MSE 465

Structural and Chemical Characterizations of Materials

Lecture 2

Fourier Transform (Series)

Reciprocal Space, and Structure Factor
 Outline
q Fourier transform (Series)
Ø FT and IFT
Ø DFT and FFT

q Real Space and Reciprocal Space

Ø Direct Lattice in Real space
Ø Reciprocal Lattice in Reciprocal space
Ø Ewald Sphere, Laue Equation and Bragg’s Law

q Structure factor
Ø Single atom scattering
Ø The structure factor
Ø Radical distribution function/Pair-distribution function

q Examples of applications of FFT

Video Link---Switch to the Zoom PC

FT/FFT:
https://www.youtube.com/watch?v=jVYs-GTqm5U

https://www.youtube.com/watch?v=nl9TZanwbBk
(Anyone can watch after class)
 Fourier Transform and Inverse Fourier Transform
qFourier Transform (FT) is a mathematical method named after J.B.J Fourier, and it
describes the analysis of any varying signal into its constituent frequency
components. For a function f(x) of some independent variable x (this may be time or
spatial position). A Fourier transform maps the function f(x) into another function
F(s) defined in the Fourier domain:
#" $%&'( #" $)(
𝐹 𝑠 = 𝓕{𝑓 𝑥 } = ∫!" 𝑓(𝑥)𝑒 𝑑𝑥= ∫!" 𝑓(𝑥)𝑒 𝑑𝑥

Physicists often use the variable k=2πs instead. For crystallography, s is more
convenient.

q Inverse Fourier Transform (IFFT): The inverse FT is defined as:

!𝟏 #" !$%&('
f 𝑥 =𝓕 𝐹 𝑠 = ∫!" 𝐹 𝑠 𝑒 𝑑𝑠
 Discrete Fourier Transform and Fast Fourier Transform
q For a discrete and periodic signal/lattice, the discrete Fourier transform, or DFT, is used. Suppose the
signal is a for n = 0...N−1, and an =an+jN for all n and j. The DFT of a, also known as the spectrum of a, is:
!"
!$% $&
Ak= ∑!"# 𝑒 # 𝑎!

More commonly written as: Ak=∑!$% (!

!"# ' 𝑎!
𝑤
!"
$&
where 𝑊! = 𝑒 #

And Wk fork=0...N−1are called the Nth roots of unity. They’re called this because, in N complex arithmetic, (Wk)
N = 1 for all k.

qFast Fourier Transform (FFT): The FFT is a fast algorithm for computing the DFT .
 Video Link---Switch to the Zoom PC

Real and Reciprocal Space in 2D and 3D:

https://www.youtube.com/watch?v=Tj3Hpf_HMk4Real
 Direct Lattices in Real Space
Unit cell Ø Direct Lattice (Bravais Lattice): “For vectors a, b, c forming a
basis of the three-dimensional vector space V3, the set L = {la + mb +
c
nc|l, m, n ∈ Z} of all integral linear combinations of a, b, c is called a
lattice in V3 and the vectors a, b, c are called a lattice basis of L.”
𝛼 b
𝛽 Ø Unit Cell of the Bravais Lattice: an array of lattice points in a specific
𝛾
Bravais lattice that, when periodically repeated, forms the entire lattice.
a
14 Bravais Lattices. ---- 230 Space groups
Crystal system --- 7 Lattice Parameters Lattice Types
Triclinic 𝑎 ≠ 𝑏 ≠ 𝑐, 𝛼 ≠ 𝛽 ≠ 𝛾 Lattice: P
Monoclinic 𝑎 ≠ 𝑏 ≠ 𝑐, 𝛼 = 𝛾 = 90° ≠ 𝛽 Lattice: P, C
Orthorhombic 𝑎 ≠ 𝑏 ≠ 𝑐, 𝛼 = 𝛾 = 𝛽 = 90° Lattice: P, C, I, F
Trigonal 𝑎 = 𝑏 ≠ 𝑐, 𝛼 = 𝛾 = 90°, 𝛽 = 120° Lattice: P, R
Tetragonal 𝑎 = 𝑏 ≠ 𝑐, 𝛼 = 𝛽 = 𝛾 = 90° Lattice: P, I
Cubic 𝑎 = 𝑏 = 𝑐, 𝛼 = 𝛽 = 𝛾 = 90° Lattice: P, I, F
Hexagonal 𝑎 = 𝑏 ≠ 𝑐, 𝛼 = 𝛾 = 90°, 𝛽 = 120° Lattice: P, R
 Bravais Lattices in Real Space
q There are two types of unit cells:
Ø Conventional unit cell (Bravais’s Cell) Ø Primitive unit cell
• Most geometrically convenient • Smallest unit cell possible
• 1 or more lattice points per unit cell • Only one lattice point
q Structure features of a “crystal”:
Ø Short-range atomic order (SRO): ~0.5nm
Ø Medium-range atomic order (MRO): 0.5~3nm
Ø Long-range atomic order (LRO):
Ø Rotation symmetry: 1, 2, 3, 4, 5, 6, 8, 10, 12—
Ø Translational symmetry: unit cell

q “Crystal Lattice” vs. “Crystal Structure”:

Ø Can a High Entropy Alloy (HEA) be called a crystal?
Ø Not in direct space by definition! Atomic structure model of fcc CoCrFeMnNi
Entropy 2013, 15(12), 5536-5548 have been reported
 Crystal Structure as Stackings of Atom Layers
Ø For close packed crystal structures, the crystal structures can be treated as layer
stackings.
High quality zinc-blende/wurtzite GaAs hetero-nanowires

Ø Convenient for defects like twin (c) and

stacking fault analysis

Ø Wurtzite (WZ) from --- ABAB --- ↔ Zinc-Blende

(ZB) --- ABCABC --- phase transformation (d,e):
Very common in III-V semiconductors. 𝐶𝑜𝑢𝑟𝑡𝑠𝑒𝑦 𝐷. 𝑆𝑝𝑖𝑟𝑘𝑜𝑠𝑘𝑎 𝑒𝑡 𝑎𝑙. , ℎ𝑡𝑡𝑝𝑠://𝑎𝑟𝑥𝑖𝑣. 𝑜𝑟𝑔/𝑝𝑑𝑓/0907.1444. 𝑝𝑑𝑓
 Crystal Structure as Stackings of Atom Layers
Ø Convenient for polymorph phase analysis

C -layer
Si -layer

Ø The crystal structure of 3C-SiC has a group symmetry of F43m, α=4.3596 Å.

Ø 6H-SiC has a hexagonal structure with a sg of P63mc and a=3.08 Å and c=15.10 Å.
International Tables for Crystallography (2006). Vol. C, Section 9.2.1, pp. 752–760.
 Reciprocal Lattice in Reciprocal Space

Unit cell q Reciprocal Lattice (inverse-space, q-space, or Fourier space):

Ø For direct lattice L ⊂ V3 with lattice basis a, b, c. Its reciprocal
c*
basis a*, b*, c* is defined by the properties a·a*=b·b*=c·c*=1 and
b·a*=c·a*=c·b*= a·b*=a·c*=b·c*=0.
𝛼* b* Ø a* is perpendicular to the plane spanned by b and c, and its length
𝛽∗
𝛾∗ along a is 1/|a| (analogously, for b* and c*). The RL L* of L is
defined as the lattice with the basis composed of a*, b*, c*.
a*

Unit Cell of the reciprocal space

In physics:
𝑏×𝑐 ∗
𝑐×𝑎 𝑎×𝑏
𝑎∗ = 2𝜋 𝑏 = 2𝜋 𝑐 ∗ = 2𝜋
𝑎 8 𝑏×𝑐 𝑎 8 𝑏×𝑐 𝑎 8 𝑏×𝑐
V = 𝒂 # 𝒃×𝒄
In crystallography:
𝑏×𝑐 𝑐×𝑎 𝑎×𝑏
∗
𝑎 = ∗
𝑏 = 𝑐∗ =
𝑎 8 𝑏×𝑐 𝑎 8 𝑏×𝑐 𝑎 8 𝑏×𝑐
 Reciprocal Lattice in Reciprocal Space

Ø The crystallographer’s definition has the advantage that the direction of a* is

just the reciprocal magnitude of a in the direction of 𝑏×c

Ø One physical interpretation of the reciprocal lattice is that it is the Fourier

transform of the real lattice.

Ø Reciprocal space is also called frequency space (K-space) or power

spectrum.
Ø The reciprocal lattice plays a fundamental role in most analytic studies of
periodic structures, particularly in the theory of diffraction. – crystal
structure solving, 3D tomography etc.
 Symmetry in Reciprocal Space: Laue Symmetry
Crystal System Laue Group --11 Point Group –32
Triclinic -1 1, -1
Monoclinic 2/m 2, m. 2/m
Orthorhombic mmm 222, mm2, mmm
Trigonal -3 3, -3
-3/m 32, 3m, -3m
Tetragonal 4/m 4, -4, 4/m
4/mmm 422, 4mm, -42m, 4/mmm
Cubic m3 23, m3
m3m 432, -43m, m3m
Hexagonal 6/m 6, -6, 6/m
6/mmm 622, 6mm, -6m2, 6/mmm

Ø Laue symmetry is the symmetry in reciprocal space (taking account the reflex intensities)
and Friedel’s law (𝐼+), = 𝐼+-). , ̅) is assumed to be true.
Ø Laue symmetry is very useful in determination of space group of a crystal using a
diffraction technique.
 Real Lattices vs. Reciprocal Lattices

Direct lattice Reciprocal lattice

Simple Cubic (SC) Simple Cubic (SC)

Face-centered cubic (FCC) Body-centered cubic (BCC)

Body-centered cubic (BCC) Face-centered cubic (FCC)

Simple hexagonal Simple hexagonal

Ø Bravais’s lattices (a, b, and c) which have 𝛼 = 𝛽 = 𝛾 = 90°, (cubic, tetragonal and
orthorhombic), have (a*, b*, and c*) parallel to their real space vectors.
Ø The reciprocal lattice is Fourier transformation of its corresponding direct lattice, and
vice versa. --- This is the key to understand the relationship between TEM images and
its Diffraction.
 Ewald Sphere
Ewald sphere construction Ewald sphere animation from
“An Interactive Course on Symmetry and
E-beam Analysis of Crystal Structure by Diffraction”
(hkl) plane By: Gervais Chapuis and Wes Hardaker

1/l

K
K0 2θ

ghkl Phkl

o Points of
1/d reciprocal lattice
Origin of the
reciprocal lattice

Ø A tool to visualize the conditions under which Bragg’s law is

satisfied and therefore a reflection (diffraction spot) will be
observable.
Ø This occurs when the surface of a sphere centered about the crystal
with radius = 1/l intersects with a point on the reciprocal lattice.
 Brillouin Zone
q The Brillouin zone is defined as a Wigner-Seitz primitive cell in the reciprocal lattice
and gives geometric interpretation of the diffraction condition.
q The degree of symmetry refers to how spherical the Brillouin zone is, the higher the
symmetry, the more spherical the BZ is.
Ø The Brillouin construction exhibits all
wavevectors k that can be Bragg reflected
by the crystal.
Ø The constructions divide the Fourier space
into fragments, out of which the first
Brillouin zone is of greatest importance.
Ø The BZ is a very important concept in
solid state physics; it plays a major role in
the theoretical understanding of the
BZ of the Hexagonal and rectangle lattices
elementary ideas of electronic energy
Courtesy R.C. Andrew et al., bands.
 The Structure Factor
q The structure factor is a mathematical description of how a material scatters incident
radiation.
012,$3456 89 :;<6 '=;336>65 ?@ ;,, ;381' $A ; BC
The Structure Factors (F) =
012,$3456 89 :;<6 '=;336>65 ?@ ;A 6,6=3>8A

q The structure factors, F(hkl), is the Fourier

transform of the electron
density function, ρ(xyz).
! # %
( +,-(% 0) 0* )
𝐹%)* = ∭'( 𝜌!,#,$ 𝑒 " $ & 𝑑𝑥𝑑𝑦𝑑𝑧

q The electron density function shows

maxima at the location of the atoms, the
internal structure of the crystals.
( ( (
! # $
'+,-(% 0) 0* ) q The F(hkl), is the resultant of all waves
𝜌!,#,$ = % % % 𝐹%)* 𝑒 / 1 2
scattered in the direction of the hkl
%&'( )&'( *&'( reflection by the n atoms contained in the
unit cell. Its mathematical expression must
Real space Reciprocal space therefore take into account the scattering
from every atom contained in it.
 Scattering by a Crystal

A
Electron Polarization factor

B
Atom Atomic scattering factor (f)

C
Unit cell (uc) Structure factor (F)
https://enthu.com/knowledge/chemistry/atomic-structure-vs-crystal-structure/
 Scattering by an Electron
Intensity of a ray Scattered by an Electron
z
For a polarized wave oscillating in z direction P

a r

Intensity of the scattered beam due to an electron (I) at a point P such that r >> l

e æ Sin a ö
4 2
I = I 0 2 4 çç 2 ÷÷
mc è r ø
1

0.8

0.6

0.4

0.2
The reason why scattering from the
protons in the nucleus can be neglected.
Cos(t)

0 t
0 30 60 90 120 150 180 210 240 270 300 330 360
-0.2

-0.4

-0.6

The scattered rays are also plane polarized

-0.8

-1
 Atomic Scattering Factor (Atomic Form Factor)
q The atomic scattering factor is also called atom form factor, as a measure of the
scattering power of an isolated atom, quantifies the efficiency of scattering from a group
of electrons in an atom. It is the Fourier transform of the electron density of an atom.
012,$3456 89 :;<6 '=;336>65 ?@ ;A ;381
Atomic Scattering Factors (f) =
012,$3456 89 :;<6 '=;336>65 ?@ ;A 6,6=3>8A

q For the diffraction condition is Δk=q=G, where q is called the scattering vector. In the
range of scattering vectors between 0 < q < 25 Å-1, the atomic form factor is well
approximated by a sum of Gaussians of the form (where the values of ai, bi, and ci can be
found in Tables): $
( "
%&! ($)) +,!
𝑓 𝐺 = $ 𝑎! 𝑒
!"#

q The atomic scattering factor depends on the scattering amplitude of an individual atom and the
Bragg angle of scattering as well as the type of radiation (X-ray, electron and neutron) involved,
which is independent of the position of the atom.
 The Structure Factor
Ø The resultant amplitude of all the waves scattered by all the atoms in the UC gives the
scattering factor for the unit cell
Ø The unit cell scattering factor is called the Structure Factor (F)
Scattering by a unit cell = f(position of the atoms, atomic scattering factors)

! ! ! !
([+, "-$ .#/$ .$0$ ]
𝐹!"#$ = : 𝑓% 𝑒 (∅% = : 𝑓% 𝑒 = : 𝑓% cos 2𝜋(ℎ𝑥% + 𝑘𝑦% + 𝑙𝑧% + 𝑖 : 𝑓% sin 2𝜋(ℎ𝑥% + 𝑘𝑦% + 𝑙𝑧% )
%&' %&' %&' %&'

For n atoms in the UC, (hkl) are Miller indices of atomic planes with the atoms

The structure factor is a complex number

 The Structure Factor

Ø Structure factor is independent of the shape and size of the unit cell

ØDescribes how atomic arrangement (uvw) influences the intensity of the

scattered beam. "#$ 2
𝐼 = 𝐹!

ØIt tells us which reflections (i.e., peaks, hkl) to expect in a diffraction pattern ---
atomic type and position dependent.

Ø Structure factor expresses the best approximation of the electron density in

terms of a single cosine wave
 Calculate Structure Factor of fcc-Au
Au toms at (0,0,0) & (½, ½, 0) equivalent positions

é i[ 2p ( 0)] i[ 2p (
h+k
)] i[ 2p (
k +l
)] i[ 2p (
l +h
)] ù
F = f êe +e 2
+e +e 2 2
ú
ë û
ip ( h + k ) ip ( k + l ) ip ( l + h )
= f [1 + e +e +e ]
Real
ip ( h + k ) ip ( k +l ) ip ( l + h )
F = f [1 + e +e +e ]
fcc Unit Cell

(h, k, l) unmixed F =4f F = 16 f

2 2 e.g. (111), (200), (220), (333), (420)

(h, k, l) mixed F =0 F =0 2
e.g. (100), (211); (210), (032), (033)

Selection / Extinction Rules

 Structure Factor for Aperiodic Matters?
Ø The unit cell scattering factor is called the Structure Factor
012,$3456 89 :;<6 '=;336>65 ?@ ;,, ;381' $A ; BC
Structure Factors =
012,$3456 89 :;<6 '=;336>65 ?@ ;A 6,6=3>8A

Ø The structures of aperiodic matters (quasicrystals and amorphous) cannot be described simply by a UC.

5* 8 10 12 ?

Ø Other methods for aperiodic matter characterization must be considered.

Radial Distribution Function/Pair Distribution Function

q Pair distribution function (PDF)/ Radial distribution function

(RDF) describes the distribution of distances between pairs of particles
contained within a given volume. Mathematically, if a and b are two particles,
the pair distribution function of b with respect to a, denoted by 𝑔;? (𝒓) is the
probability of finding the particle b at distance r from a, with a taken as the
origin of coordinates.
q It is a major descriptor for the atomic structure of amorphous materials (glasses,
polymers) and liquids. The PDF/RDF can be calculated directly from physical
measurements like light scattering, XRD, ND or ED by performing a Fourier
transform.
Radial Distribution Function/Pair Distribution Function

1 𝑑𝑛(𝑟, 𝑅 + 𝑑𝑟)
𝑔 𝑟 =
𝜌 𝑑𝑣(𝑟, 𝑟 + 𝑑𝑟)

ØCarve a shell of size r and r + dr around a center of an atom. The volume of

the shell is dv=4pr2dr
ØCount number of atoms with centers within the shell (dn)
ØAverage over all atoms in the system
ØDivide by the average atomic density <r>
 Radial Distribution Function vs. The Structure Factors
q N-point RDF:
2 2
𝑉 1 1 678(:"(&) ,<<<,:"(#)
𝑔! (𝑟' ,888, 𝑟! ) = 3
P Q 𝑑 𝑟( : 𝑒
𝑁! 𝑉 𝑍2
(&!.' ,∈5#
For a system of N particles in a volume V (for an average number density 𝜌 = 𝑁/𝑉) and at a temperature T (let us
'
also define 𝛽 = #=). The particle coordinates are ri, with i= 1, 2, ,,, N. The potential energy due to the interaction
between particles is UN (r1,--, rN) and we do not consider the case of an externally applied field.

q The (Static) Structure factor (SF):

+
The 2nd-order correlation function 𝑔 (𝑟' , 𝑟+ ) = g(r) is of special importance, as it is directly related (via a FT) to the
“Static” SF (S(q) of the system and can thus be determined experimentally using XRD or ND, ED.

𝑠 𝑞 = 1 + 𝜌 Q 𝑔(𝑟)𝑒 6(?: 𝑑𝑟
>

Ø This equation is only valid in the sense of distributions.

 Applications of Fourier Transform

q FTIR
q Power spectrum/FFT of high-resolution images
q PDF analysis from XRD, ED, ND and EELS
q For solving crystal structure
qFor 3D tomography
qImage filtering and processing

etc.,
 Direct Lattice vs. Reciprocal Lattice
HAADF SAED HAADF FFT

𝛽-Ga2O3-[010]
~12º away from 𝛽-Ga2O3-[010]

(001)𝛽-Ga2O3

(001)𝐺𝑎𝑁
SAED FFT [11-20]GaN
GaN- ~12° off [1120]

[010]Ga2O3

Ø FFT of a High resolution HAADF image has similar geometry to the corresponding SAED
Ø SAED is a FFT of its corresponding image, i.e., reciprocal lattice is a FFT of its direct lattice, and vice versa
 Fourier Image Filtering
HAADF FFT with a Band mask IFFT

HAADF FFT with selected Spots IFFT

Pair Distribution Function (PDF) Calculation-Au NCs

3D atomic configurations for

the different coordination
numbers with atomic distance,
covering the first seven peaks
in the normalized PDF profile.
Note that for the coordinate
peak at 8.65A ̊ the coordinate
number 36 is the sum of two
different interatomic distances,
[330]/ 2 and [411]/2.

H.W. Liu et al., J. Appl. Cryst. (2023). 56, 889–902

Pair Distribution Function (PDF) Calculation: Amorphous
a-SAED
 Dual Ion Beam Irradiation Experiment On Rb3NdP2O8 –on 06/07/2023
---1.2MeV Xe3+ @ 3.7 ×10-5 dpa/s and 23keV He+ @ 0.22nA /mm2
SAED SAED SAED SAED SAED

0.95min-0.21dpa 0.22dpa 0.27dpa 0.31dpa 160min-0.36dpa

PDF of Amorphized Rb3NdP2O8

40
PDF-95min PDF-100min PDF-120min
30

20 PDF-140min PDF-160min Ø In general, with the increase of

10
damage level, all the peaks in
PDF decrease.
G(r)

0
0 5 10 15 20 Ø The data could be used for
-10
understanding of structure
-20
evaluation under irradiation
-30

-40
Scatter Vector (r, A)