## The Debye equation

The Debye equation is an analytical formulation to determine the scattering that arises from some system. This equation considers the distances between particles, $r_{ij}$, to determine the scattered intensity at a given $q$-vector, $I(q)$,

where, $b_i$ and $b_j$ are the scattering lengths of atoms $i$ and $j$ respectively. While this equation is analytically-precise, there are some problems with this method. In particular, that it requires a pair-wise summation, which is very slow for large systems such as those obtained in molecular dynamics.

The Python code below is a simple implimentation of the Debye function, where the scattering length is taken as 1 for all particles.

import numpy as np

def debye(qvalues, xposition, yposition, box_length):
"""
Calculates the scattering profile from the
simulation
positions.

Parameters
----------
qvalues: float, array-like
The q-vectors over which the scattering
should be calculated
xposition: float, array-like
The positions of the particles in the x-axis
yposition: float, array-like
The positions of the particles in the y-axis
box_length: float
The length of the simulation square

Returns
-------
intensity: float, array-like
The calculated scattered intensity
"""
intensity = np.zeros_like(qvalues)
for e, q in enumerate(qvalues):
for m in range(0, xposition.size-1):
for n in range(m+1, xposition.size):
xdist = xposition[n] - xposition[m]
xdist = xdist % box_length
ydist = yposition[n] - yposition[m]
ydist = ydist % box_length
r_mn = np.sqrt(np.square(xdist) + np.square(ydist))
intensity[e] += 1 * 1 * np.sin(
r_mn * q) / (r_mn * q)
if intensity[e] < 0:
intensity[e] = 0
return intensity

from pylj import md, sample

def md_simulation(number_of_particles, temperature,
box_length, number_of_steps,
sample_frequency):
"""
Runs a molecular dynamics simulation in using the pylj
molecular dynamics engine.

Parameters
----------
number_of_particles: int
The number of particles in the simulation
temperature: float
The temperature for the initialisation and
thermostating
box_length: float
The length of the simulation square
number_of_steps: int
The number of molecular dynamics steps to run
sample_frequency:
How regularly the visualisation should be updated

Returns
-------
pylj.util.System
The complete system information from pylj
"""
%matplotlib notebook
system = md.initialise(number_of_particles, temperature,
box_length, 'square')
sample_system = sample.CellPlus(system,
'q/m$^{-1}$', 'I(q)')
system.time = 0
for i in range(0, number_of_steps):
system.integrate(md.velocity_verlet)
system.md_sample()
system.heat_bath(temperature)
system.time += system.timestep_length
system.step += 1
if system.step % sample_frequency == 0:
min_q = 2. * np.pi / box_length
qs = np.linspace(min_q, 10e10, 120)[20:]
inten = debye(qs, system.particles['xposition'],
system.particles['yposition'],
box_length)
sample_system.update(system, qs, inten)
return system

system = md_simulation(10, 3, 15, 5000, 10)