diffsim 1.0

Calculate diffraction patterns from first principles

DiffSim

Introduction

DiffSim provides an atomistic approach to efficiently simulate Bragg coherent x-ray diffraction imaging (BCDI) diffraction patterns by factorising and eliminating certain redundancies in the conventional approach. The method used is able to reduce the computation time by several orders of magnitude without compromising the recovered phase information and therefore enables feasible atomistic simulations on nanoscale crystals with arbitrary lattice distortions.

Please cite the following article when using Diffsim in published work:

Ahmed Mokhtar, David Serban and Marcus Newton, Simulation of Bragg coherent diffraction imaging, J. Phys. Commun. Volume 6, 055003 (2022)

Installation

DiffSim requires:

• Python >= 3.7
• Numba
• NumPy
• mpi4py

Installation via pip:

$ pip install diffsim

Reporting Bugs

Please send any bugs, problems, and proposals to: [e-mail] or visit: http://github.com/bonsudev/diffsim

Library Usage and Examples

Simulate ZnO Diffraction Pattern

# 
# Example simuation of ferroelectric 
# domain wall in BaTiO3 nanocrystal
# 

import numpy
from math import sqrt
from diffsim import DiffSim
from scipy import signal

d = DiffSim()
d.meta_name = "BTO_SquareWave"
# Tetragonal structure 
# unit cell in nm
crystal_a = 0.39925
crystal_b = 0.39925
crystal_c = 0.40373
# distort along x axis
d.SetLatticeVector(0,[crystal_c,0.0,0.0])
d.SetLatticeVector(1,[0.0,crystal_b,0.0])
d.SetLatticeVector(2,[0.0,0.0,crystal_a])
# Reflection
d.SetMillerIndices([1,0,1])
# Atoms in unit cell and scattering factors
d.AddAtom(55.7107, 0,0,0) # Ba
d.AddAtom(22.3470, 0.5,0.5,0.5) # Ti
d.AddAtom(8.04313, 0.5,0.5,0.0) # O
d.AddAtom(8.04313, 0.5,0.0,0.5) # O
d.AddAtom(8.04313, 0,0.5,0.5) # O


def Atom2Function(ijks): #atom function for Ti i.e atom number 2
	X= 400
	Y= 400
	Z= 400
	u = 0.01 * signal.square((2.0* numpy.pi/Z) * ijks)
	u[:,0] = u[:,2]
	u[:,1] = 0
	u[:,2] = 0
	return u

def Atom3Function(ijks):
	X=400
	Y=400
	Z=400
	u=-0.022 * signal.square((2.0 * numpy.pi/Z) * ijks)
	u[:,0] = u[:,2]
	u[:,1] = 0
	u[:,2] = 0
	return u

def Atom45Function(ijks):
	X=400
	Y=400
	Z=400
	u = -0.014 * signal.square((2.0*numpy.pi/Z)* ijks)
	u[:,0] = u[:,2]
	u[:,1] = 0
	u[:,2] = 0
	return u

d.AddAtomFunction(2, Atom2Function)
d.AddAtomFunction(3, Atom3Function)
d.AddAtomFunction(4, Atom45Function)
d.AddAtomFunction(5, Atom45Function)
#
d.SetSuperCell(5,5,10)
#d.SetShapeArray("shape.npy")
d.SetShapeArrayFromNormals([400,400,400],\
	[[5,200,200,4,200,200],\
	[395,200,200,396,200,200],\
	[200,5,200,200,4,200],\
	[200,395,200,200,396,200],\
	[200,200,5,200,200,4],\
	[200,200,395,200,200,396],\
	])
#d.SaveShapeArray("shape.npy")
d.SetDetPixelSize(50,50)
d.SetDetSize(256,256)
d.SetEnergy(9.0)
d.SetFlux(10**20)
d.SetExposureTime(100)
d.SetBeta(1.5)
d.Prepare()
d.SaveParameters()
d.CalcObject()
d.CalcObjectCoords()
d.SaveObject()
d.SaveObjectCoords()
d.CalcRockingCurveGPU()
d.SaveDiffraction()