface before comparing with observations
Round depths to integers for matching
Group by datetime and depth to handle duplicate records
Check number of matched observations after merge

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