def test_kkr(self):
energy, eps_real, eps_imag = self.ge_vasprun.dielectric
de = (energy[10] - energy[0]) / 10
def symmetrise(a):
"""Convert XX YY ZZ XY YZ XZ array to a symmetrical 3x3 matrix"""
return [[a[0], a[3], a[5]], [a[4], a[1], a[4]], [a[5], a[4], a[2]]]
eps_imag_3x3 = [symmetrise(a) for a in eps_imag]
eps_real_3x3 = np.array([symmetrise(a) for a in eps_real])
# Check difference between eps_real reported by Vasp and determined
# by Kramers-Kronig transformation of eps_im.
#
# Some discrepancy is normal, check RMS is as expected
# This is likely due to the limited precision available in vasprun
error = kkr(de, eps_imag_3x3) - eps_real_3x3
error_fracs = [
eps / eps_ref
for eps, eps_ref in zip(error.flatten(), eps_real_3x3.flatten())
if eps_ref > 1e-2
] # Exclude low-precision cases
self.assertLess(np.sqrt((np.array(error_fracs)**2).mean()), 0.1)
def dielectric_from_opt(filename, cshift=1e-6, out_filename=None):
"""Read a Questaal opt.ext file and return dielectric function
opt.ext files only provide x, y, z components so the off-diagonal terms are
set to zero.
Args:
filename (:obj:`float`):
Path to ``opt.ext`` output of LMF optics calculation. If this is
split into spin channels, the values will be recombined to a single
(observable) channel.
cshift (:obj:`float`, optional):
A small imaginary element used in Kramers-Kronig integration.
out_filename (:obj:`float`, optional):
Path to write tabulated dielectric data with columns::
energy(eV) real_xx real_yy real_zz imag_xx imag_yy imag_zz
If None, no file is written.
Returns:
:obj:`tuple`
The format imitates the ``dielectric`` attribute of
:obj:`pymatgen.io.vasp.outputs.Vasprun`: a tuple of the form::
([energy1, energy2, ...],
[[real_xx_1, real_yy_1, real_zz_1,
real_xy_1, real_yz_1, real_xz_1],
[real_xx_2, real_yy_2, real_zz_2,
real_xy_2, real_yz_2, real_xz_2], ...],
[[imag_xx_1, imag_yy_1, imag_zz_1,
imag_xy_1, imag_yz_1, imag_xz_1],
[imag_xx_2, imag_yy_2, imag_zz_2,
imag_xy_2, imag_yz_2, imag_xz_2], ...])
The off-diagonal (xy, yz, xz) terms are not given in ``opt.ext``
and are set to zero. Only the imaginary part is provided so the
real part is constructed by a Kramers-Kronig trasformation.
Energy units are converted from Ry to eV.
"""
data = np.genfromtxt(filename, skip_header=1)
if data.shape[1] == 4:
pass
elif data.shape[1] == 7:
data = np.hstack(data[:, :1], data[1:4] + data[4:7])
else:
raise ValueError("Not sure how to interpret {}; expected "
"4 or 7 columns.".format(filename))
data[:, 0] *= _ry_to_ev
de = data[1, 0] - data[0, 0]
eps_imag = [[[row[1], 0, 0], [0, row[2], 0], [0, 0, row[3]]]
for row in data]
eps_real = kkr(de, eps_imag)
# Re-shape to XX YY ZZ XY YZ XZ format
eps_imag = np.array(eps_imag).reshape(len(eps_imag), 9)
eps_imag = eps_imag[:, [0, 4, 8, 1, 5, 2]]
eps_real = eps_real.reshape(len(eps_real), 9)
eps_real = eps_real[:, [0, 4, 8, 1, 5, 2]]
if out_filename is not None:
with open(out_filename, 'wt') as f:
for e, r, i in zip(data[:, 0].flatten(), eps_real, eps_imag):
f.write((' '.join(['{:10.8f}'] * 7)).format(e, *r[:3], *i[:3]))
f.write('\n')
return (data[:, 0].flatten(), eps_real, eps_imag)