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

Difficulty in generating XANES for Ni.
by jaskirat brar 22 Apr '24

22 Apr '24

Dear list I am using feff8.2 to generate the XANES for Ni and compare it with the experimental spectra collected on pure Ni. To include the contribution from different scattering paths, I have increased the value of *r_fms* in steps. I find that the intensity ratios of the generated spectra match with that of the experimental spectra when* r_fms* is around 5 angstroms (figure below). Further increasing the* r_fms* produces a mismatch in the intensity ratios of the calculated and the experimental spectra, as shown in the figure. [image: fig.jpg] As per my understanding, increasing the *r_fms* should include more scattering paths and give a better match with the experimental spectra. Please comment on what might be the problem here. Thanks in advance. Jaskirat Brar FMP Lab, South Campus IIT Mandi, H.P., India

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Difficulty with normalization of XAS spectra
by jesse walters 15 Apr '24

15 Apr '24

Hi all, I have some spectra collected by a collaborator, Francesco Ressico, a PhD student at Uni Bologna, (see attached .h5 file below) and we are having trouble normalizing the Fe K edge spectra. The data are for serpentine group minerals and were collected in fluorescence mode. In the attached file, the correct X array value is 'energy_enc', the data type is 'xas', and the y array should be 'mu_fluo_det0'. The spectra are already normalized for the incoming beam energy (although this can also be done using 'flou_det0/i0'). There are multiple spectra in the file, any one of them can be chosen to test the procedure. After loading the spectra, I am able to plot the raw spectra correctly (see attached). But when I try to normalize the pre and post edge regions and plot the normalized spectra, the software only gives a blank plot. I have tried changing the normalization type, polynomial type, range, etc for both the pre and post edge, but nothing seems to work. I also tested different spectra, but with similar results. Does anyone have suggestions for how these data can be normalized? The h5 file is too large, so here is a dropbox link https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac… Sincerely, Jesse Walters -- Jesse B. Walters Ambizione Fellow Institut für Geologie Universität Bern

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Re: [Ifeffit] Ifeffit Digest, Vol 254, Issue 4
by Ryan Parmenter 08 Apr '24

08 Apr '24

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Peak-Fitting Process in Larix
by Ryan Parmenter 07 Apr '24

07 Apr '24

Hi All, I have some questions regarding different aspects of the peak-fitting process in Larix. I wish to repeat the process reported in similar studies, but I'm facing challenges in adapting it effectively to my dataset. * Farges 2005: 'One should model the pre-edge feature with either two or three peaks of fixed width and shape pseudo-Voigt functions of 1.3 eV 2σ width and 45% Gaussian'. * Chalmin 2009: 'The pre-edge region was extracted from the normalised XANES spectra and modelled using a series of pseudo-Voigt functions of fixed width (1.3 eV) and fixed Gaussian percent to minimise the number of variable parameters. Two contributions were modelled for Mn2+ and three for Mn3+.' Using Mn2+ as an example, after normalisation, the baseline is fitted within the pre-peak region, followed by fitting an arctangent background function to the data. The parameters for the arctangent function are initially estimated using the 'pick values from plot' feature. However, modifying these parameters doesn't result in corresponding changes in the graph, making it difficult to ascertain if it aligns with the data points. Considering this, would it be acceptable to set the arctangent's amplitude to 1 (normalised edge jump) and position its centre a couple of eV below E0? Following this, two pseudo-Voigt functions are introduced, with their parameters initially estimated. Then, to replicate the conditions of '1.3 eV 2σ width and 45% Gaussian,' do I set the pseud_fraction to 0.45 and pseud_sigma to 2? I'm uncertain about where to input the 1.3 eV width and whether this choice is optimal, especially considering that the natural width of the atomic K level at the Mn edge is 1.16 eV (Krause, 1979). Finally, I couldn't find the specific paper, but the authors stated that due to the significant processing times required for Voigt functions, they opted for pseudo-Voigt functions to model instrumental and core-hole broadening factors. With improvements in processing times, are Voigt functions now the preferred choice, or does the pseudo-Voigt function still hold advantages over both? Any insights and suggestions would be immensely valuable and greatly appreciated. Ryan

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Imidazole multiple scattering in Artemis
by Chris Pollock 02 Apr '24

02 Apr '24

Hi everyone, I've been using Artremis for quite a while, but have only recently come across a case where the inclusion of multiple scattering seems to be important for fitting some data and wanted to ask what is probably a super basic question to make sure I don't mess anything up. I've recently collected some data on a metalloenzyme with a quite histidine-rich active site and, since it's been shown previously that multiple scattering is important for fitting the longer range scattering for these types of systems, I wanted to make sure I capture this in my Artemis fits. The data appear to show scattering contributions from N3, C2, and N1 in the imidazole ring, and FEFF seems to agree that those paths are the most important, though it calculates the MS intensity to be significantly greater than the single scattering for the farther N (N1). So, my super naive question is: To include multiple scattering paths in the fits--say, the Fe-N3-N1 triangle--is it correct to include the Fe-N3-N1 multiple scattering path in addition to the Fe-N3 and Fe-N1 single scattering paths, or would that effectively be double counting the farther nitrogen (N1)? Thanks in advance!

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lithium scattering paths
by Hu, Yang (HIU) 30 Mar '24

30 Mar '24

Dear ifeffit members, I would like to ask a few questions about the FEFF calculation and fitting of scattering paths between the light lithium (scatters) and transition metals (central abs.). For materials containing Li, there are Li scattering paths in FEFF calculations, but usually with low "rank" or low "importance". Through my limited experience, I often ignored those paths when treating cations-disordered materials, where Li share the same crystallographic site with other TMs. For the pristine materials, if I include the Li paths, the fitting got unstable especially for the paths degeneracy. Things became more complicated with Li extraction/insertion in cycled cathode materials. Recently I am rechecking previous data (same cif, before XASViewer and now Larix), and I could "fit" some spectra with Li paths (the fitted parameters were not so crazy), which I never managed before (I tried a lot). I am wondering if there have been developments in FEFF or software that would allow better treats of Li scattering paths in shell fitting? The behaviour of Li and their influence on the TM local structure are quite interesting and important for our works, but I rarely see literature involving Li scattering paths. I just don't know if it is worth continuing to invest time and efforts on this...... I really appreciate if you can provide some suggestions and opinions J Thanks very much, Best regards, Yang

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Open position at BioXAS sector
by Morgane Desmau 28 Mar '24

28 Mar '24

Dear colleagues, We have a permanent position opening in the BioXAS sector (XAS/XRF) at CLS: https://urldefense.us/v3/__https://www.northstarats.com/Canadian-Light-Sour… Here are our websites: - spectroscopy: https://urldefense.us/v3/__https://bioxas-spectroscopy.lightsource.ca/__;!!… - imaging: https://urldefense.us/v3/__https://bioxas-imaging.lightsource.ca/__;!!G_uCf… with our contact information if you have any questions. If you know of a colleague who might be interested, please forward this email to her/him. Best regards, Morgane Desmau

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Re: [Ifeffit] Using Larix from Jupyter notebook
by Ryuichi Shimogawa 25 Mar '24

25 Mar '24

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Using Larix from Jupyter notebook
by Yohei Uemura 25 Mar '24

25 Mar '24

Hi all I read the documentation of Larch and Larix can generate a feff input file from a xyz file. https://urldefense.us/v3/__https://cars.uchicago.edu/xraylarch/xasviewer/ov… Does anyone have a python script to generate a feff input file from a xyz file using Larix? Best regards, Yohei -- ================================================ Yohei Uemura (Ph.D) Instrument scientist FXE beamline, European XFEL GmbH Address : Holzkoppel 4, 22869 Schenefeld, Germany Phone: +49-40-8998-6006 上村洋平所属 : FXE beamline, European XFEL GmbH, 住所 : Holzkoppel 4, 22869 Schenefeld, Germany 電話 : +49-40-8998-6006 ================================================

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Larch 0.9.75
by Matthew Newville 22 Mar '24

22 Mar '24

Hi Folks, Larch 0.9.75 has been released and is now available. You may see a prompt to install this the next time you launch the Larix GUI. It's been several months since the last release of Larch, and there have been many updates, especially for the Larix GUI, and for using Larch for XAS analysis and visualization with Jupyter notebooks. More complete release notes are at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases__;!… There have been a lot of people who helped with this release, either with code or very detailed discussions and bug reports. There are still several things on the near-term to-do list, including (in no particular order): better customizability and remembering user settings of detailed plotting preferences (themes, colors, etc) in Larix and Jupyter/plotly. Larix automatically generating Jupyter notebooks from analyses. getting a good implementation of MCR-ALS creating a self-contained set of packages so that installation can include exactly one (maybe large) download, but simplifying installation, especially on machines with poor or no internet connection. If you have any questions, trouble, or suggestions, please let us know. --Matt

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