Practical approach to EXAFS Data Analysis

by Alexei Kuzmin
Institute of Solid State Physics, University of Latvia
Kengaraga street 8, LV-1063 Riga, Latvia E-mail: a.kuzmin@cfi.lu.lv

Software for EXAFS analysis & simulations

http://www.esrf.eu/UsersAndScience/Experiments/TBS/SciSoft/Links/xafs

IFEFFIT (Athena/Artemis/Feffit) EXTRA FDMNES

A.Kuzmin, October 2011.

EXAFS Data Analysis Software Package

http://www.dragon.lv/eda/

EDAFORM: EDAXANES: EDAEES: EDAFT: EDAFIT:

converts experimental data into the EDA's file format (ASCII, 2 columns). extracts the XANES part and calculates its first and second derivatives. extracts the EXAFS part using improved algorithm for the atomic-like ("zero-line") background removal. performs Fourier filtering procedure with or without amplitude/phase correction and with the rectangular, Gaussian, Kaiser-Bessel, Hamming and Norton-Beer F3 window functions. a non-linear least-squares fitting code, based on a high speed algorithm without matrix inversion. It uses the multi-shell Gaussian/cumulant model within single-scattering approximation and allows simultaneous analysis up to 20 shells with 8 fitting parameters (Ni So2, Ri, i2, E-0i, C3i, C4i, C5i, C6i) in each. The range of values for any fitting parameter can be limited by boundaries or fixed to a constant value. The covariance and correlation matrices can be also calculated. a hybrid regularization/least-squares-fitting code allowing to determine model-independent radialdistribution-function (RDF) in the first coordination shell for a compound with arbitrary degree of disorder. performs analysis of variance of the fit results based on the Fisher's F0.95-test. general-purpose program for plotting, comparison and mathematical calculations frequently used in the EXAFS analysis (more than 20 functions !!!). extracts the scattering amplitude and phase functions from FEFF****.dat files for use with EDAFIT or EDARDF codes (works under Windows).

EDARDF:

FTEST: EDAPLOT: EDAFEFF:

A.Kuzmin, October 2011.

General scheme of the EDA package

EDAXANES EDAFORM XANES EDAEES

EDAFT EDAPLOT FTEST

EDAFIT

EDAFT+EDAPLOT

FEFF+EDAFEFF or EDAFT+EDAPLOT
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EDARDF

EDAEES: Extraction of EXAFS Signal

(E) =

STEP 1:

exp ( E ) b ( E ) 0 ( E ) 0I ( E )

STEP 2:

b ( E ) = A

B E3

0I ( E ) = Pn ( E ) 0II (k ) = Pm (k ) 0III (k ) = S3 (k , p )

n = 2,...,4

0 ( E ) = 0I ( E ) + 0II (k ) + 0III (k )
k = (2me / h )(E E0 )
2

Pn polynomial of n-order S3 smoothing cubic spline

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EDAEES: Extraction of EXAFS Signal

STEP 3: STEP 4:

I (k ) = ( E ) 0I ( E )

II (k ) = I (k ) 0II (k )

0II (k ) = Pm (k )
m = 1,...,7
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0III (k ) = S3 (k , p )
p 0 smoothing spline parameter

EDAEES: Extraction of EXAFS Signal

STEP 5:

0 ( E ) = 0I ( E ) + 0II (k ) + 0III (k )

Influence of zero-line on the EXAFS.

exp ( E ) b ( E ) 0 ( E ) (E) = 0I ( E )

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EDAEES: Extraction of EXAFS Signal

Influence of zero-line removal on the FT of the EXAFS.

A.Kuzmin, October 2011.

Fourier transform (FT)

Window function W(k):

W(k)
A~1-2

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Back-Fourier transform (BFT)

AMPL((k))

Rmin

Rmax

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Influence of backscattering amplitude and phase on EXAFS and FT

N.B. The RDF G(R) is the same for each atoms pair !
0.6
2.0 1.5 Model: 2 2 N=1, R=2 , =0

Backscattering amplitude f(,k,R)

EXAFS (k)k ( )

W
0.4

-2

1.0 0.5 0.0 -0.5 -1.0 -1.5

0.2

Ni O

Ni-O Ni-Ni Ni-W

0 2 4 6 8 10 12 14
-1

0.0

10

12

14
-1

16

18

20

-2.0

16

18

20

Wavenumber k ( )
4

Wavenumber k ( )

Total backscattering phase l (,k,R)=(,k,R)+c (k)

FT (k)k ( )

-5

Ni-O Ni-Ni Ni-W

2
-3

1 0 -1 -2 -3

Ni-O Ni-Ni Ni-W

-10

-15

Model: 2 2 N=1, R=2 , =0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0

-20

10

12

14
-1

16

18

20

-4 0.0

Wavenumber k ( )

Distance R ()

FEFF8 simulations for the Ni K-edge

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Simulation of the EXAFS signal

The EXAFS signal (k) can be described by the following equations depending on the way how the RDF G(R) is described.

1. The parametrized multi-component Gaussian/cumulant model (EDAFIT):

2. The general RDF model (EDARDF):

model ( k ) = S 02

R max

R min

G (R) f ( , k , R ) sin( 2 kR + ( , k , R )) dR kR 2

3. The splice model (EDAPLOT + EDAFT):

Reconstructed from cumulant

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Experimental

=0

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Where to get amplitude f(,k,R) and phase (,k,R) ?

Ab initio theory: FEFF8,
Crystal atoms.inp structure parameters
feff.inp feff****.dat

ATOM

FEFF8

EDAFEFF

amp****.dat pha****.dat

Absolute amplitude and phase

Reference compound: a crystal with well known structure

Experimental EXAFS ref(k)
AMPL(k) PHASE(k)

EDAFT: FT+BFT

EDAPLOT
Crystal structure parameters: N, R

Relative amplitude and phase

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Gaussian/cumulant parametrization of the EXAFS signal

(k ) = S
2 0

2 Ri Ni 2 4 f l ( , k , Ri ) exp( 2 i2k 2 + C4i k 4 C6i k 6 ) exp kR 2 (k ) 3 45 i =1 i 4 4 3 sin 2kRi C3i k + C5i k 5 + l ( , k , Ri ) + 2 cl (k ) l 3 15

M

k = (2me / h 2 )E0
Correlation between parameters
in the amplitude of EXAFS function: S02N, 2, C4, C6 in the phase of EXAFS function: R, C3, C5, E0 Example:
E0 = 1 eV R 0.005 E0 = 5 eV R 0.025 E0 = 10 eV R 0.048 N = 0.5 2 0.001 2 N = 1.0 2 0.002 2

1.Fix E0 2.Fix N
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Relationship between the k and R space Nyquist theorem

From the properties of Fourier transform: if (k) is given in the k-space from kmin=0 to kmax with a step dk, then G(R) will be given in the R-space from Rmin=0 to Rmax/2dk with the spatial resolution R 1/2kmax. For example: R = 0.03 for kmax = 16 -1. The total number of parameters Mmax used in the model must be less than that given by the Nyquist theorem:

For a single shell, k = kmax - kmin = 15 -1 and R = Rmax - Rmin = 1 , then Mmax 11.5.
E.O. Brigham, The Fast Fourier Transform (Prentice Hall, Englewood Cliffs, New Jersey, 1974). E.A. Stern, Phys. Rev. B 48 (1993) 9825.
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Fishers F0.95 test

The FTEST program allows one to perform the analysis of variance of the results of the multi-shell fit using the Fishers F0.95 test. The experimental EXAFS exp(k) is given from kmin to kmax and corresponds to the range of the back-Fourier transform R. It was fitted by two models 1(k) and 2(k) having the number of fitting parameters M1 and M2. The variance is
N M max ( exp (ki ) mod el (ki ))2 D= N (M max M fit ) i =1

According to the Fishers F0.95 test (95% probability), the second model should be accepted when

Dfit1 > F0.95 Dfit 2

D.J. Hudson, Statistics Lectures on Elementary Statistics and Probability (CERN, Geneva, 1964)

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Example of Fishers F0.95 test

Analysis of the experimental Re L3-edge EXAFS exp(k) from the first coordination shell (Re-O1) in ReO3. Back-FT in the interval from Rmin=0.7 to Rmax=2.1 : R=1.4 . Best-fit of (k) in the interval from kmin = 1.5 -1 to kmax = 15 -1. Model1 1(k,N,R,2,E0): the number of fitting parameters M1=4. Model2 2(k,N,R,2,E0,C3,C4,C5,C6): the number of fitting parameters M2=8. The variance is
N M max ( exp (ki ) mod el (ki ))2 D= N (M max M fit ) i =1

Dfit1 > F0.95 Dfit 2

D1=4.02 10-4 and D2=6.3710-4, so D1/D2=0.63 < F0.95 =4.1

According to the Fishers F0.95 test, the second model should not be accepted !

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Amplitude ratio and phase difference analysis within the Gaussian/cumulant approximation
This method can be used to find relative variations of parameters in the EXAFS formula when the single shell EXAFS signal can be isolated.

P. Fornasini, S. a Beccara, G. Dalba, R. Grisenti, A. Sanson, M. Vaccari, F. Rocca, Phys. Rev. B 70 (2004) 174301:1-12.
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EXAFS Data Analysis: how to do ?

Change E0
2.5
4 2

6 4

1 shell
EXAFS (k)k ( )
-2 2

EXAFS (k)k ( )

X-ray Absorption

-2

2.0 1.5 1.0 0.5 0.0 8100

FT (k)k ( )

-3

0 -2 -4 -6

2 0 -2 -4

EDAEES
8400 8700 9000 9300 9600

EDAFT
0 2 4 6 8 10 12 14
-1

EDAFIT
0 2 4 6

-1

16

18

-2

Energy E (eV)

Wavenumber k ( )

Distance R ()

10
-1

12

14

Wavenumber k ( )

C ha n

ge E

Compare (k) phase

FEFF(k)
Crystal structure model
atoms.inp feff.inp feff****.dat

ATOM

FEFF8

EDAFEFF

amp****.dat pha****.dat

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Examples of EXAFS data analysis by different approaches

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Gaussian, cumulant and RDF models

experiment model RDF

Gaussian-model Cumulant-model RDF model

Gaussian-model Cumulant-model RDF model

A. Kuzmin, J. Physique IV (France) 7 (1997) C2-213-C2-214.

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The RDFs derived by the splice and RDF techniques for several kmax values

Dashed line splice method Solid line RDF method Circles experiment (model RDF)

A. Kuzmin, J. Physique IV (France) 7 (1997) C2-213-C2-214.

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The RDFs for the 1st shell in ReO3, WO3 and MoO3 derived by the splice and RDF techniques

Dashed line experiment Solid line RDF method Dotted line splice method

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Examples of best fits of the EXAFS signals in k-space

EDAFIT (Gaussian model) EDARDF

Re L3-edge in rhenium trioxide ReO3

A. Kuzmin, J. Purans, G. Dalba, P. Fornasini, F. Rocca, J. Phys.: Condensed Matter 8 (1996) 9083-9102.
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Examples of best fits of the EXAFS signals in k-space by EDAFIT (Gaussian model)
1st shell Ni-O 2nd shell Ni-Ni

Ni K-edge in polycrystalline and thin film nickel oxide NiO

Solid lines experiment, dashed lines - model
A. Kuzmin, J. Purans, A. Rodionov, J. Phys.: Condensed Matter 9 (1997) 6979-6993.
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Examples of best fits of the EXAFS signals in k-space

EDAFIT (Gaussian model) EDARDF

Ag K-edge in Ag2O-B2O3 glasses

Dashed lines experiment, solid lines - model
A. Kuzmin, G. Dalba, P. Fornasini, F. Rocca, O. ipr, Phys. Rev. B 73 (2006) 174110:1-12.
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Thank you for attention !

Get more details at: http://www.dragon.lv/eda and http://www.dragon.lv/exafs

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