April 2024 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Origin of noise in Ag K-Edge
by Sebastian Kunze 30 Apr '24

30 Apr '24

Dear Shelly, Robert, Matt, thank you for your kind replies, I think I should give more information about the measurement. The sample is a sealed battery anode consisting of silver particles that should undergo alloying with Lithium during charging. This is done at constant temperature and applied pressure. I repeated this experiment under different conditions several times, and each time there is less noise before a certain time during the charging process, after which is persists even when the battery is at rest (not charging/discharging). I0 also did not fluctuate much, and the integration time for each point is indeed the same. Therefore I think it is not instrumental, but rather something happening in the sample. As you can see from the spectra, the silver particles experience a strong decrease of uniform structure when they lithiate. For me, this at least explains why the noise in the post-edge increases, but can it also explain the noise in the edge and pre-edge? In any case, thank you very much for your answers! Best, Sebastian

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question concerning the limitations of the webatoms program
by I. D. 30 Apr '24

30 Apr '24

Dear All, We are studying the gallium oxide polymorph (gamma phase). The *.cif file used is in the appendix. After testing this file with the webatoms program, I believe that there is a limitation of the number of atoms in the list between between 256 and 299. As can be seen in the *.cif file considered structure contains 426 atoms. If we try to use the webatoms program to generate the feff.inp file, error like that appears: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." Also there is no possibility to change the cluster size and select the desired absorption atom for generating feff.inp file. Can anyone help and explain how to solve the existing problem? Best regards, Iraida.

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Origin of noise in Ag K-Edge
by Sebastian Kunze 29 Apr '24

29 Apr '24

Greetings, I recently did in-situ QEXAFS at Ag K-edge, expecting to see structure loss starting from crystalline (metallic) state. While we can see that, in addition we also see an increase in noise(?) in the xanes region (compare start and end in the attached image). I am confused by this because the amount of material did not change, so I did not expect a difference in the signal/noise ratio at the absorption edge. And it is reproducible across several samples, so not instrument related. Could anyone point me in the right direction as to what I am missing? Thank you! Best, Sebastian Kunze

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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 08 Apr '24

08 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 03 Apr '24

03 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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