Analysing X-ray data using GudrunX
2.0
Ca60Mg25Cu15
Ca60Mg20Cu20
X-ray i(Q)
1.5
Ca60Mg15Cu25
1.0
0.5
0.0
-0.5
-1.0
0
2
4
6
8
10
-1
Q (Å )
12
14
16
18
Outline
• Planning an experiment
– Absorption
– Fluorescence
– Beam size
• Data required
• Outline of analysis process
• Step by step guide through
analysis
• Practice with some data!
– SiO2
– H2O
– Tellurite glass
Planning an experiment
• Before starting an experiment it is important to have a very good idea of
your sample composition and density.
• This information will help identify any potential problems which may
arise, such as:
– Absorption +capillary size
– Beam size
– Measurements required
– Fluorescence (We’ll return to this later)
• A good idea of potential problems will help you plan the length of your
experiment too.
– Strongly absorbing/weakly scattering or strongly fluorescent samples
may require longer data collection
• Consider what your data will be used for and what quality you require.
Planning an experiment: Absorption
If we accept 60% loss of
flux, we can estimate the diameter of capillary to use:
Linear (µ) and mass (µ/ρ) absorption
coefficients can be calculated from programs
such as XOP(1)
L
H2O : µ = 0.656
ln(0.4)/-6.626 = 1.4 cm
d ~ 1.8 cm
Al2O3 : µ = 6.626
d ~ 2 mm
GeO2 : µ = 96.906
d ~ 0.12 mm
2r
Area = πr2
Y2O5 : µ = 186.756
d ~ 0.07 mm
L =(πr2)/2r = π/4 d
~ 3/4 d
TeO2 : µ = 68.607
d ~ 0.18 mm
PbO : µ = 549.499
d ~ 0.03 mm
Ge (32)
Y (39)
Te (52)
Ag
1000
Increase Z → increased energy at
which K edge occurs.
100
for region around Ag
(Z > Ag) µ/ρ < (Z <Ag)
10
1
0.1
10000
100000
Energy (eV)
HOWEVER, there is also density to consider
Mass Absorption coefficient (Ag K)
Mass Attenuation coefficient
Planning an experiment: Absorption
100
Ag
80
60
40
20
0
0
10
20
30
40
50
Element
60
70
80
90
Planning an experiment: Absorption
Example: β filter
A Material chosen as a β filter must have an
absorption edge which lies between the Kα
and Kβ peaks.
For an Ag tube, Rh is used.
linear absorption coefficient cm
-1
800
600
K
K
400
200
0
20000
25000
Energy (eV)
30000
Planning an experiment: Beam size
Diameter of sample (L)
PDS angle (θ)
PDS θ (rad) = L/r
240 mm (r)
Capillary
ASS= PDS x 2
PRS (mm) = L
PDS ASS
size
0.5
1/8 1/4
1
1/4 1/2
1.5
1/2
1
2
1/2
1
2.5
1
2
3
1
2
Table 1: PDS and ASS
settings
Anti scatter
slit
Mask
Prog. Div. slit
Soller slit
Kβ filter
X-ray tube
Prog. Rec. slit
Soller slit
Detector
Measurements needed
Once the experimental setup has been
decided up, three measurements are
required – as with Neutron analysis,
these are:
Background
Sample in capillary
Empty capillary
The current set up is to collect data at
0.2° intervals from 3.2 – 156°.
All these measurements need to be
taken under the SAME CONDITIONS.
At each point, data is collected of 30
seconds.
There is the option to collect two sets
of data:
Several repeat scans from 3.2 to 156°
Additional scans from 35 to 156° to
improve statistics at high Q
GudrunX: What does it do?
• Calculating the coherent scattering
Measured data
background data
Krogh-Moe – Norman normalisation
Compton scattering
Polarisation
raw data
corrected for
absorption &
polarisation
5
6x10
5
5x10
Absorption
5
Intensity
4x10
5
3x10
5
2x10
5
1x10
0
0
2
4
6
8
10
12
-1
Q (Å )
14
16
18
20
22
GudrunX: What does it do?
Experimental data
Self scattering
120
100
S(Q)
40
20
0
S(Q)
60
40
-20
-40
-60
-80
20
-100
4
8
12
16
20
Q
0
20
40
60
80
100
120
140
0.6
2
• Calculating F(Q)
S(Q)
0.4
0.2
Effect of normalisation:
0.0
sample
<f>2
<f2>
%diff
SiO2
100
108
8%
Ga2O3
309.7
448
44%
S(Q)
Intensity
80
-0.2
-0.4
-0.6
-0.8
-1.0
5
10
15
Q
20
Installing GudrunX
The X-ray diffractometer webpages can be found at
http://www.isis.stfc.ac.uk/support-laboratories/xrd/xrd9446.html
OR as a link from the disordered materials group web page.
Instrument panel:
The required files are all located in the gudrunX folder.
•User may wish to alter the Q range of the F(Q) produced, depending on the
quality of the data.
•The Qmax should be set to the final Qmax you chose for you data.
Beam panel:
Requires minimal alteration.
•Edit the beam size if the beam is smaller that the sample.
•Ensure the correct bremsstrahlung file is chosen.
Normalisation panel:
User must choose which method of normalisation they wish to apply to the
data.
Altering Breit-Dirac factor and Overlap factor can give some improvements to
the extracted F(Q). Maintain default values initially.
Sample background panel:
Select an appropriate sample background panel.
‘Read data’ will display the information from the .XRDML file, including number
of scans and the range of angles over which the chosen data set has been
measured.
Set sample background factor (between 0.9 and 1)
Sample specific information required:
Once the instrument and background information has been checked, new tabs
need to be added to give sample specific information.
As with GUDRUN this includes a sample and a sample container tab.
Information required includes:
Sample specific information:
•Composition
•Effective density
•Sample size
•Fluorescence - a problem for elements in the same row as Ag (Rb – Te)
•Multiple scattering
Experimental setup:
•Polarisation - 0
•Compton scattering - 1
•Bremsstrahlung - 0.4
Container panel:
Composition, container size (inner and outer dimensions), effective density.
For density either the measured effective density can be given, with a tweak
factor = 0
Or the bulk density can be used with the tweak factor altered
Effective density = bulk density/tweak factor
Sample panel:
Basic information + fluorescence, multiple scattering etc.
Ensure that packing fraction is sensible (measure or estimate it ~60%)
Vary effective density and multiple scattering first, then bremsstrahlung.
Only apply fluorescence for samples containing Rb – Te.
GudrunX: Output files
.subcan
X = 2θ
Y1 = experimental data
Y2 = single atom scattering
Y6 = Bremsstrahlung
GudrunX: Output files
.soq
X=Q
Y1 = F(Q)
F(Q) will have been
normalised to either <f>2
or <f2>. Ensure that you
have a record of which you
used!
GudrunX: Output files
.gofr
X=r
Y1 = G(r)
Quality of G(r) can be improved by
varying parameters in GudrunX.
Alternatively, the fourier transform
software in Open Genie can be used.
Daniel will be discussing the relationship
between various correlation functions
Fluorescence
4000
Ca bioglass
Ca/Sr bioglass
Empty SiO2 capillary
3500
Intensity (cps)
3000
2500
2000
Fluorescence provides a background
which is uniformly distributed across
the angular range
1500
1000
500
0
0
20
40
60
80
100
120
Angle
10000
Mass absorption coefficient
X-ray energy > absorption edge in
sample → Fluorescence
Ca
Sr
Ag K edge
1000
100
10
1
1000
10000
Energy (eV)
100000
Fluorescence
4000
Ca bioglass
Ca/Sr bioglass
Empty SiO2 capillary
3500
Intensity (cps)
3000
Multiplying the data measured for the
empty capillary and Ca/Sr glass data
by a scale factor to match the Ca glass
data (at high angle) gives:
2500
2000
1500
3000
2500
500
0
20
40
60
80
100
120
Angle
10000
Ca
Sr
Ag K edge
1000
Intensity (cps)
0
Mass absorption coefficient
Ca bioglass
Ca/Sr bioglass
Empty SiO2 capillary
1000
2000
1500
1000
500
0
100
0
40
60
80
100
Angle
10
1
1000
20
10000
Energy (eV)
100000
The shape of the capillary and calcium
data are well matched.
Problem with strontium sample.
120
Fluorescence
4000
Ca bioglass
Ca/Sr bioglass
Empty SiO2 capillary
3500
Intensity (cps)
3000
However, if a constant background is
subtracting from the Ca/Sr data and
THEN the data is scaling:
2500
2000
1500
3000
2500
500
0
20
40
60
80
100
120
Angle
10000
Ca
Sr
Ag K edge
1000
Intensity (cps)
0
Mass absorption coefficient
Ca bioglass
Ca/Sr bioglass
Empty SiO2 capillary
1000
2000
1500
1000
500
0
100
0
40
60
80
100
Angle
10
1
1000
20
The characteristic X-ray shape is once
again present in the data
10000
Energy (eV)
100000
120