# Dynamic structure factor¶

This feature is under testing.

From Eq. (3.120) in the book “Thermal of Neutron Scattering”, coherent one-phonon dynamic structure factor is given as

$S(\mathbf{Q}, \nu, \omega)^{+1\text{ph}} = \frac{k'}{k} \frac{N}{\hbar} \sum_\mathbf{q} |F(\mathbf{Q}, \mathbf{q}\nu)|^2 (n_{\mathbf{q}\nu} + 1) \delta(\omega - \omega_{\mathbf{q}\nu}) \Delta(\mathbf{Q-q}),$
$S(\mathbf{Q}, \nu, \omega)^{-1\text{ph}} = \frac{k'}{k} \frac{N}{\hbar} \sum_\mathbf{q} |F(\mathbf{Q}, \mathbf{q}\nu)|^2 n_{\mathbf{q}\nu} \delta(\omega + \omega_{\mathbf{q}\nu}) \Delta(\mathbf{Q-q}),$

with

$F(\mathbf{Q}, \mathbf{q}\nu) = \sum_j \sqrt{\frac{\hbar}{2 m_j \omega_{\mathbf{q}\nu}}} \bar{b}_j \exp\left( -\frac{1}{2} \langle |\mathbf{Q}\cdot\mathbf{u}(j0)|^2 \rangle \right) \exp[-i(\mathbf{Q-q})\cdot\mathbf{r}(j0)] \mathbf{Q}\cdot\mathbf{e}(j, \mathbf{q}\nu).$

where $$\mathbf{Q}$$ is the scattering vector defined as $$\mathbf{Q} = \mathbf{k} - \mathbf{k}'$$ with incident wave vector $$\mathbf{k}$$ and final wavevector $$\mathbf{k}'$$. Similarly, $$\omega=1/\hbar (E-E')$$ where $$E$$ and $$E'$$ are the energies of the incident and final particles. These follow the convention of the book “Thermal of Neutron Scattering”. In some other text books, their definitions have opposite sign. $$\Delta(\mathbf{Q-q})$$ is defined so that $$\Delta(\mathbf{Q-q})=1$$ with $$\mathbf{Q}-\mathbf{q}=\mathbf{G}$$ and $$\Delta(\mathbf{Q-q})=0$$ with $$\mathbf{Q}-\mathbf{q} \neq \mathbf{G}$$ where $$\mathbf{G}$$ is any reciprocal lattice vector. Other variables are refered to Formulations page. Note that the phase convention of the dynamical matrix given here is used. This changes the representation of the phase factor in $$F(\mathbf{Q}, \mathbf{q}\nu)$$ from that given in the book “Thermal of Neutron Scattering”, but the additional term $$\exp(i\mathbf{q}\cdot\mathbf{r})$$ comes from the different phase convention of the dynamical matrix or equivalently the eigenvector. For inelastic neutron scattering, $$\bar{b}_j$$ is the average scattering length over isotopes and spins. For inelastic X-ray scattering, $$\bar{b}_j$$ is replaced by atomic form factor $$f_j(\mathbf{Q})$$ and $$k'/k \sim 1$$.

Currently only $$S(\mathbf{Q}, \nu, \omega)^{+1\text{ph}}$$ is calcualted with setting $$N k'/k = 1$$ and the physical unit is $$\text{m}^2/\text{J}$$ when $$\bar{b}_j$$ is given in Angstrom.

## Usage¶

Currently this feature is usable only from API. The following example runs with the input files in example/NaCl.

#!/usr/bin/env python

import numpy as np
from phonopy.spectrum.dynamic_structure_factor import atomic_form_factor_WK1995
from phonopy.phonon.degeneracy import degenerate_sets
from phonopy.units import THzToEv

def get_AFF_func(f_params):
def func(symbol, Q):
return atomic_form_factor_WK1995(Q, f_params[symbol])
return func

def run(phonon,
Qpoints,
temperature,
atomic_form_factor_func=None,
scattering_lengths=None):
# Transformation to the Q-points in reciprocal primitive basis vectors
Q_prim = np.dot(Qpoints, phonon.primitive_matrix)
# Q_prim must be passed to the phonopy dynamical structure factor code.
phonon.run_dynamic_structure_factor(
Q_prim,
temperature,
atomic_form_factor_func=atomic_form_factor_func,
scattering_lengths=scattering_lengths,
freq_min=1e-3)
dsf = phonon.dynamic_structure_factor
q_cartesian = np.dot(dsf.qpoints,
np.linalg.inv(phonon.primitive.get_cell()).T)
distances = np.sqrt((q_cartesian ** 2).sum(axis=1))

print("# [1] Distance from Gamma point,")
print("# [2-4] Q-points in cubic reciprocal space, ")
print("# [5-8] 4 band frequencies in meV (becaues of degeneracy), ")
print("# [9-12] 4 dynamic structure factors.")
print("# For degenerate bands, dynamic structure factors are summed.")
print("")

# Use as iterator
for Q, d, f, S in zip(Qpoints, distances, dsf.frequencies,
dsf.dynamic_structure_factors):
bi_sets = degenerate_sets(f)  # to treat for band degeneracy
text = "%f  " % d
text += "%f %f %f  " % tuple(Q)
text += " ".join(["%f" % (f[bi].sum() * THzToEv * 1000 / len(bi))
for bi in bi_sets])
text += "  "
text += " ".join(["%f" % (S[bi].sum()) for bi in bi_sets])
print(text)

if __name__ == '__main__':
primitive_matrix='F',
unitcell_filename="POSCAR")

# Q-points in reduced coordinates wrt cubic reciprocal space
Qpoints = [[2.970000, -2.970000, 2.970000],
[2.950000, 2.950000, -2.950000],
[2.930000, -2.930000, 2.930000],
[2.905000, -2.905000, 2.905000],
[2.895000, -2.895000, 2.895000],
[2.880000, -2.880000, 2.880000],
[2.850000, -2.850000, 2.850000],
[2.810000, -2.810000, 2.810000],
[2.735000, -2.735000, 2.735000],
[2.660000, -2.660000, 2.660000],
[2.580000, -2.580000, 2.580000],
[2.500000, -2.500000, 2.500000]]

# Mesh sampling phonon calculation is needed for Debye-Waller factor.
# This must be done with is_mesh_symmetry=False and with_eigenvectors=True.
mesh = [11, 11, 11]
phonon.run_mesh(mesh,
is_mesh_symmetry=False,
with_eigenvectors=True)
temperature = 300

IXS = True

if IXS:
# For IXS, atomic form factor is needed and given as a function as
# a parameter.
# D. Waasmaier and A. Kirfel, Acta Cryst. A51, 416 (1995)
# f(Q) = \sum_i a_i \exp((-b_i Q^2) + c
# Q is in angstron^-1
# a1, b1, a2, b2, a3, b3, a4, b4, a5, b5, c
f_params = {'Na': [3.148690, 2.594987, 4.073989, 6.046925,
0.767888, 0.070139, 0.995612, 14.1226457,
0.968249, 0.217037, 0.045300],  # 1+
'Cl': [1.061802, 0.144727, 7.139886, 1.171795,
6.524271, 19.467656, 2.355626, 60.320301,
35.829404, 0.000436, -34.916604]}  # 1-
AFF_func = get_AFF_func(f_params)
run(phonon,
Qpoints,
temperature,
atomic_form_factor_func=AFF_func)
else:
# For INS, scattering length has to be given.
# The following values is obtained at (Coh b)
# https://www.nist.gov/ncnr/neutron-scattering-lengths-list
run(phonon,
Qpoints,
temperature,
scattering_lengths={'Na': 3.63, 'Cl': 9.5770})


The output of the script is:

# [1] Distance from Gamma point,
# [2-4] Q-points in cubic reciprocal space,
# [5-8] 4 band frequencies in meV (becaues of degeneracy),
# [9-12] 4 dynamic structure factors.
# For degenerate bands, dynamic structure factors are summed.

0.009132  2.970000 -2.970000 2.970000  0.977517 1.648183 19.035705 30.535702  0.000000 706.475380 0.000000 16.137386
0.015219  2.950000 2.950000 -2.950000  1.640522 2.747087 18.994893 30.479078  0.000000 262.113412 0.000000 16.366740
0.021307  2.930000 -2.930000 2.930000  2.298710 3.841226 18.935185 30.395654  0.000000 138.116831 0.000000 16.619581
0.028917  2.905000 -2.905000 2.905000  3.116160 5.200214 18.836546 30.256295  0.000000 78.225945 0.000000 16.965983
0.031961  2.895000 -2.895000 2.895000  3.441401 5.740457 18.790421 30.190463  0.000000 65.174556 0.000000 17.112970
0.036526  2.880000 -2.880000 2.880000  3.927209 6.546550 18.714922 30.081791  0.000000 51.288627 0.000000 17.341206
0.045658  2.850000 -2.850000 2.850000  4.890522 8.140492 18.544488 29.832346  0.000000 34.845699 0.000000 17.819327
0.057833  2.810000 -2.810000 2.810000  6.154512 10.217882 18.286153 29.444246  0.000000 23.864605 0.000000 18.476926
0.080662  2.735000 -2.735000 2.735000  8.440068 13.902951 17.731951 28.589254  0.000000 15.762830 0.000000 19.591803
0.103491  2.660000 -2.660000 2.660000  10.559231 17.071210 17.175478 27.602958  0.000000 0.000000 14.349345 20.000676
0.127842  2.580000 -2.580000 2.580000  12.497611 16.203093 19.926659 26.474218  0.000000 0.000000 18.814845 17.496644
0.152193  2.500000 -2.500000 2.500000  13.534679 15.548262 21.156819 25.813428  0.000000 0.000000 34.134746 6.765951