Example 3: Phonon Calculation

This example demonstrates phonon calculations and thermal property analysis.

Source Code

See examples/03_phonon_calculation.py

What You'll Learn

• Calculating phonon frequencies
• Checking dynamical stability
• Computing thermal properties
• Plotting phonon DOS

Code Walkthrough

Setup

from mace_inference import MACEInference
from ase.io import read

calc = MACEInference(model="medium", device="auto")
atoms = read("structures/si_diamond.cif")

Optimize Unit Cell

Phonon calculations require well-relaxed structures:

# optimize() returns Atoms directly
atoms = calc.optimize(atoms, fmax=0.001, optimize_cell=True)

Calculate Phonons

result = calc.phonon(
    atoms,
    supercell_matrix=[2, 2, 2],  # Supercell for force constants
    displacement=0.01,            # Displacement in Å
    temperature_range=(0, 500, 10) # For thermal properties
)

Check Stability

frequencies = result['frequencies']
imaginary = frequencies[frequencies < -0.1]  # Threshold for numerical noise

if len(imaginary) > 0:
    print("⚠️ Structure is dynamically unstable!")
    print(f"Imaginary modes: {imaginary}")
else:
    print("✓ Structure is dynamically stable")

Thermal Properties

# Thermal properties available if temperature_range was specified
if 'thermal' in result:
    thermal = result['thermal']
    print(f"Thermal properties calculated for {len(thermal['temperatures'])} temperatures")

Plot DOS

import matplotlib.pyplot as plt

dos = result['dos']
plt.figure(figsize=(8, 5))
plt.fill_between(dos['frequencies'], dos['total_dos'], alpha=0.5)
plt.plot(dos['frequencies'], dos['total_dos'])
plt.xlabel("Frequency (THz)")
plt.ylabel("DOS (states/THz)")
plt.title("Phonon Density of States")
plt.axvline(0, color='k', linestyle='--', lw=0.5)
plt.savefig("phonon_dos.png", dpi=150)

Expected Output

============================================================
Example 3: Phonon Calculation
============================================================

1. Loading structure: Si8

2. Optimizing structure...
   Converged in 1 steps

3. Calculating phonons...
   Supercell: (2, 2, 2) = 64 atoms
   Displacements: 6
   ✓ Force constants calculated

4. Analyzing results...
   Gamma-point frequencies (THz):
     0.00, 0.00, 0.00 (acoustic)
     12.45, 12.45, 12.45
     15.23, 15.23, 15.23
     ...

   ✓ No imaginary frequencies - structure is stable

5. Thermal properties at 300 K:
   Free energy: 0.2341 eV
   Entropy: 0.4521 meV/K
   Heat capacity: 0.3892 meV/K

✅ Example 3 completed successfully!

Key Points

1. Supercell Size: Larger supercells give more accurate results but are slower
2. Optimization: Tight force tolerance (< 0.001 eV/Å) is important
3. Imaginary Modes: Small negatives near zero are numerical noise; large negatives indicate instability
4. Units: Frequencies in THz, thermal properties per atom