April 2004 - Ifeffit - millenia.cars.aps.anl.gov

RE: [Ifeffit] S02-Interpretation
by Kelly, Shelly D. 16 Apr '04

16 Apr '04

Hi Matt > > 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, > > How do you mean this? Is this the 'plot three curves of sigma2 v. > S02 curves for three different k-weights' again? I find this > approach puzzling and dangerous. I do not understand why the slope > (correlation) of sigma2 v. S02 should depend on k-weight in > any systematic way -- does anyone else know why it should?? > What you want is the S02 and sigma2 that gives the lowest > chi-square, not where these lines cross. I have found that usually there is a "larger than one would like" correlation between the amplitude and phase terms in the EXAFS equation. But the different terms have different k-dependencies. Low k-weights will give more weight to an accurate E0, whereas higher k-weights will give a more accurate deltar. Although the errors will be large. If you plot the dependence of these variables on the k-weight, or better yet use all three k-weights in the fit, you will find that the best-fit value is consistent with the one k-weight value but that the uncertainty is lower because you are distinguishing between the two coorelated variables by including the k-dependence in the fit. Shelly

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[HELP!] Athena and Artemis doesn't start
by mauro＠rulp.org 16 Apr '04

16 Apr '04

Hi to all, This morning the "story" started with some .TRAP files during an Artemis fit. From one of this I have understood the problem was again with conflicts between the compiled-by-hand horae version and Carlo's .deb (automatically installed) package. Here the ARTEMIS.TRAP file: # This file created at 10:32:53 on 16 April, 2004 # using linux, perl 5.008003, Tk 800.025, and Ifeffit 1.2.5 The following message was trapped by Artemis on a SIGWARN: Artemiswarn/home/mauro/.horae/stash/ARTEMIS.TRAPCODE(0x95e0a4c) at /usr/bin/artemis line 1491 main::__ANON__('Use of uninitialized value in concatenation (.) or string at ...') called at /usr/bin/artemis line 5809 main::set_degeneracy(1) called at /usr/lib/perl5/Tk.pm line 225 eval {...} called at /usr/lib/perl5/Tk.pm line 225 Tk::__ANON__('Tk::Menu=HASH(0x96c8228)','active') called at /usr/lib/perl5/Tk/Menu.pm line 531 Tk::Menu::Invoke('Tk::Menu=HASH(0x96c8228)',1) called at /usr/lib/perl5/Tk.pm line 347 eval {...} called at /usr/lib/perl5/Tk.pm line 347 Tk::MainLoop() called at /usr/bin/artemis line 1627 After this, I decided to reinstall everything. I have completely removed the previous software from "/usr/local" and I have used apt-get to reinstall horeae and ifeffit (also). The result is: Artemis and Athena doesn't start! These the errors: mauro@mac6npd2:~$ artemis Can't load '/usr/lib/perl5/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/auto/Ifeffit/Ifeffit.so: undefined symbol: PL_sv_undef at /usr/lib/perl/5.8/DynaLoader.pm line 225. at /usr/bin/artemis line 49 Compilation failed in require at /usr/bin/artemis line 49. BEGIN failed--compilation aborted at /usr/bin/artemis line 53. mauro@mac6npd2:~$ athena Can't load '/usr/lib/perl5/auto/Ifeffit/Ifeffit.so' for module Ifeffit: /usr/lib/perl5/auto/Ifeffit/Ifeffit.so: undefined symbol: PL_sv_undef at /usr/lib/perl/5.8/DynaLoader.pm line 225. at /usr/bin/athena line 55 Compilation failed in require at /usr/bin/athena line 55. BEGIN failed--compilation aborted at /usr/bin/athena line 59. I really don't know what to do. I've tried different times reinstalling the ..deb package o recompiling the source. Please, help me! -- Mauro Rovezzi <mauro(a)rulp.org> - Physics student University of Rome "Tor Vergata", ESRF Beamline BM8 - GILDA

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Re[2]: a question about background refinement
by Stanislav Stoupin 16 Apr '04

16 Apr '04

To Matt: >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? No, I can not. 1.5A is around the minimum value in Chi(R) magnitude where the first peak can be separated from the others. However, the peak is a result of superposition of background, oxygen path and also the alloy structure. As for the correlation between Ru-O variables and the background parameters, they are somewhat correlated I think If I do not play with the rmin value and keep it equal to 1.0A these correlations are: delr_ru_o and bkg01_05 --> 0.5440 delr_ru_o and bkg01_04 --> -0.3878 dwf_pt_pt and bkg02_11 --> 0.3551 x_o and bkg01_01 --> -0.2856 delr_ru_o and bkg01_03 --> 0.2760 delr_ru_ru and bkg01_05 --> 0.2709 dwf_ru_o and bkg01_01 --> -0.2614 x_o and bkg01_02 --> 0.2600 dwf_ru_o and bkg01_02 --> 0.2595 delr_ru_pt and bkg02_11 --> 0.2562 x_o means the amplitude of Ru-O path e0 for Ru-O path is constrained to be the same as for all paths with Ru central atom To Jeremy: >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. I have two e0 parameters in the model that correspond to ru and pt data sets (they are e0_ru and e0_pt) the same e0_ru I use for Ru-O path Typical values that they take are about: e0_pt = 7.2318013 +/- 1.0171952 (0.0000) e0_ru = -9.1526876 +/- 0.7730603 (0.0000) and this is consistent through all data that I have and also their values almost do not depend on whether I use rmin=1.0A or 1.5A the same I can say about Ru-O distance. Typical value is: delr_ru_o = -0.0899771 +/- 0.0406058 (0.0000) To Bruce: >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? My advisor (Carlo Segre) has already answered this question I just want to add that the observed amplitude of Ru-O path (0.3)is approximately in agreement with the number of atoms on the nanoparticle surface. This may indicate that all Ru atoms are on the surface and all they have oxygen bonds. Stanislav

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

15 Apr '04

> 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

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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 15 Apr '04

15 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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