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"""QHA example of Si."""
import tarfile
import matplotlib.pyplot as plt
import numpy as np
from phonopy import Phonopy
from phonopy.interface.vasp import Vasprun, read_vasp
def get_force_sets(index):
"""Parse vasprun.xml and return forces."""
with tarfile.open("vasprun_xmls.tar.lzma", "r:xz") as tr:
with tr.extractfile("vasprun_xmls/vasprun.xml-%d" % index) as fp:
vasprun = Vasprun(fp, use_expat=True)
forces = vasprun.read_forces()
return forces
def get_frequency(poscar_filename, force_sets):
"""Calculate phonons and return frequencies."""
unitcell = read_vasp(poscar_filename)
volume = unitcell.volume
phonon = Phonopy(
unitcell,
[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
)
disps = np.zeros_like(force_sets)
disps[0] = [0.01, 0, 0]
phonon.dataset = {
"natom": len(force_sets),
"first_atoms": [
{"number": 0, "displacement": [0.01, 0, 0], "forces": force_sets}
],
}
phonon.produce_force_constants()
return phonon.get_frequencies([0.5, 0.5, 0]), volume
def main():
"""Run QHA."""
frequencies = []
volumes = []
for i in range(-5, 6):
poscar_filename = "POSCAR-%d" % i
force_sets = get_force_sets(i)
fs, v = get_frequency(poscar_filename, force_sets)
frequencies.append(fs)
volumes.append(v)
for freq_at_X in np.array(frequencies).T:
freq_squared = freq_at_X**2 * np.sign(freq_at_X)
# np.sign is used to treat imaginary mode, since
# imaginary frequency is returned as a negative value from phonopy.
plt.plot(volumes, freq_squared, "o-")
# for v, f2 in zip(volumes, freq_squared):
# print("%f %f" % (v, f2))
# print('')
# print('')
plt.title("Frequeny squared (THz^2) at X-point vs volume (A^3)")
plt.show()
if __name__ == "__main__":
main()
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