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Basic Tutorials on XAS data analysis using y g

Athena & Artemis


Dr. Wantana Klysubun
(Manager of Beamline 8, wantana@slir.or.th)
Workshop at Kantary Hills Hotel, Chiang Mai
2 September 2011 2 September 2011
By Monte Carlo Simulation and Molecular Dynamics in physics Research
Laboratory, CMU and ThEP
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Standard procedure for XAS data processing
1. Get to know data file from BL8 : Which columns store photon energy and
absorption values?
2. Data processing with Athena
2 1 O d t fil f l 2.1 Open data files of your sample
2.2 Plot all spectra, inspect them, delete the bad ones
2.3 Align spectra
2.4 Merge spectra into one spectrum (from now on, the merged spectrum will be g p p ( , g p
processed)
2.5 Normalize spectrum
2.6 Save all your work and a text file of normalized spectrum
3. Linear combination fit by Athena
4. Peak fit by Athena
5. Fitting EXAFS spectrum by Artemis
5.1 Import merged spectrum
5.2 Create atomic model by Atom
5 3 Generate scattering paths by FEFF 5.3 Generate scattering paths by FEFF
5.4 Select important paths and define parameters of each path
5.5 Fit parameters
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1. Get to know data formats at BL8
At BL8 d t fil di t (1) t f l At BL8 we name a data file according to (1) type of sample,
(2) Mode of XAS measurement, (3) type of detector, (4)
XANES or EXAFS spectrum and (4) time when the file was
Saved. For examples,
-Open a file with Notepad or Wordpad to see data stored in
each column.
What column is photon energy ?
File#1 : NiNO3 EXAFS 0623_1
File#2: NiNO3 EXAFS 0623_2

File#6: NiNO3 EXAFS 0623_6


What column is I0?
What column is absorption?
The file name #1 tells that it is an EXAFS spectrum of NiNO3
(which actually is Ni(NO3)2), measured in transmission mode,
saved at 6:23 am on that day. There are six successive scans
for this sample.
What column is absorption?
File#7 : C029 FLGe EXAFS 2233_1
Sample =C029
Mode =Fluorescence yield
Detector =13-element Ge detector
File contains EXAFS data
File#8: xxx FLSi 0000 File#8 : xxx FLSi 0000
Sample =xxx
Model =Fluorescent yield
Detector =Si drift detetor
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2. Data processing with Athena
4 Plot multiple spectra
EXERCISE 1 : Normalize NiNO3 EXAFS data
1. Run Athena
2. > File> open files
select all NiNO3 EXAFS xxxx files
4. Plot multiple spectra
select spectra, then
click on
and
select all NiNO3 EXAFS xxxx files
mark column 1 for photon energy
mark column 6 for numerator
3. Plot one spectrum
highlight filename then click highlight filename, then click
on
plot in mu (E)
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2. Data processing with Athena
5 Plot all spectra
- plot as smoothedderivative
5. Plot all spectra
6. Delete bad spectrum, if any
highlight filename > group actions > remove
group
plot as smoothed derivative
- fit as smoothed derivative
- Click on
Are they consistent?
7. Align spectra
Athena will do the followings:
> Data > Align scans
- select standard spectrum that we think there is no
shift of energy
- select other spectrum that will be aligned to the
standardspectrum
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standard spectrum
2. Data processing with Athena
8 Align all other spectra 8. Align all other spectra
9. Return to the main window
see E shift on each spectrum
We can calculate the mean value of E shifts and use
it as the uncertainty in photon energy of your
experiment !
10 Plot all spectra 10. Plot all spectra
11. Merge all spectra
> Merge> merge marked data in mu(E)
12. Rename merged spectrum
double click on the old name (merge)
andreplace with NiNO3 mergedEXAFS and replace with NiNO3 merged EXAFS
13. Save all your work
> File > Save entire project
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2. Data processing with Athena
14 Normalized merged spectrum 14 . Normalized merged spectrum
-highlight NiNO3 merged EXAFS
- mark to plot pre-edge line and
post edge line
-Select good region that can be fit by a linear function
Pre-edge range from eV to eV
relative to E0
- What is E0?
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2. Data processing with Athena
- What is E0? - What is E0?
- Plot the 1
st
derivative of the spectrum, select E0 at the center of the first peak to get
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2. Data processing with Athena
-- select regionafter the edge which -- select region after the edge which
will be your normalization range.
Arthena will fit data in this range with
a polynomial function (purple line)
of order 1, 2 or 3
Normalization range from . eV to eV
- Click on to select
the order of the polynomial function
- Recall that normalized (E) =(E)/A
A is the edge step =post(E0)
- Never flatten the normalized spectrum, so unclick it
g p p ( )
- What is your edge step ?
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2. Data processing with Athena
15 Plot normalized spectrum 15 . Plot normalized spectrum
19. Plot all normalized spectra
16 . Save your work
17 S t t fil f th li d t 20 E t t EXAFS ill ti Chi(k) 17. Save a text file of the normalized spectrum
> File > Save norm(E)
18. Normalize other spectra with the same
parameters
20. Extract EXAFS oscillation or Chi(k)
- Highlight NiNO3 merged EXAFS, plot mu(E)
and background
Highlight NiNO3 merged EXAFS, mark all other
spectra
> Value > Set all marked group to the current
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2. Data processing with Athena
21. Plot EXAFS in k space
- click on
- select region for background absorption, Athena will
use a spline function (red line) to fit background of
the data in this region
_(E) = {(E)- 0(E) }/ A
0(E) =background absorption(red line)
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0(E) =background absorption (red line)
2. Data processing with Athena
22 Pl t ll t i k 24 S hi(k) 22. Plot all spectra in k space 24. Save chi(k)
> File > Save chi(k) > k^2*chi(k)
25. Fourier transform
- set good k range for the Fourier transform
-mark to show the Fourier transform function
that you have selected
If you have more scans, you will get less noise, especially
i hi h k i !
that you have selected.
in high k region !
23. Plot EXAFS in k space with other k-weight
- click on
What different do you see?
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2. Data processing with Athena
Pl hi(R) li k - Plot chi(R), click on
-What are k range, dk of the window and window type
26 S hi(R)
g yp
suitable for this chi(k) data ?
k range from .. to
dk = window type =..
26. Save chi(R)
> File > Save chi(R)
27. Save your entire project
End of Athena Tutorial !
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5. Fitting the EXAFS spectrum by Artemis
EXERCISE 2 Fi i h NiNO3 d EXAFS 2 R A t i EXERCISE 2 : Fitting the NiNO3, merged EXAFS
spectrum
1. Search information on the atomic arrangement for
Ni(NO3)2.6H2O that will help to model this molecule.
2. Run Artemis
> File > open files
- select NiNO3 EXAFS. prj, hightlight on NiNO3 merged
EXAFS, click on
( ) p
- Ni is surrounded by six oxygen atoms in octahedral
geometry. We will start with this simple model. g y p
+y
+z
R
Ni
+x
R =2
Ni
O
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5. Fitting the EXAFS spectrum by Artemis
2 C t t th t i d l > f ff i 2. Construct the atomic model
> Theory > Quick first shell theory
- set Absorbing atom to Ni
Edge to K
Scattering atom to O
> feff.inp
- see that Artemis creates one atom of Ni and six atoms of
oxygen
g
Distance to 2.0 A
Coordination to octahedral
- click do it
+y
+z
R
+x
R
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+x
5. Fitting the EXAFS spectrum by Artemis
2 P iti Ni d t f f ff i
- see that Feff generates five scatteringpaths
2. Position Ni and oxygen atoms from feff.inp
- see that Feff generates five scattering paths
4. Lets fit the data with path#1
- click on path 1
+z
+y
3. Click Run Feff , then > interpretation
+x
- Draw scattering route of photoelectron wave leaving
from the Ni atom and coming back to the Ni atom
+y
+z
Path #1
+x
-How many routes are equivalent to this one?
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Degeneracy (degen) =Number of equivalent routes
5. Fitting the EXAFS spectrum by Artemis
- Set which parameters should be varied or fixed.
> Guess, Def, Set
- What is Reff?
Effitive view
of
multiple
scattering
R
2
R
3
R =(R
1
+R
2
+R
3
)/2
scattering
is R
1
4. Define parameters of path#1
- Edit the 1
st
row to rename amp as S02
Set S02 =1 andGuess it (to be varied) - Set S02 =1 and Guess it (to be varied)
- EXAFS equation of path#1 is - Set enot =0 and Guess it
- Set delr =0 and Guess it
- Set ss =0.003 and Guess it
- By default, Artemis defines amp =S0^2 and use N =1
- Rename amp to S02 and set N =6
- R1 =Reff +delr
-Note that enot =E0 is the energy different between initial 1s
state and the final p state, i.e. the edge energy .
-At E =E0, k =0 because
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5. Fitting the EXAFS spectrum by Artemis
6 Define the fitting range to fit the data with path#1 6. Define the fitting range to fit the data with path#1
- Click on NiNO3 merged EXAFS, set R-range =1 to 3
5. Plot chi(R) from path#1
- Highlight the data and path 1
-try setting S02 =0.7, What different dose it make?
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5. Fitting the EXAFS spectrum by Artemis
-To see fitting result, >highlight fit 1 and click on
parameter report
- Keep in mind that number of variables (parameters that you
set them to Guess must be lower than independent points.
-Are the values of variables determined by Artemis y
reasonable?
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5. Fitting the EXAFS spectrum by Artemis
-Always check how good the fit is to the real part and
imaginary part of _(R)
-Always check how good the fit is to the original _(k)
- What do you think ?
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5. Fitting the EXAFS spectrum by Artemis
fi h d i h h#1 d h#2 7. Lets fit the data with path#1 and path#2
-Highlight Ni-O, then path #2, right click on it, add
and jump to feff0002.dat
+y
+z
Path #2
+x
-Study the atom coordinates and draw scattering route from
the Ni atomto oxygen atoms and on the way back to the Ni
- Can you identify all of 24 equivalent routes?
-How many routes are equivalent to this one?
the Ni atom to oxygen atoms and on the way back.to the Ni
Degeneracy (degen) =Number of equivalent routes - What is Reff of path #2 ?
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5. Fitting the EXAFS spectrum by Artemis
8. Define parameters of path#2
- ss2 is different from ss1 because each oxygen atom
contribute mean square variation of path lenght.
- Right click on ss2 >make ss2 a Guess and jump
This is a short cut to
Guess, Def, Set window
Edit ss2 0 003 then hit Enter
- S02 is the scaling factor, it should be equal for all paths
generated from the same atomic model. However, if there
are more than one structure in the sample, S02 can be
different.
-Edit ss2 =0.003, then hit Enter
-Plot data, path#1 and path#2
- E0 is equal for all paths by the same reason as above.
- Why set delR =delr*1.707?
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5. Fitting the EXAFS spectrum by Artemis
L t t ib ti f th#1 d#2 i th k
-Extend R range for fitting, from R =1 to 4
- Click on Fit
- See fitting results and plot contribution from each path
-Lets see contribution of path#1 and #2 in the k space.
-Because ss2 is very large, the sine wave damps quickly in
k, as e
-2k^2*ss2
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5. Fitting the EXAFS spectrum by Artemis
9 fi h d i h h#1 #2 d #3
C id tif ll f 6 i l t t ?
9. Lets fit the data with path#1, #2 and #3
-Highlight Ni-O, then path #3, right click on it, add
and jump to feff0003.dat
-Study the atom coordinates and draw scattering route.
- Can you identify all of 6 equivalent routes?
Wh t i R ff f th #3 ? - What is Reff of path #3 ?
8. Define parameters of path#3
+y
+z
Path #3
+x
- make ss3 a Guess and jump, edit ss3 =0.003, click Enter.
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5. Fitting the EXAFS spectrum by Artemis
Pl d h#1 #2 d #3
Pl t d t fit d h th
- Plot data, path#1, #2 and #3.
- Plot data, fit, and each path
- Click Fit
- See fitting results
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5. Fitting the EXAFS spectrum by Artemis
10 C f th i th fit? Wh t i i 10. Can we further improve the fit? What are we missing
in the model?
12. Draw all 12 hydrogen atoms in the model
+
+z
+y
11. Lets add hydrogen atoms ( from water molecules)
in the model
Water molecule : O-H bond =0.957 A
+x
u =104.5 deg
x1 =0.957cos(u/2)=0.586
y1 =0.957sin(u/2) =0.757
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y ( )
5. Fitting the EXAFS spectrum by Artemis
13 Add H atoms in the model 14 R n Feff and see the scattering paths generated 13. Add H atoms in the model
- Click on feff.inp , Edit it to add 12 hydrogen atoms in the
model.
14. Run Feff and see the scattering paths generated.
- Note that paths #1,#5,#7,#8 and #9 are what we had before
(see p. 16), but now Feff makes new paths #2, #3, #4 and
#6 from scattering with the hydrogen atoms !.
Th i l tt i Ni H ( th #2) d lti l The single scattering Ni-H (path #2) and multiple
scattering Ni-O-H (path #3) are comparably strong as the
multiple scattering from Ni-O-O (#7& #5)
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5. Fitting the EXAFS spectrum by Artemis
15 To start the new fit we must delete paths 1 3 in the 15. To start the new fit, we must delete paths 1-3 in the
last fit.
17 I l d Ni H th #2 d d fi it t 17. Include Ni-H path #2 and define its parameter as
follows:
16. Include oxygen paths #1, #5 and #7 and define their
parameters the same way as you did before.
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5. Fitting the EXAFS spectrum by Artemis
Cli k Fi b d l k h fi i l if - Click on Fit button and look at the fitting results, see if
they have sensible values.
- Note that R factor is much smaller, so the fit including
Ni-H is better.
-Its recommended to check the fit by plotting the imaginary
part in R space and k space.
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5. Fitting the EXAFS spectrum by Artemis
19. Add Ni-O-H scattering, path #3, define its paramaters
and fit.
From the atomic coordinates in Feff.inp, the program calculated
Reff of the path #3 from (R1+R2+R3)/2 where R1 =2.0 A, R2 =
2 695A R3 =0 957A
Th fit l k b tt d
2.695 A, R3 =0.957 A.
Lets allow the program to vary the position of hydrogen atom
freely, so we add a variable (a) in R3 and define delR of the
path #3 as (delr+delrH+a)/2
The fit looks better and
R factor is smaller !
R1+AR
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5. Fitting the EXAFS spectrum by Artemis
S
19. If you think you this is the best fit that you can get,
then make a table to report the fitting parameters.
-Calculate R from Reff+delR for each path, e.g. Reff of Path #1 (Ni-O)
=2.0 A and delR =0.0413 A from the fit., So R =2.0413 A with
Recommended XAS websites
for more tutorials by
XASFS ld id iti
Coordination N R (A) o
2
uncertainty from that of delR (0.00064 A)
XASFS worldwide communities
(www.xafs.org)
Thailand XAS Society
Ni-O 6 2.041+/-0.006 0.007+/-0.001
Ni-H 12 2.903+/-0.093 0.007+/-0.012
Thailand XAS Society
(www. slri.or.th)
- Additionally, we can also calculate the bond length of O-H and the
angle of O-H bond from the obtained parameters of path#3 (Ni-O-H).
-Bond length of O-H =0.957+a =0.957+0.143 =1.10 A
- Angle between two O-H bonds =47.2x2 =94.4 deg.
Contact me: wantana@slri.or.th
Office phone: 044-217-040
2.041
47.2
O
Office phone: 044-217-040
Cell phone: 087-239-0026
Synchrotron Light Research Insititute
P.O. Box 93, Nakhorn Ratchasima 30000, Thailand
End of Artemis Tutorial !
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