phono3py

import numpy as np from phonopy import Phonopy from phonopy.structure.atoms import PhonopyAtoms from phono3py import Phono3py # Define a simple silicon unit cell (diamond structure) for demonstration a = 5.43 # Lattice parameter for Si # Unit cell basis vectors (face-centered cubic) lattice = np.array([ [a/2, a/2, 0], [a/2, 0, a/2], [0, a/2, a/2] ]) # Atoms in the unit cell (fractional coordinates) positions = np.array([ [0, 0, 0], [0.25, 0.25, 0.25] ]) symbols = ['Si', 'Si'] # Create a PhonopyAtoms object for the unit cell unit_cell = PhonopyAtoms(cell=lattice, scaled_positions=positions, symbols=symbols) # Define supercell matrix (e.g., 2x2x2 supercell) supercell_matrix = np.diag([2, 2, 2]) # Initialize Phonopy object (a prerequisite for Phono3py) phonon = Phonopy(unit_cell, supercell_matrix) # Define a primitive matrix if different from the unit cell. # For FCC structures, a typical primitive cell matrix is: primitive_matrix = np.array([ [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0] ]) # Initialize Phono3py object with the Phonopy object and supercell matrix ph3 = Phono3py(phonon, supercell_matrix, primitive_matrix=primitive_matrix) print("Phono3py object initialized successfully.") print(f"Number of atoms in primitive cell: {ph3.primitive.numbers.shape[0]}") print(f"Number of atoms in supercell: {ph3.supercell.numbers.shape[0]}")