Inspecting Aragog NetCDF output

This is a quick how-to for opening, inspecting, and plotting variables from Aragog’s NetCDF snapshot files. This how-to assumes you have output out/first_output.nc from the First Run tutorial, but is applicable to any output file.

1. Quick command-line inspect

Show metadata, dimensions, and available variables:

ncdump -h out/first_output.nc

Print a variable (example: temp_b):

ncdump -v temp_b out/first_output.nc | head

2. Python option A: xarray

Install once:

pip install xarray

Open and inspect:

import xarray as xr

ds = xr.open_dataset("out/first_output.nc")
print(ds)          # dimensions, variables, attrs
print(ds.attrs)    # global metadata
print(ds.data_vars)

List variable names:

print(list(ds.data_vars))

Grab a variable as a NumPy array:

temp = ds["temp_b"].values

3. Plot a variable vs radius/pressure (xarray + matplotlib)

Temperature vs pressure

import matplotlib.pyplot as plt
import xarray as xr

ds = xr.open_dataset("out/first_output.nc")

P = ds["pres_b"].values     # GPa
T = ds["temp_b"].values     # K

plt.figure()
plt.plot(T, P)
plt.gca().invert_yaxis()
plt.xlabel("Temperature (K)")
plt.ylabel("Pressure (GPa)")
plt.title("Temperature profile")
plt.tight_layout()
plt.show()

Total heat flux vs radius

import matplotlib.pyplot as plt
import xarray as xr

ds = xr.open_dataset("out/first_output.nc")

r = ds["radius_b"].values    # km
F = ds["Ftotal_b"].values    # W m-2

plt.figure()
plt.plot(F, r)
plt.xlabel("Total heat flux (W m$^{-2}$)")
plt.ylabel("Radius (km)")
plt.title("Total heat flux profile")
plt.tight_layout()
plt.show()

4. Python option B: netCDF4 (no extra dependencies needed)

import netCDF4 as nc

ds = nc.Dataset("out/first_output.nc")

print(ds.dimensions)
print(ds.variables.keys())

temp_b = ds.variables["temp_b"][:]  # read variable
print(temp_b)

ds.close()