/usr/share/python-ase/doc/ase/phonons.py is in python-ase-doc 3.15.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | # creates: Al_phonon.png Al_mode.gif Al_mode.pdf
import matplotlib.pyplot as plt
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.dft.kpoints import ibz_points, bandpath
from ase.phonons import Phonons
# Setup crystal and EMT calculator
atoms = bulk('Al', a=4.05)
calc = EMT()
# Phonon calculator
N = 6
ph = Phonons(atoms, calc, supercell=(N, N, N))
ph.run()
# Read forces and assemble the dynamical matrix
ph.read(acoustic=True)
# High-symmetry points in the Brillouin zone
points = ibz_points['fcc']
G = points['Gamma']
X = points['X']
W = points['W']
K = points['K']
L = points['L']
U = points['U']
point_names = ['$\Gamma$', 'X', 'U', 'L', '$\Gamma$', 'K']
path = [G, X, U, L, G, K]
path_kc, q, Q = bandpath(path, atoms.cell, 100)
omega_kn = 1000 * ph.band_structure(path_kc)
# DOS
omega_e, dos_e = ph.dos(kpts=(50, 50, 50), npts=5000, delta=1e-4)
omega_e *= 1000
# Plot phonon dispersion
plt.figure(1, (8, 6))
plt.axes([.1, .07, .67, .85])
for n in range(len(omega_kn[0])):
omega_n = omega_kn[:, n]
plt.plot(q, omega_n, 'k-', lw=2)
plt.xticks(Q, point_names, fontsize=18)
plt.yticks(fontsize=18)
plt.xlim(q[0], q[-1])
plt.ylim(0, 35)
plt.ylabel("Frequency ($\mathrm{meV}$)", fontsize=22)
plt.grid('on')
plt.axes([.8, .07, .17, .85])
plt.fill_between(dos_e, omega_e, y2=0, color='lightgrey', edgecolor='k', lw=2)
plt.ylim(0, 35)
plt.xticks([], [])
plt.yticks([], [])
plt.xlabel("DOS", fontsize=18)
plt.savefig('Al_phonon.png')
# Write modes for specific q-vector to trajectory files
ph.write_modes([l / 2 for l in L], branches=[2], repeat=(8, 8, 8), kT=3e-4,
center=True)
# Generate png animation
from subprocess import call
from ase.io import Trajectory, write
trajfile = 'phonon.mode.2.traj'
trajectory = Trajectory(trajfile, 'r')
for i, atoms in enumerate(trajectory):
write('picture%02i.png' % i, atoms, show_unit_cell=2,
rotation='-36x,26.5y,-25z')
# Flatten images for better quality
call(['convert', '-flatten', 'picture%02i.png' % i, 'picture%02i.png' % i])
# Make static pdf image for pdflatex
call(['convert', 'picture00.png', 'Al_mode.pdf'])
# Concatenate to gif animation
call(['convert', '-delay', '5', '-loop', '0', '-dispose', 'Previous',
'picture*.png', 'Al_mode.gif'])
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