April 2007 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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large Eo's and neg. D-W factors
by Richard Mayes 02 May '07

02 May '07

Greetings! I have inherited a vanadium EXAFS data set (due to a group member graduating - lucky dog!) that is giving me major fits. I am getting consistent numbers with all my fits which visually look fantastic, that is until I look at the numbers...one Debye-Waller factor is negative (a V-O path) and the Eo's are large, the V-Cl path is on the order of -20 eV, the V=O path is on the order of 17 eV, and the V-O path falling at -11 eV. ARe there any "tricks" outside of restraints or constraints that I can attempt to get more realistic values? (I understand that a large Eo can be realistic, but a negative Debye-Waller factor doesn't make sense.) I can restrain the V-O Debye-Waller factor and get a positive value, but then the V=O D-W factor is negative. If I restrain both D-W factors, the fit falls apart, suggesting something else is wrong that I just can't find. Another issue I'm having involves something in Artemis that's confusing me. Sometimes after a fit, the Artemis Pallet shows the V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6 Angstroms, completely reversed to the FEFF model. I have seen this when I separated the chlorides as well (I attempted to model the Cl at different distances as reported by Deguns, et. al. (attached) due to the immediate environment around the V in our sample being similar to the one they report in scheme 1-(I), p5008). Attached is a text file that shows an Artemis Pallet output illustrating what I'm trying to describe for the V=O and V-O paths. The Artemis project that generated the output is also attached. At this point, I'm wandering what I'm missing. Any help is greatly appreciated!! Many thanks in advance! Rich Mayes Barnes Group 450/452 Buehler Hall Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996 Project title : Fitting SA_162deglitch-merge.chi Comment : Fit #1 Prepared by : Contact : Started : 15:46:44 on 17 April, 2007 This fit at : 15:58:01 on 18 April, 2007 Environment : Artemis 0.8.007 using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 Figure of merit : 3 ============================================================ Independent points = 14.027343750 Number of variables = 9.000000000 Chi-square = 45.640992098 Reduced Chi-square = 9.078550099 R-factor = 0.012557807 Measurement uncertainty (k) = 0.000687372 Measurement uncertainty (R) = 0.023895029 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): enot = 17.1999060 +/- 3.4058600 (0.0000) delr = 0.1588460 +/- 0.0081480 (0.0000) ss = -0.0022720 +/- 0.0007180 (0.0030) enot_O2 = -11.0384940 +/- 9.8688920 (guessed as enot) delr_O2 = -0.2214820 +/- 0.0356500 (0.0000) ss_O2 = 0.0027560 +/- 0.0021290 (0.0030) enot_Cl = -16.0026700 +/- 3.5982940 (guessed as enot) delr_Cl = -0.0118230 +/- 0.0104780 (0.0000) ss_Cl = 0.0016470 +/- 0.0004220 (0.0030) Set parameters: amp = 0.93 CN_O1 = 1 CN_O2 = 1 CN_Cl = 2 Correlations between variables: enot_Cl and delr_Cl --> 0.9479 enot_O2 and delr_O2 --> 0.9104 enot and enot_Cl --> 0.8766 enot and enot_O2 --> -0.8755 ss and delr_Cl --> 0.8737 delr_O2 and enot_Cl --> -0.8655 ss and enot_Cl --> 0.8469 enot_O2 and enot_Cl --> -0.8220 ss and delr_O2 --> -0.8025 enot and delr_Cl --> 0.7864 enot and delr_O2 --> -0.7825 delr_O2 and delr_Cl --> -0.7817 enot_O2 and ss_O2 --> 0.7535 delr_O2 and ss_O2 --> 0.7259 enot_O2 and delr_Cl --> -0.7080 ss and enot_O2 --> -0.6872 enot and ss --> 0.6795 delr_O2 and ss_Cl --> -0.6271 delr and ss_Cl --> -0.6217 ss_O2 and enot_Cl --> -0.6173 ss and ss_Cl --> 0.5740 ss_O2 and ss_Cl --> -0.5640 enot and ss_O2 --> -0.5314 enot_Cl and ss_Cl --> 0.5264 ss and ss_O2 --> -0.5084 enot_O2 and ss_Cl --> -0.4750 ss_O2 and delr_Cl --> -0.4747 delr_Cl and ss_Cl --> 0.4701 delr and ss_O2 --> 0.4134 enot and delr --> 0.3090 enot and ss_Cl --> 0.2693 All other correlations are below 0.25 ===== Data set >>SA 162deglitch-merge<< ======================================== file: C:\Program Files\Ifeffit\horae\stash\artemis.project.2\chi_data\SA_162deglitch-merge.chi title lines: Self absorption correction of 162deglitch-merge using method of Troger et al. + V K edge + Formula=H24.75 C8.25 O21.48 Si12.125 Cl4.7 V1.48 Merge in e space of: ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.001 ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.002 ** D:/200600603/Barnes-lab/EXAFS/NSLS/EXAFS/MYL-JULY-2006/all-VOCl3/162-Me2SiCl2+V5/162.003 k-range = 2.388 - 15.000 dk = 2.000 k-window = hanning k-weight = 2 R-range = 1.200 - 3.000 dR = 0.200 R-window = hanning fitting space = R background function = none phase correction = none R-factor for this data set = 0.01256 ===== Paths used to fit SA 162deglitch-merge FEFF1: Path 1: [O] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0001.dat id = reff= 1.6819, nlegs= 2, path= V<->O label = r = 1.840746 degen = 1.000000 s02 = 0.930000 e0 = 17.199906 dr = 0.158846 ss2 = -0.002272 3rd = 0.000000 4th = 0.000000 ei = 0.000000 FEFF1: Path 2: [O] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0002.dat id = reff= 1.8269, nlegs= 2, path= V<->O label = r = 1.605418 degen = 1.000000 s02 = 0.930000 e0 = -11.038494 dr = -0.221482 ss2 = 0.002756 3rd = 0.000000 4th = 0.000000 ei = 0.000000 FEFF1: Path 3: [Cl] .. feff = C:\Program Files\Ifeffit\horae\stash\artemis.project.2\data0.feff1\feff0003.dat id = reff= 2.1121, nlegs= 2, path= V<->Cl label = r = 2.100277 degen = 1.000000 s02 = 1.860000 e0 = -16.002670 dr = -0.011823 ss2 = 0.001647 3rd = 0.000000 4th = 0.000000 ei = 0.000000

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Potential Postdoctoral Position in XAFS
by Bare, Simon R 30 Apr '07

30 Apr '07

POSTDOCTORAL POSITION in XAFS and XRD UOP LLC There is a potential opening for a postdoctoral position in synchrotron radiation research of catalysts and adsorbents with UOP LLC. The successful candidate with work with UOP LLC research scientists and will support UOP LLC exploratory and fundamental industrial research activities primarily at the Advanced Photon Source (APS) at Argonne National Laboratory. UOP LLC, a Honeywell Company, located in northwest suburban Chicago, is an international leader in technology, products, and services for the petroleum processing and separation industries (www.uop.com <http://www.uop.com/> ). The successful candidate will participate in all aspects of experiments related to operating a beamline, collecting, analyzing and interpreting the data. This position requires expertise in techniques of XAFS (preferably with knowledge of Athena/Artemis or Iffeffit software) and XRD, together with hands-on experience with electronic control and measuring equipment and beamline components. A CV with publications list, and the names and addresses of two references, should be sent via e-mail to Dr. Simon Bare at: simon.bare(a)uop.com.

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sum path NAN?
by Mauro Rovezzi 27 Apr '07

27 Apr '07

Dear all, Do you have any idea of what means NAN (Not A Number?) in "sum path" Ifeffit output during the fit? I've already posted this issue in a post dated 2006/10/04 and Bruce asked to me to give him something to reproduce this issue on his computer but this behavior is very unstable and I don't understand how to exactly reproduce it. I would like to know in your opinion what could bring a variable during the minimization process to NAN. In addition, what exactly means the four numbers visible in the "sum path #1 #2 #3 #4" output? It seems to me that, for each path, #2 = delr and #3 = sigma2, isn't it? M. -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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mailing list downtime
by Matt Newville 20 Apr '07

20 Apr '07

Hi Folks, Sorry to bother you with non-XAFS related mail, but I wanted to let you know that the Ifeffit mailing list, web pages (everything on http://cars9.uchicgo.edu, http://millenia.cars.aps.anl.gov, and http://xafs.org) will be unavailable tomorrow (Apr 21), starting around 6am Central Daylight Time (11am UTC) and lasting for around 12 hours. This is due to a scheduled complete power outage to the building housing the server and network equipment. I assume the network equipment and server will come back from the power outage just fine, but will be watching for signs of life. Mail sent to the mailing list during the down time should queue up until the server is back up, but I wouldn't want to guarantee that mail won't get bounced over the weekend. Sorry for the inconvenience, --Matt

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Several Questions
by Edward L. Kunkes 20 Apr '07

20 Apr '07

Hello everyone, I am currently using IFEFFIT to fit LIII edge data collected for Pt, Re and PtRe bi-metallic Nan particles supported on carbon, and I have several questions: 1. I get an So2 value of 0.54 from a first coordination shell fit on Re-foil (this So2 value also seems to work when fitting NH4ReO4-) Has anyone ever worked with Re before and gotten a similar value for So2 ? 2. I model the path for the a single coordination shell as 6 octahedrally arranged nearest neighbor atoms surrounding the absorber atom at a distance equal to that of inter -atomic spacing in the metal. When comparing the IFEFFIT predicted EXAFS for this model to one that is generated by using the first path from a crystallographic model, the two seem slightly different. The nanoparticles are very small (amorphous to XRD), and probably consist of a disordered phase, so I cannot assign a crystal structure. What should I do in this case? 3. I often get high correlations the coordination number and ss, or delEo and dR (the correlations are ~0.8). Using multiple k-weights doesn’t decrease the correlations. What is an acceptable value for these correlations? Thank you very much for taking the time to answer my questions -Ed Kunkes

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Re: [Ifeffit] Structures with multiple crystallographic sites
by Vadim G Palshin 20 Apr '07

20 Apr '07

Matt, Bruce - thank you! I believe I found the problem - Artemis does seem to choke even on 200 paths, especially with the "fit background" option on. At least it does on my office PC - relatively old and weak machine, will start begging for a new one shortly. Sometimes it would generate a long error message starting with "use of uninitialized value in abs at artemis line 12984."; sometimes there is no error message but results would look really strange. Had me so confused that I started to doubt my fitting method. I have since trimmed down the number of paths and variables to a minimum (didn't need that many anyway), and the problem seems to be solved. Thanks again for your responses, gentlemen! Vadim.

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Structures with multiple crystallographic sites
by Vadim G Palshin 20 Apr '07

20 Apr '07

>Do a Feff calculation with each unique Co site as the absorbing atom, >then use paths from each calculation, weighted by the fractional site >occupancy. >Cheers, >--Matt Thanks, Matt! Yes, that's exactly what I tried doing. It's a simple cubic lattice with 20 atoms per unit cell, 8 of one type (Co1) and 12 of the other (Co2). So I did two FEFF runs in the same Artemis project, with Co1 and Co2 as the core atom, and multiplied their respective amplitudes by 0.4 and 0.6. Then I noticed that if I calculate a sum of all included paths I get a different FT spectrum than if the sums are calculated separately for the two FEFF runs and averaged (with correct weighting) outside of Artemis. Of course, it is a bit late here and I could be missing some obvious mistake. On the other hand, I am trying for 1.6-5.5 angstrom fitting range, which involves 70+ paths for Co1 core and ~120 for Co2. Is it possible that Artemis does not like to deal with too many paths and/or variables? I better go check the manual... :o) Regards. Vadim.

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Structures with multiple crystallographic sites
by Vadim G Palshin 19 Apr '07

19 Apr '07

Hello, everyone! I am trying to fit various metallic Co spectra (nanoparticles) and one of the structural models, the epsilon-Co phase, has two unique crystallographic sites for Co. How does one tackle fitting a dataset with multiple crystallographic sites? Thanks! Vadim.

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