6a Fundamentals of Rietveld Refinement XRD Simulation
6a Fundamentals of Rietveld Refinement XRD Simulation
6a Fundamentals of Rietveld Refinement XRD Simulation
2000
0
4000 Quartz
3000
2000
1000
0
Cristobalite
4000
2000
0
20 30 40 50
Position [°2Theta] (Copper (Cu))
1
hkl
2
• dhkl* is the reciprocal of dhkl: d * 2
d hkl
bc sin
a*
• dhkl is calculated based on the reciprocal abc
space units of the lattice parameters cos cos cos
cos *
sin sin
• the diffraction peak position is a product
of the average atomic distances in the
crystal
• anything that changes the average bond
distances (temperature, pressure, etc.)
will change dhkl and therefore change the
diffraction peak positions
The amplitude of light scattered by a crystal is determined
by the arrangement of atoms in the diffracting planes
2
𝐼ℎ𝑘𝑙 ∝ 𝐹ℎ𝑘𝑙
Fhkl N j f j exp 2ihx j ky j lz j
m
j 1
j 1
2
B sin 2 q
f
2
f 0 exp f '
f ' ' 2
l 2
The atomic scattering factor f0 can be found using tables or
equations determined experimentally or from quantum
mechanical approximations
40
• f0 at 0° is equal to the number of
Y
electrons around the atom 35 Y(3+)
– Y and Zr are similar, but slightly Zr
different, at 0° 30 Zr(4+)
– Zr and Zr4+ are slightly different at O(2-)
0° 25
fo
– Y3+ and Zr4+ are identical at 0°
20
• the variation with (sin θ)/λ depends
on size of atom
15
– larger atoms drop off quicker
– at higher angles, the difference 10
between Y3+ and Zr4+ is more
readily discerned 5
– at higher angles, the difference
between different oxidation states 0
(eg Zr and Zr4+) is less prominent 0 0.5 1 1.5
(sin q/l
Thermal motion of the atom changes the scattering
factor 2
B sin q
f f 0 exp
• the efficiency of scattering by an atom l 2
is reduced because the atom and its 40
B=0
electrons are not stationary 35 B=1
– the atom is vibrating about its B=10
equilibrium lattice site 30
– the amount of vibration is quantified by
25
the Debye-Waller temperature factor:
B=8π2U2 20
f
• U2 is the mean-square amplitude of the
vibration 15
– this is for isotropic vibration: sometimes
10
B is broken down into six Bij anistropic
terms if the amplitude of vibration is not 5
the same in all directions.
– aka temperature factor, displacement 0
factor, thermal displacement parameter 0 0.5 1 1.5 2
(sin q/l
Anomalous scattering of X-rays with energies near the
absorption edge of the atom changes the scattering factor
2
B sin q
2
f
2
f 0 exp f '
f ' ' 2
l 2
• publications
• Commercial Databases
– ICDD PDF4+ Inorganic
– Inorganic Crystal Structure Database (ICSD)
– Linus Pauling File (LPF)
• this is included in ICDD PDF4+ Inorganic
– NIST Structural Database (metals, alloys, intermetallics)
– CCDC Cambridge Structure Database (CSD) (organic materials)
• Available online http://beta-www.ccdc.cam.ac.uk/pages/Home.aspx
• MIT Site license available for download from IS&T website
• Free Online Databases
– Crystallography Open Database http://www.crystallography.net/
– ICSD- 4% available as demo at http://icsd.ill.eu/icsd/index.html
– Mincryst http://database.iem.ac.ru/mincryst/index.php
– American Mineralogist http://www.minsocam.org/MSA/Crystal_Database.html
– WebMineral http://www.webmineral.com/
– Protein Data Bank http://www.rcsb.org/pdb/home/home.do
– Nucleic Acid Database http://ndbserver.rutgers.edu/
– Database of Zeolite Structures http://www.iza-structure.org/databases/
A Crystal Structure
• ZrO2
• Space Group Fm-3m (225) site occupancy factor,
• Lattice Parameter a=5.11 sof, is equivalent to N
in the Fhkl equation
Zr 4a 0 0 0 1.14 1
• each letter in the Wyckoff notation specifies a site that sits on a different
combination of symmetry elements
– The Wyckoff site indicates if x, y or z are can change or if they must be fixed to preserve the
symmetry of the crystal
– An element on the 4a site in the Fm-3m space group can only occupy 0,0,0
• Moving the element to a different position would change the surroundings of the site and
would represent a change in the interaction between that atom and its neighbors
– An element on the 32f site in the Fm-3m space group will occupy x,x,x (indicating that the x,
y, and z positions must be the same number)
• the number in the Wyckoff notation indicates the number of atoms put into the
unit cell if the atom is on that site
– 4a- an atom on the a site will populate the unit cell with 4 atoms
– 8c- an atom on the c site will populate the unit cell with 8 atoms
– Wyckoff notation gives you a quick way to check if stoichiometry is correctly preserved
when you create a crystal structure
– you can deduce z, the number of molecules per unit cell, from the Wyckoff notation (z=4 for
ZrO2)
Retrieve information about space groups using the
Symmetry Explorer in HighScore Plus
j 1
• Desktops can be
changed in the menu:
– View > Desktops
• You can type the element symbol or select from a drop-down menu
– The element can be an atom or ion (select oxidation state)
• the use of oxidation states in modifying the scattering factor for an atom is set in
Customize>Program Settings, in the Rietveld tab
• by default it is set to “Ignore Oxidation States”
• This is not just useful for these tutorial purposes, but also
for anticipating what your real data might look like and
for evaluating limits of detection
To change values for the simulation
fo
change the SOF of O to 0.5, then 20
recalculate the pattern
15
• Remember, the atomic scattering
factor, f0, is equal to the number of 10
electrons around the atom
5
– Zr atoms scatter much more
strongly than O, so the XRD 0
diffraction pattern is more sensitive 0 0.5 1 1.5
to the Zr atoms (sin q/l
We can predict the change in peak intensities
when we dope the sample
40
• change thermal parameter for Zr B=0
– reset the SOF of Zr to 1 and the SOF 35 B=1
of the other 4a atom (Ce or Y) to 0 B=10
30
• the diffraction pattern will be
representative of ZrO2 with no doping 25
f
diffraction pattern
15
• change from 1.14 to 2.3
• change to 5 10
• change to 0.1 5
0
0 0.5 1 1.5 2
(sin q/l
B sin 2 q
f f 0 exp
l 2
These simulations do not necessarily represent the
data that your diffractometer will produce
• There are more factors that contribute to the diffraction pattern that
you collect with an instrument
32
Pk r 2 cos2 k r 1 sin 2 k
k is the angle between the preferred orientation vector and the
normal to the planes generating the diffracted peak
r is a refinable parameter in the Rietveld method
• Absorption Correction
– accounts for the transmission and absorption of the X-rays through the irradiated
volume of the sample.
– depends on sample geometry: flat plate or cylindrical
– depends on the mass absorption coefficient of the sample
• significant for cylindrical or transmission samples with a high sample absorption
• significant for a flat plate sample with a low sample absorption
• Extinction Correction
– Secondary diffraction of scattered X-rays in a large perfect crystal can decrease
the observed intensity of the most intense peaks
– scattering by uppermost grains limits the penetration depth of a majority of X-
rays, causing a smaller irradiated volume
– want “ideally imperfect” crystals– grains with enough mosaicity to limit extinction
– better to reduce extinction by grinding the powder to a finer size
• These two corrections are rarely used. Caution is advised. Always check to
make sure that the correction values are physically meaningful.
We now know how to calculate the diffraction peak
intensity, but there a couple of more factors involved in
simulating real diffraction data
• The intensity, Yic, of each individual data point i is calculated using the
equation: k2
Yic Yib Gik Ik
k k1
• We already know how to calculate IK, the intensity of the Bragg diffraction
peak k: IK=SMKLK|FK|2PKAKEK
• Yib is the intensity of the background at point i in the pattern
• k1 - k2 are the reflections contributing to data point i in the pattern
– sometimes multiple Bragg diffraction peaks overlap, resulting in multiple
contributions to the observed intensity at a single data point
• Gik is the peak profile function
– this describes how the intensity of the diffraction peak is distributed over a range
of 2theta rather than at a single point
– this profile is due to instrument broadening, sample broadening, etc
Diffraction peaks have profiles that must be
empirically modeled
• The intensity equation Ik predicts that diffraction peak intensity occurs at a
single point 2theta– but in reality the diffraction peak intensity is spread out
over a range of 2theta
– The total area of the diffraction peak profile is the predicted intensity Ik
• Diffractometers contribute a characteristic broadening and shape to the
diffraction peak based on their optics and geometry
– each separate combination of divergence slit apertures, Soller slits, beta filter
or monochromators, and detectors will have their own characteristic
instrument profile
50
Profile Parameters
Peak Shape
51
The Cagliotti equation describes how peak width
varies with 2theta
H k U tan q V tan q W
2
1/ 2
53
Diffraction Peaks from laboratory diffractometers
are a mixture of Gaussian and Lorentzian profiles
Counts
Counts
4000
2000
1000
1000
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0
42 44 46 48 50
45.50 46
Position [°2Theta]
Position [°2Theta]
54
Several different functions can be used to describe the
mixing of Gaussian and Lorentzian contributions
G jk
2
H k
1 4 X 2jk
1
1
C11/ 2
H k 1/ 2
exp C1 X 2
jk
1 2 2q 3 2q 2
• The parameters 1, 2, and 3 are the refinable shape parameters,
listed as Peak Shape 1, Peak Shape 2, and Peak Shape 3 in the
Refinement Control list
– Usually Peak Shape 1 is the only one used
• Hk is the Cagliotti peak width function
• C1 is 4 ln 2
2q i 2q k
• Xkj is X jk
Hk
Background can be empirically fit with an equation,
manually fit, or evaluated with a blank sample
• refinement of a polynomial function
• refinement using a type I or II Chebyshev polynomial function
• By amorphous sinc function
• linear interpolation between base points
• independent data collection run without the sample in place
– It is difficult to use this technique effectively– it requires careful evaluation of the validity of the background fit
57
Systematic error in diffraction peak positions can
also be calculated
59
What is Physically Meaningful?
Wel (1975)
60