- Ifeffit - millenia.cars.aps.anl.gov

RE: [Ifeffit] crucial information -oops
by SCHLEGEL Michel 177447 15 Apr '04

15 Apr '04

oops.. sorry, it's the Greek goddess Aphrodite > -----Message d'origine----- > De : SCHLEGEL Michel 177447 > Envoyé : jeudi 15 avril 2004 15:04 > À : 'XAFS Analysis using Ifeffit' > Objet : RE: [Ifeffit] crucial information > > > > > the correct greek prononciation were > > "hephaistos" which is the god of "smiths" > > But this is from "old Europe", > > Yep, and he was the unfortunate husband of Venus. > So Bruce, if you are planing some versatile > companion software for "Hephaistus"... > > Best regards, > > Michel Schlegel > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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crucial information
by Bruce Ravel 15 Apr '04

15 Apr '04

Hey, I've now been asked several times how to pronounce the word "Hephaestus". Although I am fairly confident that each of the people who asked owns a dictionary, here's some linkage to Merriam-Webster. The page includes a .wav file of someone saying it (click on the little red speaker icon). http://www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=hephaestus&x=0&y=0 ;-) B -- Bruce Ravel ----------------------------------- ravel(a)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/

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"FEFFs order" bug corrected in Artemis 0.7.003
by Stanislav Stoupin 14 Apr '04

14 Apr '04

From: Bruce Ravel <ravel(a)phys.washington.edu> >BTW, Does the new release of Artemis seem to address the many problems >you reported with your multiple data set, multiple feff calculation >fits? It does! I have just performed a couple of tests where I opened old-style project that had "incorrect" FEFF order: data_set1 FEFF0 FEFF1 FEFF4 data_set2 FEFF2 FEFF3 test #1 1. fit the data and saved as another project 2. opened the saved project no missing FEFFs were found nothing changed test#2 1. change data in the project 2. fit and saved as another project 3. opened the saved project again no missing FEFFs were found and no other suspicious behaviour was observed These things did't work before Stanislav

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RE: [Ifeffit] S02-Interpretation
by Kelly, Shelly D. 14 Apr '04

14 Apr '04

> To my knowledge, S02 accounts for intrinsic as well as > extrinsic losses in the > sample. Now, if I have two samples and determined the S02 > value according to > the way which Bruce has in his supplement to the FEFFIT > course, I find two > differing values for electrochemically prepared oxide (0.74) > and crystalline > gold oxide (0.92). This difference is independent of > beamlines I measured and > I can exclude quite safely that it is just a measurement > error - it comes up > with any spectrum I recorded on these systems. > > When discussing this with my colleagues, we interpreted the > S02 difference as > an indication of more disorder in case of the electrochemical > system (which > would well fit to my picture of the whole thing). > > BUT: Is there any physical reason to assign a difference in S02 (for > "chemically equivalent" systems, where just the preparation > is different) to > a structural disorder? > > Regards, > > Norbert Hi Norbert, I believe that the value for S02 should be the same in these two samples. But S02 is not the only amplitude term in the EXAFS equation. The degeneracy of the path, sigma2, and the step height normalization are also amplitude terms. One needs to be careful in processing the data so that the change in the amplitude between the two signals really belongs to the correct parameter. Here is a recipe for how I would try to solve the problem: 1st: Double check the step height normalization in Athena. 1) Make sure that Ezero is the same for both data set and that the data sets are aligned in energy. 2) Plot the xmu data along with the pre-edge and post-edge lines and check the step height that Athena reports...make sure it seems reasonable. 3) plot both chi(k) data sets with kweight of 1, and then 2 and then 3. You are looking to see if the change in amplitude between the data sets is the same for all k-range or if the ampliude changes more at high or low k. 4) you could also Fourier filter the data and do this again. If the change in amplitude is the same for all k, then the difference is because of SO2 or degeneracy or step height normalization. If the change in amplitude is more at high k than at low k the change is because of sigma2 term. If the change is more at low k than at high k then I would say different bkg curves or self absorption effects. 2nd: Say you think that the difference is due to a sigma2 term. I would fit both data sets with the same parameters for SO2 and different parameters for sigma2 for what ever paths you decide to include in your fit. If you want to prove that the change is a sigma2 and not a SO2 parameter then you do the fit using kweight of 1, and 2 and 3 all at the same time for both data sets, trying two different models, 1) where SO2 is different for both data sets but sigma2 is the same, and 2) another where sigma2 is different but SO2 is the same. You should see a difference in the goodness-of-fit parameters that is greater than one standard deviation. Using all three k-weights helps Artemis "see" the changes that you saw in Athena, by comparing the two data sets with the different k-weights. I just read Bruce's comment, If you think that the change should be in the coordination number then you should repeat the above models with the coordination numbers allowed to vary. To decouple SO2 and N you need to have more than one shell in the fit, otherwise they are exactly the same variable. H.T.H Shelly

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new Debian packages of horae-033
by Carlo U. Segre 14 Apr '04

14 Apr '04

Hello All: There are now new Debian packages of the latest horae available. Bruce, I noticed that you removed tkformula and apt in favor of the new combined application called Hephaestus. Hopefully I didn't miss any other big changes in the programs. The sources and binaries can be obtained at For the stable (woody) distribution deb http://fermi.phys.iit.edu/debian/woody binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ For the unstable (sid) distribution deb http://fermi.phys.iit.edu/debian/sid binary/ deb-src http://fermi.phys.iit.edu/debian/sid source/ Carlo -- 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 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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a question about background refinement
by Stanislav Stoupin 13 Apr '04

13 Apr '04

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

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RE: [Ifeffit] a question about background refinement
by Kropf, Arthur Jeremy 13 Apr '04

13 Apr '04

Stanislav, You mention that the amplitude remains consistent at about 0.3. However, what is happening to R and E0? Are these values also reasonable? I have found that, on occasion, a negative DWF is telling me that oxygen may not be the correct nearest neighbor. In these cases, R and E0 are always anomalous for the metal-oxygen path. Jeremy Kropf Chemical Engineering Division Argonne National Laboratory -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Stoupin, Stanislav A. Sent: Tuesday, April 13, 2004 5:01 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] 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 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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[Ifeffit] Re: from I.Demchenko (PhD student at the Institute of Physics PAS)
by Bruce Ravel 07 Apr '04

07 Apr '04

Hi Iraida, I hope you don't mind that I CC my reply to the ifeffit mailing list. I have some suggestions for you, but I thought it might be helpful to you to see if anyone else has anything to contribute. (The attachments to Iraida's email included a couple of screenshots showing the plotting window with a very good-loooking fit. She also sent the artemis log file showing many of the numbers she quotes below.) On Tuesday 06 April 2004 12:12 pm, Iraida Demchenko wrote: > I have a problem with fitting of my data for 0.5 microns of Ge on > Si(001) substrate (grown by MBE). The spectrum for K-edge of Ge was > collected by TY mode. This sample is a standard for my next > fitting. >From this fitting (for 1 shell) I want to draw > So^2... But, if I apply a "trick" with k-weight determination as 1 > and So^2 value changing from 0.7 to 1.1 and repetition of this > operation for k^1, k^2, k^3, I get three parallel lines for > sigma^2(Ge-Ge) as function of So^2 :(. They aren't crossed in this > area. This is kind of surprising to me. I have used the three-lines trick many times and have never seen the situation of three parallel lines. I am a little confused how that is even possible. One might expect this trick to do strange things in the case of a first shell that is not well separated from higher shells, but my memory of Ge is that the first shell is well separated. Another situation that might lead to trouble is if strain induced by the substrate splits the first shell into two well-separated peaks. However, that does not seem to be the case for you either. 1/2 micron is (I think) thick enough so that the film should be bulk-like. Sadly, I am stumped. Has anyone else ever seen this? > On the other hand, I tried to fit my data (3 shells, k-w=2; dk=2; > Hanning; k(3.5-12.3)) and I've obtained: reduced chi-square=10.33; > R-factor=0.011; So^2=1.22 +/- 0.34; dr_1=0.0107+/-0.006; > sigma^2_1shell=0.0037+/-0.0019; sigma^2_2=0.0068+/-0.0033; > sigma^2_5=0.0096+/-0.0041(3 shell) (of course, that errors were > recalculated(following FEFFIT, p.44). I doubt about the obtained > value for So^2=1.22 +/-0.34. Within the error, of course, I can say, > that this value is in the range from 0.6 to1. But, the correlations > between variables are: amp (So^2) and sigma2_1: 0.916 :(; amp and > sigma^2_2: 0.498; amp and sigma^2_5: 0.49; sigma^2_1 and sigma^2_2: > 0.47; sigma^2_1 and sigma^2_5: 0.45.....all other correlations are > below 0.25. In the attachment there is a log file for this fitting, > as you can see sigma^2_3 is -0.0055+/-0.016 :(. > > Are there any other ways to determine our So^2? Or these actual results > (So^2=1.22) we can consider as good? What do You think about this fit? First, as you say, your value for S02 is not unreasonable in that the error bar covers a value that one might expect. Still, you are right that 1.22 is an oddly large best fit value and suggests that something else might be happening in the data. Second, I wouldn't be so concerned about the high correlation between S02 and sigma^2. It's normal. Here is a nice short piece by Matt about correlations: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-February/000713.html The rest of thread might be of interest to you, as well. At another point in that thread, there is some discussion of how the normalization is done. Have you examined that carefully? If the post-edge line intersects E0 at an oddly low value, then the edge-step used in the normalization might be rather too small. This is certainly a possibility in fluorescence data where the region after the edge sometimes sweeps upward. In that case, the normalization range is such that the regressed post-edge line can be below the data near E0. I explained this in some more detail at http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-February/000711.html That could be the cause of a best-fit S02 that is larger than 1, That's my best guess, given that I have not seen the mu(E) data, for what is happening. I was bit confused by thing about sigma^2_3. I saw in the log file that it was, as you said, negative. But none of the sigma^2 values for the paths were negative. It wasn't clear how that sigma^2 value was being used. Hope that helps, B P.S. I could tell from the log file that you sent me that you are using a *very* old version of Artemis and presumably of ifeffit as well. You may want to download the latest ifeffit installation package from http://cars9.uchicago.edu/ifeffit/download.html and then let the automatic updater bring your computer completely up to date. -- Bruce Ravel ----------------------------------- ravel(a)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/

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simultaneous fitting of multiple data sets in ifeffit
by Stanislav Stoupin 05 Apr '04

05 Apr '04

Hello! First of all I would like to thank Bruce for answering my questions. As a beginner I very much appreciate your help. Now I am trying to compare my results using two possible ways of doing EXAFS analysis : 1. Artemis 2. ifeffit command line (loading input files) Here is my question: When I use ifeffit commands it is not clear to me how to assing different kmin/kmax (rmin/rmax) values to different data sets in a multiple data set fit. My current understanding of the problem is as follows: As ifeffit documentation says all variables are global. At the same time ifeffit tries to evaluate all parameters of feffit() command first and does the fit only after determination of kmin kmax rmin rmax. What happens is that the last given values are assigned to these variables. Could somebody show me an example of a script that allows to assing different values of kmin kmax rmin and rmax for different data sets? Stanislav

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A question about the new Artemis version
by Stanislav Stoupin 31 Mar '04

31 Mar '04

Hello all I just upgraded to the newest horae-031 package It looks to me that the new Artemis version (0.7.001) doesn't have that nice button "use previous background" anymore. If I am not mistaken the button allowed to subtract background fitted previously. Am I? Is it somehow hidden in the new version? Thank you in advance Stanislav

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