hi, please don't think wrong about my question, but from my experience sometimes problems are on the other side of analysis... Simply, I want to be clearly sure what you did. as I understand: you aligned and calibrated spectra in Athena (by reference sample) and than you imported the apj file to Artemis? Then you fitted your experimental data to the model of the unit cell? If you say "fitted E0 in Artemis" you mean usually named "delE0" in path or "Enot" fitting parameter from "Guess, Def, Set" window? I asked about changes of the set-up of beamline, simply because I had met with such problems... kicaj W dniu 11-06-06 10:17, Brandon Reese pisze:

Ahh, it sounds I wasn't entirely clear on what I doing. The measurements were at the In edge, so I aligned all the scans such that the peak in the first derivative of the reference foil was at 27940 eV. The peak of the first derivative in the samples was ~27944 eV. The 1st derivative peaks of samples grown without additional oxygen ("conducting") compared to the samples grown with additional oxygen ("intrinsic") were ~0.5 eV different or less.

Using the peak of the first derivative in Athena for the background subtraction, the refined E0 in Artemis was ~7 eV for conducting samples and ~5.5 eV for intrinsic samples. I also tried setting the E0 in Athena to the peak of the whiteline, which was about 27950 eV. Again the spread between the white line peak values was ~0.5 eV between samples. With this value for the background subtraction in Athena, Artemis refined the E0's to be ~1.5 eV for the conducting samples and ~0 eV for the intrinsic samples.

Another piece of information is that the refined CN's for the samples had an inverse correlation to shift in E0. So the conducting samples with a higher E0 (by 1.5 eV) had a lower CN of about 0.1. The calculated correlation in Artemis for the two variables was ~35%.

I didn't intentionally change anything on the beamline setup. I measured all of the conducting samples and then all of the intrinsic samples. So if there was a sudden change in *something* in between the sample groups, it would be consistent. The sample changes took ~10 minutes at most, so the change would have to happen on that time scale. The only other consistency I noticed is the conducting samples had to be shifted ~0.7 eV to get the metal foil to line up, and the intrinsic samples only had to be shifted about 0.1 eV.

Brandon

2011/6/6 "Dr. Dariusz A. Zając" mailto:kicaj@ifj.edu.pl>

Hi Brandon, before someone gives you correct answer, could you shortly inform us, what is the E0 for reference foil, for each experimental data. As I understand you have a shift of 7eV between samples, but measured on samples, thus would be nice to see what is the shift for reference. The second question comes for me automatically - have you done something with the beamline set-up between experiments ? kicaj

W dniu 11-06-06 08:56, Brandon Reese pisze:

...

Hi all,

I am looking at EXAFS of thin film metal oxides. I am varying both metal content and the oxygen content of the films. I aligned the scans with a metal reference foil collected simultaneously. In Artemis, I have noticed that when changing between films with no extra oxygen versus those with extra oxygen there is a shift in the fitted E0 of ~1.5 eV (after aligning to the foil). I tried setting the E0 in Athena to the peak of the 1st derivative and the peak of the white line with the same result (~7 eV difference). I was a little surprised by the offset because in Athena the E0 values varied by <0.5 eV. I am not sure if the argument could be made that this shift is a result in a changing oxidation state because it doesn't show up in the XANES (at least qualitatively). Are there other experimental effects that could cause a shift like this, or is this likely something real in my material? If anyone want to see a representative group of data, let me know.

I also have an unrelated quick (I think) question on the EXAFS equation. In some references I see a term 1/(k R)^2 and in others it is 1/(k R^2). I couldn't really see any reason for the difference, unless it is to correct for subtle differences in how the other terms are defined.

Thanks Brandon

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Kicaj and Matt, Thanks for the replies. It is certainly reasonable to ask about the experimental setup, that seems like a good first place to look for oddities. Sorry about using E0 in two different contexts (Athena and Artemis). I'll switch to using E0 for the chosen parameter in Athena's background subtraction and Enot for the guess parameter in Artemis. I aligned the scans in Athena using the reference foil absorption edge. I ended up shifting the scans in energy by ~1 eV or less based on the reference foil. I then set the E0 parameter in Athena to the peak of the first derivative. This value varied by about 0.5 eV (or less) between the different samples. This is what I considered when I made the statement about not seeing the oxidation change in the XANES. There is a shift of about 4 eV compared to the reference foil, which I would expect because I am looking at oxides. I then extracted the chi(k) into Artemis, and used the same Feff calculations/paths for each sample. In the Artemis fits I am seeing Enot shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this seemed a little on the big side, I also tried setting E0 to be the top of the white line, in that case Enot came out to be ~1 eV. The Enot shift between samples was about the same either way. Could an argument be made that there is a small shift in the overall oxidation state of the films, possibly contributing to the changes in the conductivity changes in the films? Does anyone have any references about using Enot shifts in this way? Scott - The amplitudes of the XANES features are very close. in the normalized spectrum the difference practically 0, and in the derivative the amplitudes are ~5% off. There is bit larger of a difference in amplitude between the samples (in fluorescence) and a pure In2O3 powder (in transmission) of ~10% in the first derivative. The samples are sputtered from oxide sources, so the presence of metallic In should be pretty small. I am interested about your comment on the relative sizes of the first derivative peaks. Comparing my samples to the foil the oxide peak amplitude is bigger than the metal peak by 10% or so. Could this be due to the differences between fluorescence and transmission or not optimizing the experiment to measure the foil? Or could it be due to something else more heinous? I noticed on individual fits that the dR for the first shell came out nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the Enot's had the 1-2 eV shift between the samples. I tried to fit the two types of samples simultaneously while constraining the dR's (and a few 2nd shell parameters) to be equal to each other and letting the Enot's float. The relative Enot values came out close to what they were before. If I let dR values fit independantly, there was no real change present. In other words the multiple data set fit just made my EB's a bit smaller, but the relative shifts stayed about the same. Would there be some reasonable way in a multi-data set fit to constrain the Enot's? Brandon On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville wrote:

HI Brandon,

If I understand right (and to echo Darius's questions), it seems like you measure samples with a metal reference, and aligned the spectra in Athena so that the references matched. That's a fine way to go. I would ask: how big were the needed energy shifts? Are the experimental mu(E) spectra aligned well at this point? If you're studying metal oxides with different oxygen content, you might very well see oxidation in the XANES. If I understand correctly, you're saying you don't see this.

Then, you extracted the chi(k) from the aligned spectra. How much did E0 vary for the shifted spectra in this background-subtraction step?

Then, you pulled these chi(k) into Artemis, and see different E0 shifts in the fits. This E0 is a little different, in that it is the E0 shift applied to the Feff calculation to match the experimental spectra. If you use different paths or different calculations, such E0 shifts might happen, and wouldn't be highly meaningful.

I know that's not a complete answer, but hopefully that and Darius's questions will help,

--Matt

PS on Q2: 1/ (kR)^2 vs 1 / kR^2

This is probably either a typo, or a different convention based on the definition of f(k) as the electron scattering amplitude. In the Feff world, it should be 1/kR^2, but using 1/(kR)^2 would just map f(k) to k*f(k). _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Chris - I have done it both ways, but I generally leaned to constraining them all to some reasonable value. Thanks Brandon On Mon, Jun 6, 2011 at 7:55 PM, Christopher Patridge wrote:

Brandon,

I have a question about your method. You mention that you pick E0 based on the 1st peak of the derivative for each sample then extract chi(k). Have you tried constraining E0 across the set? I have thought that in order to make a good comparison between samples in a set, a common E0 should be chosen in order to replicate closely the background function across the whole set. Constraining may also provide a trend in the fitting.

Buena salud,

Chris

On Jun 6, 2011, at 6:46 PM, Brandon Reese wrote:

Kicaj and Matt,

Thanks for the replies. It is certainly reasonable to ask about the experimental setup, that seems like a good first place to look for oddities. Sorry about using E0 in two different contexts (Athena and Artemis). I'll switch to using E0 for the chosen parameter in Athena's background subtraction and Enot for the guess parameter in Artemis.

I aligned the scans in Athena using the reference foil absorption edge. I ended up shifting the scans in energy by ~1 eV or less based on the reference foil. I then set the E0 parameter in Athena to the peak of the first derivative. This value varied by about 0.5 eV (or less) between the different samples. This is what I considered when I made the statement about not seeing the oxidation change in the XANES. There is a shift of about 4 eV compared to the reference foil, which I would expect because I am looking at oxides.

I then extracted the chi(k) into Artemis, and used the same Feff calculations/paths for each sample. In the Artemis fits I am seeing Enot shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this seemed a little on the big side, I also tried setting E0 to be the top of the white line, in that case Enot came out to be ~1 eV. The Enot shift between samples was about the same either way. Could an argument be made that there is a small shift in the overall oxidation state of the films, possibly contributing to the changes in the conductivity changes in the films? Does anyone have any references about using Enot shifts in this way?

Scott - The amplitudes of the XANES features are very close. in the normalized spectrum the difference practically 0, and in the derivative the amplitudes are ~5% off. There is bit larger of a difference in amplitude between the samples (in fluorescence) and a pure In2O3 powder (in transmission) of ~10% in the first derivative. The samples are sputtered from oxide sources, so the presence of metallic In should be pretty small. I am interested about your comment on the relative sizes of the first derivative peaks. Comparing my samples to the foil the oxide peak amplitude is bigger than the metal peak by 10% or so. Could this be due to the differences between fluorescence and transmission or not optimizing the experiment to measure the foil? Or could it be due to something else more heinous?

I noticed on individual fits that the dR for the first shell came out nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the Enot's had the 1-2 eV shift between the samples. I tried to fit the two types of samples simultaneously while constraining the dR's (and a few 2nd shell parameters) to be equal to each other and letting the Enot's float. The relative Enot values came out close to what they were before. If I let dR values fit independantly, there was no real change present. In other words the multiple data set fit just made my EB's a bit smaller, but the relative shifts stayed about the same.

Would there be some reasonable way in a multi-data set fit to constrain the Enot's?

Brandon

On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville < newville@cars.uchicago.edu> wrote:

...

HI Brandon,

If I understand right (and to echo Darius's questions), it seems like you measure samples with a metal reference, and aligned the spectra in Athena so that the references matched. That's a fine way to go. I would ask: how big were the needed energy shifts? Are the experimental mu(E) spectra aligned well at this point? If you're studying metal oxides with different oxygen content, you might very well see oxidation in the XANES. If I understand correctly, you're saying you don't see this.

Then, you extracted the chi(k) from the aligned spectra. How much did E0 vary for the shifted spectra in this background-subtraction step?

Then, you pulled these chi(k) into Artemis, and see different E0 shifts in the fits. This E0 is a little different, in that it is the E0 shift applied to the Feff calculation to match the experimental spectra. If you use different paths or different calculations, such E0 shifts might happen, and wouldn't be highly meaningful.

I know that's not a complete answer, but hopefully that and Darius's questions will help,

--Matt

PS on Q2: 1/ (kR)^2 vs 1 / kR^2

This is probably either a typo, or a different convention based on the definition of f(k) as the electron scattering amplitude. In the Feff world, it should be 1/kR^2, but using 1/(kR)^2 would just map f(k) to k*f(k). _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Hi Brandon, that was a reason why I wanted to clarify which parameters you use. E0 (as a Fermi level) in Athena can be taken (but do not must) as a valence state of measured ion for K edges, whereas in Artemis delE0 can correspond to the potential of the one of nearest atoms to the measured one. If you talk about Artemis and calculations, would be also helpful to know the version of feff. It is known that for version up to 6. can be problem with fitting values of Enot. And of course Matt answered you more clearly... The difference of 0.5eV between spectra of reference sample can be simply related with the energy resolution of the beam (beamline). Maybe this will helps you more: http://cars9.uchicago.edu/pipermail/ifeffit/2004-June/005607.html http://cars9.uchicago.edu/pipermail/ifeffit/2006-February/006811.html kicaj W dniu 11-06-07 00:46, Brandon Reese pisze:

Kicaj and Matt,

Thanks for the replies. It is certainly reasonable to ask about the experimental setup, that seems like a good first place to look for oddities. Sorry about using E0 in two different contexts (Athena and Artemis). I'll switch to using E0 for the chosen parameter in Athena's background subtraction and Enot for the guess parameter in Artemis.

I aligned the scans in Athena using the reference foil absorption edge. I ended up shifting the scans in energy by ~1 eV or less based on the reference foil. I then set the E0 parameter in Athena to the peak of the first derivative. This value varied by about 0.5 eV (or less) between the different samples. This is what I considered when I made the statement about not seeing the oxidation change in the XANES. There is a shift of about 4 eV compared to the reference foil, which I would expect because I am looking at oxides.

I then extracted the chi(k) into Artemis, and used the same Feff calculations/paths for each sample. In the Artemis fits I am seeing Enot shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this seemed a little on the big side, I also tried setting E0 to be the top of the white line, in that case Enot came out to be ~1 eV. The Enot shift between samples was about the same either way. Could an argument be made that there is a small shift in the overall oxidation state of the films, possibly contributing to the changes in the conductivity changes in the films? Does anyone have any references about using Enot shifts in this way?

Scott - The amplitudes of the XANES features are very close. in the normalized spectrum the difference practically 0, and in the derivative the amplitudes are ~5% off. There is bit larger of a difference in amplitude between the samples (in fluorescence) and a pure In2O3 powder (in transmission) of ~10% in the first derivative. The samples are sputtered from oxide sources, so the presence of metallic In should be pretty small. I am interested about your comment on the relative sizes of the first derivative peaks. Comparing my samples to the foil the oxide peak amplitude is bigger than the metal peak by 10% or so. Could this be due to the differences between fluorescence and transmission or not optimizing the experiment to measure the foil? Or could it be due to something else more heinous?

I noticed on individual fits that the dR for the first shell came out nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the Enot's had the 1-2 eV shift between the samples. I tried to fit the two types of samples simultaneously while constraining the dR's (and a few 2nd shell parameters) to be equal to each other and letting the Enot's float. The relative Enot values came out close to what they were before. If I let dR values fit independantly, there was no real change present. In other words the multiple data set fit just made my EB's a bit smaller, but the relative shifts stayed about the same.

Would there be some reasonable way in a multi-data set fit to constrain the Enot's?

Brandon

On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville mailto:newville@cars.uchicago.edu> wrote:

HI Brandon,

If I understand right (and to echo Darius's questions), it seems like you measure samples with a metal reference, and aligned the spectra in Athena so that the references matched. That's a fine way to go. I would ask: how big were the needed energy shifts? Are the experimental mu(E) spectra aligned well at this point? If you're studying metal oxides with different oxygen content, you might very well see oxidation in the XANES. If I understand correctly, you're saying you don't see this.

Then, you extracted the chi(k) from the aligned spectra. How much did E0 vary for the shifted spectra in this background-subtraction step?

Then, you pulled these chi(k) into Artemis, and see different E0 shifts in the fits. This E0 is a little different, in that it is the E0 shift applied to the Feff calculation to match the experimental spectra. If you use different paths or different calculations, such E0 shifts might happen, and wouldn't be highly meaningful.

I know that's not a complete answer, but hopefully that and Darius's questions will help,

--Matt

PS on Q2: 1/ (kR)^2 vs 1 / kR^2

This is probably either a typo, or a different convention based on the definition of f(k) as the electron scattering amplitude. In the Feff world, it should be 1/kR^2, but using 1/(kR)^2 would just map f(k) to k*f(k). _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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