February 2023 - Ifeffit - millenia.cars.aps.anl.gov

XAS viewer unit detection during data reading
by van der Veer, Siebe 02 Mar '23

02 Mar '23

Dear all, I am not sure if this mailing list is the correct medium for this question. Apologies, if not. I am looking to import files in XAS viewer, which worked fine in ATHENA, but in XAS viewer the correct units of the data are not detected and I cannot manually change them. I can get a plot of the data, but the data is not recognized by the software as XAS data, i.e. a lot of plotting/conversion options do not show. I hope the following screenshots provide sufficient information to illustrate my issue. Reading in a .dat file of fluorescence data. I can't change the units in the marked area. [image: image.png] The data can be read into the XAS viewer, but I don't have the regular plotting options in these dropdown menus. [image: image.png] Any advice would be much appreciated. Kind regards, -- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer(a)rug.nl |

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Re: [Ifeffit] Ifeffit Digest, Vol 240, Issue 14
by van der Veer, Siebe 28 Feb '23

28 Feb '23

Dear Edmund, Thank you for the prompt reply. That did work. Cheers, Siebe On Tue, Feb 28, 2023 at 1:39 PM <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: XAS viewer unit detection during data reading (Welter, Edmund) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 28 Feb 2023 13:37:03 +0100 (CET) > From: "Welter, Edmund" <edmund.welter(a)desy.de> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XAS viewer unit detection during data reading > Message-ID: > <1505460518.63098920.1677587823196.JavaMail.zimbra(a)desy.de> > Content-Type: text/plain; charset="utf-8" > > Dear Siebe, > > did you try to change the data type from "raw" to XAS. If you click on the > small arrow on the right you should have the choice between xas and raw. On > my computer that works and after that I can choose the unit for the X-axis. > For some reason "raw" seems to be the preset choice. Maybe Matt could > change that, I fell into this trap several times. > > Cheers, > Edmund > > > From: "van der Veer, Siebe" <s.van.der.veer(a)rug.nl> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Tuesday, 28 February, 2023 13:16:18 > Subject: [Ifeffit] XAS viewer unit detection during data reading > > Dear all, > I am not sure if this mailing list is the correct medium for this > question. Apologies, if not. > > I am looking to import files in XAS viewer, which worked fine in ATHENA, > but in XAS viewer the correct units of the data are not detected and I > cannot manually change them. I can get a plot of the data, but the data is > not recognized by the software as XAS data, i.e. a lot of > plotting/conversion options do not show. > > I hope the following screenshots provide sufficient information to > illustrate my issue. > > Reading in a .dat file of fluorescence data. I can't change the units in > the marked area. > > > > The data can be read into the XAS viewer, but I don't have the regular > plotting options in these dropdown menus. > > > > Any advice would be much appreciated. > > Kind regards, > > > -- > Siebe van der Veer | PhD student > Nanostructures of Functional Oxides | Zernike Institute for Advanced > Materials > University of Groningen | Nijenborgh 4, 9747 AG Groningen | The > Netherlands > Email: [ mailto:s.van.der.veer@rug.nl | s.van.der.veer(a)rug.nl ] | > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

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Dumb question
by Roberta Candela 17 Feb '23

17 Feb '23

Hi all, I am attempting to graph a simple plot of intensity vs time for some supplemental info on a paper (from XAFS data from beamtime). I thought it should be simple enough since I can export I0 and If from Athena and I know the run time and time per data point but I can’t get anything that looks remotely like the logarithmic graph it should be. Am I missing some big fundamental point for why this isn’t possible? My apologies if this is way too vague!/I feel like I’m missing something super obvious Thank you for your time!Sincerely -B Sent from Yahoo Mail for iPhone

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Error importing CIF files using Larch/ XAS Viewer
by Jack Geary 15 Feb '23

15 Feb '23

Hello, I have encountered an issue recently where any CIF file I attempt to open in XAS Viewer for Feff calculations returns an error that the file cannot be imported. This occurs with any CIF I have tried (all downloaded from CCDC). Is there a workaround for this? Thanks ---- Jack Geary Pronouns: he/him PhD Candidate, Xiao Group <https://xiaolab.org/> University of Washington

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Y2O3 E0
by Otal Eugenio 14 Feb '23

14 Feb '23

Hi all, I am aligning in energy Y substituted sample but using Zr foil as a reference, no Y metal is available at the BL. Does anyone have well-calibrated in-energy Y2O3 spectra? Best regards. (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Dept. of Materials Chemistry Shinshu University 4-17-1 Wakasato, Nagano 380-8553, JAPAN eugenio_otal(a)shinshu-u.ac.jp https://sites.google.com/view/zettsu-laboratory/news-updates

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Zr K edge EXAFS analysis of amorphous materials
by Angshuman Gupta 11 Feb '23

11 Feb '23

Dear everyone, I am working on alumina based amorphous materials containing ZrO2. I am interested in finding the bond length between Zr and O atoms and coordination number (N). Zr K edge spectra were collected at room temperature at 300K along with Zr foil as reference. Extracted So2 from reference (Zr foil) spectra was used to find N in the amorphous material. Local environment around Zr was modelled with harmonic and quasi harmonic models using a third cumulant of the distributions. Theoretical spectra fit well using quasi-harmonic models with large bond length (2.21 A) while harmonic models without third cumulants do not fit the spectra properly and calculating higher N value with 2.16 A as Zr-O bond length. I will be thankful if you kindly let me know what else we can do to improve the fitting and get some meaningful outcome. Any relevant journal articles are also helpful. I have attached the Artemis files. Thanking you Angshuman Gupta PhD research scholar IIT Bombay, Mumbai

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Parameters for parent function in wavelet transform analysis
by Scott Calvin 08 Feb '23

08 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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Upcoming symposium on spectroscopy at large-scale facilities
by Dugan Hayes 08 Feb '23

08 Feb '23

Dear colleagues, The 76th International Symposium on Molecular Spectroscopy to be held June 19-23, 2023 at the University of Illinois Urbana-Champaign is now open for registration. The conference is highly student-oriented, aiming to give any student the opportunity to give an oral contribution. Each year, the ISMS spotlights topics of special interest in mini-symposia, typically lasting three or four half-day sessions. This year, Renske van der Veen, Joost Bakker, and I are organizing a mini-symposium entitled “Spectroscopy at Large-Scale Facilities: from Steady-State to Ultrafast.” The aim is to showcase how spectroscopy at large-scale facilities is practiced and what types of scientific questions can be addressed using the unique capabilities such facilities provide. Below is a short description of the mini-symposium, and more information on ISMS is available at the conference website: https://isms.illinois.edu/ The deadline for abstract submission is *March 1st*. We hope you would be willing to bring ISMS, and in particular our mini-symposium, to the attention of your Ph.D. students and postdocs - and of course urge them to come! Please also pass this announcement along to any other group leaders at your institute and beyond who may be interested. Regards, Dugan Hayes (University of Rhode Island) Joost Bakker (Radboud University, HFML-FELIX) Renske van der Veen (Helmholtz-Zentrum Berlin, BESSY) --------------------------------------------------------- *Spectroscopy at Large-Scale Facilities: from Steady-State to Ultrafast* The general topic of the symposium is IR/XUV/X-ray spectroscopy at synchrotrons and free-electron lasers, applied to, but not limited to the following topics: - Ion/gas-phase/cluster chemistry - Astro- and atmospheric chemistry - Molecules for catalysis and solar energy - Reaction dynamics - Photophysics of organic molecules and transition-metal complexes Symposium description: Large-scale facilities offer unique capabilities for spectroscopic investigations of, e.g., dilute solution-phase samples, clusters, or time-resolved molecular dynamics. With the recent advent of free-electron laser (FEL) facilities, yet a new era of molecular spectroscopy has begun. The goal of this symposium is to bring together the lab-based molecular spectroscopy community (historically largely represented at ISMS) with people from recently emerged fields such as (ultrafast) IR/XUV/X-ray spectroscopy at synchrotrons and FEL facilities. -- Dugan Hayes Assistant Professor | Department of Chemistry | University of Rhode Island Beaupre 374E | 140 Flagg Road | Kingston, RI 02881 (401) 874-5516 | (*he/him*) http://www.chm.uri.edu/hayesgroup/

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FDMNES Simulation for ZnO
by Chen, Danting 06 Feb '23

06 Feb '23

Dear All, I tried to run some simulations through FDMNES about XANES of ZnO with the absorber of Zn, and there are the results for simulated ZnO (red) compared with the experimental one (Green curve). The white line matches well but the two additional peaks are not shown in the spectrum of simulated ZnO. I attached the input file for FDMNES here. Do you have any idea to improve it? I am quite new to running the simulation and would appreciate if you can give me some directions to modify it. Best Wishes, Danting [cid:image001.png@01D937EA.4B65FBB0]

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