a question about background refinement
Hello all, Recently, I was able to improve fitting results in one of my projects using background refinement/subtraction in some "strange" way. I have got reasonable results but I was not totally sure if that was a valid approach. So, any feedback is appreciated. Here is the story: The system I am working on is Ru-Pt fcc alloy in a form of nanoparticles which may be oxidized. There is a reason to suspect presence of Ru-O bonds in the system. For the moment I am doing only the first shell analysis and the model I am using includes a part that models alloy first shell structure and also Ru-O path. If I don't use the Ru-O path in my model all the alloy parameters that I get from the fit are reasonable but the fit works bad in low R region. In that region there is a broad peak around 1.3A. The rmin parameter which is responsible for background refinement is set to 1A ( the same value was used when I did initial background subtraction in Athena). What I found a long time ago is that the fit could be significantly improved if I add the Ru-O path in my model (all alloy parameters were even better in that case). However, the DWF of Ru-O bond always went negative (about -0.005). At the same time I got reasonable value for the Ru-O amplitude which was about 0.3. I attempted to get rid of the negative DWF value many times. For example, if I fixed or restrained the DWF to a reasonable value (0.01 is what I expect) it didn't help. Finally, I decided to play with background refinement and what I have done can be described as follows: 1. Set rmin to about 1.5 A 2. Fit with my model which included Ru-O path with fixed delr = 0 and DWF = 0.01 ( the Ru-O amplitude was allowed to vary). Backgound fitting was turned on. 3. Subtracted the background from the data 4. Moved rmin back to 1A and allowed Ru-O delr to vary (the DWF remained fixed to 0.01) 5. Fit again with no background fitting A very decent looking fit came out as a result. (Chi-square was improved) The Ru-O amplitude was about 0.3 (as expected) and I had the DWF set to 0.01. Thanks for you patience if you read it all the way through. My own impression of what I have done is that it looks very artificial and the fact that I use AUTOBK two times bothers me a lot. The second time it is supposed to remove all structural information below 1.5A (rmin value). However, with this approach I hope to get rid of the background that dominates the fine structure in the low R region (Ru-O scattering) using some preliminary knowledge about the compound. I will be happy to hear any point of view. Thank you in advance. If you are interested and want more details please let me know. Stanislav -------------------------------- Stanislav Stoupin Research Assistant/PhD student BCPS Department Illinois Institute Of Technology E-mail:stousta@iit.edu
Hi Stanislav, Yes, that makes me a little bit uneasy too. If we choose to be optimistic, we could be reassured that the amount of Ru-O is fairly independent of how you do (or re-do) the background refinement. For the most part, I don't find re-doing the background subtraction a problem. One can view autobk/spline() as the crude approach and including the background in the fit as refining this crude background. And, we _know_ that the normal use of autobk/spline() (that is, without a 'standard') is imperfect: the idea that chi(R) should be as small as possible below Rbkg is not strictly correct, as there should be non-zero contributions 'leaking' to low-R from the first shell (especially when it's oxygen, which is a large fraction of the EXAFS on interest!). The repeated background subtractions do not by themselves make me uneasy. The slightly negative sigma2 doesn't bother me too much either, as that's close enough to zero to be influenced by non-ideal normalization, energy resolution, S02, and how the Ru-metal shell fit is done. It seems that you're finding that the first shell sigma2 is correlated with the background parameters, so that setting sigma2 to 0.010 and re-determining the background works simply by altering the background function. That seems like a reasonable constraint on the background function. I've usually found E0 to be most highly correlated with the background parameters, but the first shell sigma2 and R are also correlated with these. (if they weren't somewhat correlated, it would make no difference how you did the background subtraction). The thing that makes me the most uneasy is the relatively large values of Rbkg/Rmin (that is rbkg in spline() and rmin in feffit(do_bkg=1,....) which also refines the background) and how they change around in your analysis. Normally, you'd want to keep Rbkg/Rmin below the 'first shell peak', which is sometimes difficult to define for the asymmetric peak common with short metal-oxygen distances, but if the peak is around 1.3Ang, the Rbkg/Rmin of 1.5Ang seems like it might be too high. Can you get decent results with a lower Rbkg/Rmin? Just to be clear, spline() with Rbkg=1.5 *tries* to remove the component below 1.5Ang, but it's always incomplete and not a shart cut-off. In feffit(), setting do_bkg=1 makes the fit really use an R-range of [0,Rmax], and adds variables for the refined spline according to Rmin, but the correlation between spline and structural parameters gets messy around Rmin -- which is why you do the refinement of the background. I'm not sure that's very clear, but I hope it helps, --Matt On Tue, 13 Apr 2004, Stanislav Stoupin wrote:
Hello all,
Recently, I was able to improve fitting results in one of my projects using background refinement/subtraction in some "strange" way. I have got reasonable results but I was not totally sure if that was a valid approach. So, any feedback is appreciated.
Here is the story:
The system I am working on is Ru-Pt fcc alloy in a form of nanoparticles which may be oxidized. There is a reason to suspect presence of Ru-O bonds in the system. For the moment I am doing only the first shell analysis and the model I am using includes a part that models alloy first shell structure and also Ru-O path.
If I don't use the Ru-O path in my model all the alloy parameters that I get from the fit are reasonable but the fit works bad in low R region. In that region there is a broad peak around 1.3A. The rmin parameter which is responsible for background refinement is set to 1A ( the same value was used when I did initial background subtraction in Athena).
What I found a long time ago is that the fit could be significantly improved if I add the Ru-O path in my model (all alloy parameters were even better in that case). However, the DWF of Ru-O bond always went negative (about -0.005). At the same time I got reasonable value for the Ru-O amplitude which was about 0.3.
I attempted to get rid of the negative DWF value many times. For example, if I fixed or restrained the DWF to a reasonable value (0.01 is what I expect) it didn't help.
Finally, I decided to play with background refinement and what I have done can be described as follows:
1. Set rmin to about 1.5 A 2. Fit with my model which included Ru-O path with fixed delr = 0 and DWF = 0.01 ( the Ru-O amplitude was allowed to vary). Backgound fitting was turned on. 3. Subtracted the background from the data 4. Moved rmin back to 1A and allowed Ru-O delr to vary (the DWF remained fixed to 0.01) 5. Fit again with no background fitting
A very decent looking fit came out as a result. (Chi-square was improved) The Ru-O amplitude was about 0.3 (as expected) and I had the DWF set to 0.01.
Thanks for you patience if you read it all the way through. My own impression of what I have done is that it looks very artificial and the fact that I use AUTOBK two times bothers me a lot. The second time it is supposed to remove all structural information below 1.5A (rmin value). However, with this approach I hope to get rid of the background that dominates the fine structure in the low R region (Ru-O scattering) using some preliminary knowledge about the compound.
I will be happy to hear any point of view. Thank you in advance. If you are interested and want more details please let me know.
Stanislav
Stanislav, Matt said:
The thing that makes me the most uneasy is the relatively large values of Rbkg/Rmin (that is rbkg in spline() and rmin in feffit(do_bkg=1,....) which also refines the background) and how they change around in your analysis. Normally, you'd want to keep Rbkg/Rmin below the 'first shell peak', which is sometimes difficult to define for the asymmetric peak common with short metal-oxygen distances, but if the peak is around 1.3Ang, the Rbkg/Rmin of 1.5Ang seems like it might be too high. Can you get decent results with a lower Rbkg/Rmin?
I have a question for you. Are you trying to determine the oxide content? That is, do you want to know what fraction of the Ru atoms are in an oxide environment? Or are you trying to account for the oxide so that you better measure the metallic component? If you don't need a good measurement of the oxide, then perhaps the thing to do is to consider the oxide to be inseparable from the background, and just let the spline to remove that oxide contribution from the fit. That's not as silly as it might sound. As Matt explained, the purpose of the spline is to remove components below Rbkg. Another way of saying that is that the components above Rbkg are the interesting ones and the components below Rbkg are not part of your analysis problem. One often use the AUTOBK spline to remove the step function, the so-called AXAFS, and the low-frequency contributions due to multi-electron excitations. One removes all those things because they are not the portion of the XAS spectrum that you want to fit. All I am suggesting is that you might lump the oxide in that category as well, if you are only concerned about the metallic component. Of course, you may find that the Ru-Ru path from the oxide contributes in a frequency range similar to the metallic first shell. But that's another story. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Bruce: We are definitely interested in the oxide component. We want to have a way of understanding the number of Ru atoms in the nanoparticle which "see" oxygen. Eventually we need to determine if this changes as a function of fuel cell operating conditions or particle size, etc. Carlo On Tue, 13 Apr 2004, Bruce Ravel wrote:
Stanislav,
Matt said:
The thing that makes me the most uneasy is the relatively large values of Rbkg/Rmin (that is rbkg in spline() and rmin in feffit(do_bkg=1,....) which also refines the background) and how they change around in your analysis. Normally, you'd want to keep Rbkg/Rmin below the 'first shell peak', which is sometimes difficult to define for the asymmetric peak common with short metal-oxygen distances, but if the peak is around 1.3Ang, the Rbkg/Rmin of 1.5Ang seems like it might be too high. Can you get decent results with a lower Rbkg/Rmin?
I have a question for you. Are you trying to determine the oxide content? That is, do you want to know what fraction of the Ru atoms are in an oxide environment? Or are you trying to account for the oxide so that you better measure the metallic component?
If you don't need a good measurement of the oxide, then perhaps the thing to do is to consider the oxide to be inseparable from the background, and just let the spline to remove that oxide contribution from the fit.
That's not as silly as it might sound. As Matt explained, the purpose of the spline is to remove components below Rbkg. Another way of saying that is that the components above Rbkg are the interesting ones and the components below Rbkg are not part of your analysis problem. One often use the AUTOBK spline to remove the step function, the so-called AXAFS, and the low-frequency contributions due to multi-electron excitations. One removes all those things because they are not the portion of the XAS spectrum that you want to fit. All I am suggesting is that you might lump the oxide in that category as well, if you are only concerned about the metallic component.
Of course, you may find that the Ru-Ru path from the oxide contributes in a frequency range similar to the metallic first shell. But that's another story.
B
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
participants (4)
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Bruce Ravel -
Carlo U. Segre -
Matt Newville -
Stanislav Stoupin