August 2022 - Ifeffit - millenia.cars.aps.anl.gov

Parameters for parent function in wavelet transform analysis
by Scott Calvin 09 Feb '23

09 Feb '23

Hi all, I’ve never actually tried wavelet transform analysis before, so I’m trying to understand it better, but there’s one aspect that’s puzzling me: The Morlet wavelet has two parameters, eta and sigma. Eta controls how fast it wiggles, and sigma how quickly the function dies out. (Essentially, it’s like the basis function for a Fourier transform multiplied by a Gaussian envelope.) In wavelet analysis we pick a parent function, which is often a Morlet wavelet with particular values of eta and sigma that we have chosen. We then create a set of child functions from the parent function by shifting and dilating the function in k-space. Each child function is then used as a basis function for a transform of chi(k) calculated by integrating over a range of k-values, much like what is done to calculate a Fourier transform. Since the Morlet wavelet is localized in k-space, and the child functions are shifted to focus on different regions of k-space, our wavelet transform produces plots which are a function of k. But since dilating the parent function by different amounts yields child functions with different frequencies, the plots are also a function of R. Therefore the result is a two-dimensional (k and R) contour plot. So far, so good. But what I’m wondering about is the effect of the initial choice of eta and sigma for the parent function. The dimensionless product of eta and sigma has a clear effect. If (eta)(sigma) is small, the parent function will not have very many oscillations of significant size; it it’s large, it will have a lot of oscillations. So if we want good resolution in R (and thus relatively poor resolution in k), we want a big value of (eta)(sigma). In the limit as (eta)(sigma) becomes arbitrarily large, we recover the Fourier transform. If we want good resolution in k, we use a small value for (eta)(sigma). In the limit as (eta)(sigma) becomes arbitrarily small we recover chi(k). That still makes sense to me! But what difference do sigma and eta make individually? In other words, how is sigma = 0.5 and eta = 10.0 different from sigma = 1.0 and eta = 5.0? Since we end up creating child functions that dilate the parent function anyway, I can’t see that it should have any effect at all. And if those two parameters don’t make an independent effect, why do we pretend there are two independent-looking parameters? I’ve seen at least one early paper that suggests choosing eta so that it’s close to the path length you’re most interested in probing, but I can’t see how that actually makes any difference, given the dilation. I expect there’s a good chance I’m missing something obvious, or have a fundamental misunderstanding of part of the process, and look forward to learning more! Best, Scott Calvin Lehman College of the City University of New York

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XAFS fitting in xas_viewer and reset of customized variables after save & load cycle
by juejing.liu＠gmail.com 04 Sep '22

04 Sep '22

Hi all, I am using xas_viewer, version 0.9.65, to fit some XAFS data. In a typical situation I will also fit the coordination numbers of atoms by add customized variables in the amplitude boxes (image below). It works fine during my fitting. However, when I save my result as a larch session and load it later, all my customized parameters are disappeared, and the amplitude boxes are reset. Therefore, I need to refill all the variables after each save & load cycle. This becomes increasingly tedious when dealing with about 20 different paths. Is there any workaround of this problem? Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

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Simultaneous multispectral fitting in Larch?
by Van Stappen, Casey M 30 Aug '22

30 Aug '22

To whom it concerns, I wanted to inquire regarding how best to perform multispectral fitting (i.e. fitting several EXAFS spectra simultaneously with shared parameters) in Larch? This was something that could be done with (relative) ease in Artemis, but I was hoping to perform this at a larger scale (6 spectra, >10 restrictions) in Larch. I’ve hunted through Dr. Newville’s excellent Youtube tutorials, but didn’t find this specific information. Thank you for your help! Best, Casey Van Stappen ------------------------------------------------------------------------ Dr. Casey Van Stappen University of Texas at Austin Robert A. Welch Hall, 4.318 2350 Speedway Austin, TX 78705 USA Phone: +1 (512) 775-2658 E-mail: casey.vanstappen(a)austin.utexas.edu

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XAFS short course at BNL: November 2-4
by Anatoly Frenkel 29 Aug '22

29 Aug '22

Dear subscribers, This is a reminder about the annual XAFS short course at BNL. The dates are: November 2-4. It will be virtual. The level will be intermediate to advanced As in the past, lectures, discussions and software demonstration sessions will be on Wednesday and Thursday, and the full day data analysis practicum will be on Friday. The course agenda and the link to the application form are available at the BNL web site: https://www.bnl.gov/xafscourse/index.php and at the web site of the Synchrotron Catalysis Consortium: https://you.stonybrook.edu/scc2/xafs-workshops/ Registration deadline is September 11. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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Question related to an example of EXAFS fitting using Larch
by Andy Zhang 29 Aug '22

29 Aug '22

Dear all, I am learning Larch and read the manual of Larch online. In the "13.8.10. Example 3: Fit 3 datasets with 1 Path" of the webpage https://xraypy.github.io/xraylarch/xafs_feffit.html#example-3-fit-3-dataset…, it shows an example that fitting Cu at different temperatures. Einstein model was used to simulate the sigma2, as shown in the figure below. [image: image.png] However, in some papers (eg. Radiation Physicsand Chemistry137 (2017) 93–98) that model EXAFS at elevated temperatures, they separates the total sigma2 to static and thermo components (Sigma^2 = Sigma_static^2 + Sigma_thermo^2), which is different from the above Larch example. I am a little confused about the utilization of Einstein model. I wonder if the Sigma2 obtained by Einstein model can reflect the total sigma2 or can only reflect the thermo part. Many thanks for your help! Best regards, Harry

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Re: [Ifeffit] XAFS fitting in xas_viewer and reset of customized
by juejing.liu＠gmail.com 28 Aug '22

28 Aug '22

Hi Matt, Here is the session file for the UO2 fitting. The screenshot blow shows what the customized variables look like right before saving this session. Please feel free to let me know if you need any extra information. Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

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Re: [Ifeffit] XAFS fitting in xas_viewer and reset of customized variables after save & load cycle
by Liu, Juejing 28 Aug '22

28 Aug '22

Hi Matt, Thanks for the quick response. I just noticed that the data in the screenshot is unpublished data so I may not be able to send you that one. But I will send you a typical UO2 fitting later today (in the larch session) so that you can look. Best, Juejing Liu Guo Group Materials Science and Engineering program Alexandra Navrotsky Institute for Experimental Thermodynamics Washington State University Pullman, WA 99164-4630 Office: Fulmer Hall, Room 630 Phone: 208-206-7304

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Quick Absorption and Scattering (QAS) beamline scientist position at NSLS II
by Stavitski, Eli 26 Aug '22

26 Aug '22

Dear all, We are looking for a beamline scientist for Quick Absorption and Scattering (QAS) beamline (https://www.bnl.gov/nsls2/beamlines/beamline.php?r=7-BM) The full job description is available here https://jobs.bnl.gov/job/upton/beamline-scientist-quick-x-ray-absorption-an… ____________________________________ Eli Stavitski, PhD, Physicist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 631 344 8641 istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> https://www.bnl.gov/ps/beamlines/beamline.php?r=8-ID

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third cumulant in Larch
by Andy Zhang 19 Aug '22

19 Aug '22

Dear all, I have a quick question related to EXAFS fitting using Larch. I wonder how to include the third cumulant in the fitting. I tried to add "third" in the "pars" section, but it seems it did not work. [image: image.png] Thanks a lot for your help! Have a nice day! Best, Harry

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Environmental geochemist position at DOE-National Energy Technology Laboratory
by Mengling Stuckman 18 Aug '22

18 Aug '22

Dear ifeffit members, Recently we are interested in hiring an environmental geochemist for our critical mineral sustainability program at NETL, Pittsburgh, PA. Synchrotron experience is a plus. U.S. citizens are strongly preferred. Here is the specific job posting. https://leidos.wd5.myworkdayjobs.com/External/job/Pittsburgh-PA/Environment… Feel free to pass along this information to your students who are interested. If you have any questions related to the post, feel free to contact me at mengling.stuckman(a)netl.doe.gov Thanks and have a nice day, Mengling -- Mengling Stuckman Leidos Technical Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

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