Comparing similar peak positions in Fourier transform with fitting results
Greetings to all, I am working on Zn binding to Fe and Al oxides and I am trying to fit the second and third shells. I have three spectra from three samples that differ in a particular treatment. Visually speaking, the Fourier transforms for all these spectra show second and third shells at 2.6 and 3.2A (uncorrected for phase shift), respectively. I fit the second shell with Fe and the third shell with Al. From the fitting results I obtained the Zn-Fe and Zn-Al radial distances for the second and third shells. However, these Zn-Fe and Zn-Al radial distances were different among the samples. For example, the Zn-Fe radial distance was 3.18A for sample 1, 3.44A for sample 2 and 3.51A for sample 3. My question is: if the peaks in the Fourier transforms are at the same position for all samples, why is it that the fitting shows that the radial distances are actually different? NOTE: I fit the 1st,2nd and 3rd shells(R range:1.0-3.2A) together. Thank you, Hashem Stietiya School of Plant, Soil and Environmental Sciences Louisiana State University
On Wednesday 22 July 2009 04:04:19 am Hashem Stietiya wrote:
Greetings to all,
I am working on Zn binding to Fe and Al oxides and I am trying to fit the second and third shells. I have three spectra from three samples that differ in a particular treatment. Visually speaking, the Fourier transforms for all these spectra show second and third shells at 2.6 and 3.2A (uncorrected for phase shift), respectively. I fit the second shell with Fe and the third shell with Al. From the fitting results I obtained the Zn-Fe and Zn-Al radial distances for the second and third shells. However, these Zn-Fe and Zn-Al radial distances were different among the samples. For example, the Zn-Fe radial distance was 3.18A for sample 1, 3.44A for sample 2 and 3.51A for sample 3. My question is: if the peaks in the Fourier transforms are at the same position for all samples, why is it that the fitting shows that the radial distances are actually different? NOTE: I fit the 1st,2nd and 3rd shells(R range:1.0-3.2A) together. Thank you, Hashem Stietiya School of Plant, Soil and Environmental Sciences Louisiana State University
Hashem, It is hard to say without examining the details of your problem, but this sounds like a common sort of problem. There is nothing about an EXAFS spectrum that actually identifies itself as being due to a particular type of atoms. All that the Fourier transform of your EXAFS data tells you is at what frequencies (or distances, as you wish...) your spectrum has large Fourier components. We than propose a structural model based on a physical understanding of the sample in question, do a Feff calculation on that structural model, and use the Fourier components of the Feff calculation to model the Fourier components in the data. If it works and the model yields physically sensible numbers, then we say "yay!". The problem is that the parameters we use to fit the Fourier components of the Feff caluclation to the Fourier components of the data are not independent of one another. There are correlations. In a numerical sense, those correlations mean that the fitting algorithm might be equally happy with two (or more) different sets of parameter values, so long as the fitting metric is minimized. What I suspect is happening in your case is that the parameters used for the Fe scatterer are not very robust parameters in the sense that different values can be made to give numerically reasonable fits to the data. When this happens, you usually see that the Fe parameters are highly correlated to other parameters in the problem and that error bars on the Fe parameters are quite large. Is that the case? Are the uncertainties in difference large compared to the different distances you are seeing? Are the delR parameters for the Fe highly correlated with otgher parameters -- specifically other parameters that effect things in the same range of radial distance as the Fe atom? When you have an instability in the fit, you need to figure out some way to address it. It is hard to say in general what that might be, but it could include making some assumptions about your structure, constraining two or more parameters to not be floated independently of one another, or something else. In any case, you need to draw on some other source of knowledge -- possibly the results of other EXAFS fitting problems, the results of other kinds of measurements on the samples, the results of theoretical calculations, and so on. Good luck, B PS: Remember that the XAFS conference is next week. A lot of the people who might otherwise answer questions will be fairly unavailable until the following week. -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Hashem, You might find it useful to plot the data and the path using the real part of the FT with an offset for all three data sets and the same path for all three data sets. To do this you need to set the offset value in the "traces" tab in Artemis. Then highlight all the data sets and the path. HTH, Shelly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Bruce Ravel Sent: Thu 7/23/2009 3:12 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Comparing similar peak positions in Fourier transformwith fitting results On Wednesday 22 July 2009 04:04:19 am Hashem Stietiya wrote:
Greetings to all,
I am working on Zn binding to Fe and Al oxides and I am trying to fit the second and third shells. I have three spectra from three samples that differ in a particular treatment. Visually speaking, the Fourier transforms for all these spectra show second and third shells at 2.6 and 3.2A (uncorrected for phase shift), respectively. I fit the second shell with Fe and the third shell with Al. From the fitting results I obtained the Zn-Fe and Zn-Al radial distances for the second and third shells. However, these Zn-Fe and Zn-Al radial distances were different among the samples. For example, the Zn-Fe radial distance was 3.18A for sample 1, 3.44A for sample 2 and 3.51A for sample 3. My question is: if the peaks in the Fourier transforms are at the same position for all samples, why is it that the fitting shows that the radial distances are actually different? NOTE: I fit the 1st,2nd and 3rd shells(R range:1.0-3.2A) together. Thank you, Hashem Stietiya School of Plant, Soil and Environmental Sciences Louisiana State University
Hashem, It is hard to say without examining the details of your problem, but this sounds like a common sort of problem. There is nothing about an EXAFS spectrum that actually identifies itself as being due to a particular type of atoms. All that the Fourier transform of your EXAFS data tells you is at what frequencies (or distances, as you wish...) your spectrum has large Fourier components. We than propose a structural model based on a physical understanding of the sample in question, do a Feff calculation on that structural model, and use the Fourier components of the Feff calculation to model the Fourier components in the data. If it works and the model yields physically sensible numbers, then we say "yay!". The problem is that the parameters we use to fit the Fourier components of the Feff caluclation to the Fourier components of the data are not independent of one another. There are correlations. In a numerical sense, those correlations mean that the fitting algorithm might be equally happy with two (or more) different sets of parameter values, so long as the fitting metric is minimized. What I suspect is happening in your case is that the parameters used for the Fe scatterer are not very robust parameters in the sense that different values can be made to give numerically reasonable fits to the data. When this happens, you usually see that the Fe parameters are highly correlated to other parameters in the problem and that error bars on the Fe parameters are quite large. Is that the case? Are the uncertainties in difference large compared to the different distances you are seeing? Are the delR parameters for the Fe highly correlated with otgher parameters -- specifically other parameters that effect things in the same range of radial distance as the Fe atom? When you have an instability in the fit, you need to figure out some way to address it. It is hard to say in general what that might be, but it could include making some assumptions about your structure, constraining two or more parameters to not be floated independently of one another, or something else. In any case, you need to draw on some other source of knowledge -- possibly the results of other EXAFS fitting problems, the results of other kinds of measurements on the samples, the results of theoretical calculations, and so on. Good luck, B PS: Remember that the XAFS conference is next week. A lot of the people who might otherwise answer questions will be fairly unavailable until the following week. -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Bruce Ravel -
Hashem Stietiya -
Kelly, Shelly