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

Larch 0.9.60
by Matt Newville 23 May '22

23 May '22

Hi Folks, Larch version 0.9.60 has been released. It should now be installed by default using all installation mechanisms, and you should see a notice to update, perhaps the next time you run XAS Viewer. There are several bug fixes and feature improvements in XAS Viewer. This version also adds some important new features to XAS Viewer and Larch. These are described in a bit more detail at https://github.com/xraypy/xraylarch/releases/tag/0.9.60 Briefly, the new features for XAS Viewer are: 1. Each data "Group" has a processing Journal, with a time-stamped history of processing events. This will document the main processing steps. 2. Many preferences for XAS Viewer can now be set program-wide and saved for future sessions. Copying processing parameters between groups now works better. 3. A Session or Project file can now be saved at any time. This will contain all the arrays for a Group and also include fitting models and per-group fit histories for Pre-edge Peaks, Linear-Combination analyses, Feff-fitting (including Feff Paths), and so on. These Session files can be read back in and fit models and histories are restored in XAS Viewer. That is, these files are intended to be suitable for exchanging by email and archiving, etc. Session files are also "auto-saved" periodically and can be used to recover the last session on startup. There are several changes here. I'm confident with the basic functionality and have been testing myself on all platforms. But GUI actions are hard to test thoroughly, so it is reasonable to expect some new bugs or misfeatures. With upcoming workshops in July, I expect to need a release focused on bug and feature fixes in about a month. So, I hope you will be able to test and make any suggestions, comments, or error reports. Cheers, --Matt PS: For Python users, all of Python 3.7, 3.8, 3.9, and 3.10 should work, though the main installers are still using either Python 3.8 or Python 3.9.

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Simulated XANES spectra does not match with experimental spectra in the white line region
by Monica Bairagi 23 May '22

23 May '22

Dear IFEFFIT members, Using FEFF10, I am simulating XANES spectra of copper complexes in which aspartic and glutamic acid are primary ligands. The experimental XANES spectra show a broadened peak with two weak humps, in the white line as shown in the accompanying figure. In the simulated spectra I am not getting a broadened white line, it shows a peak-like structure. My question is whether FEFF10 can show in the simulated spectra a broadened white line. As is known the white line structure is due to molecular orbital of 4p orbitals. Does FEFF10 takes into account of the molecular orbital also, if so, then why I am not able to reproduce the white line structure as is obtained in the experimental spectra. Please find attached screenshots of Experimental and theoretical spectra of copper complex (in which asp is ligand). Kind regards. Monica Bairagi, Ph.D. Student, India.

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Save and load XAFS fittings in xas_viewer, Larch
by Liu, Juejing 21 May '22

21 May '22

Hi all, I have another quick question about saving & loading Feff fittings. Let's say I have a good Feff fitting for my XAFS spectrum. How to save my fitting project for the future refinement? I checked the xas_viewer document in the Larch site. It only mentioned how to save a pre-edge peak fitting, and there is no content about saving and loading about Feff fittings. The file bottom at the tool bar of the Feffit Result window seems saves everything (e.g., paths used, fitting parameters, and even fitting plots). But there is no "load" bottom at that window, therefore the saved fittings are not recoverable. Best, Juejing 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 [cid:image001.png@01D86D1D.2A250CE0]

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Re: [Ifeffit] Using Larch to analyze uranium compounds
by juejing.liu＠gmail.com 21 May '22

21 May '22

Hi All, Thank you for the information. I double-checked my Feff calculation and noticed that I did not change the uranium edge from K (default, but not reasonable for uranium) to L3 (what I used in experiment). After using the correct uranium edge to run the Feff calculation, the fitting result looks good. I previously used Artemis. The Feff function in this software would automatically pick the common edge for the absorbing elements (in my case, L3-edge for uranium or thorium). That makes me ignore the edge box in Larch. Best, Juejing -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, May 21, 2022 12:26 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 231, Issue 14 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: Using Larch to analyze uranium compounds (John J Rehr) ---------------------------------------------------------------------- Message: 1 Date: Sat, 21 May 2022 12:25:21 -0700 From: John J Rehr <jjr(a)uw.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Using Larch to analyze uranium compounds Message-ID: <CAMw-=E-W8=7eksBMTkFkftn_8fbLo=RSPpPLBR11r5J0sO+PZw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Juejing, It also wasn't clear to me which edge you were measuring, but U XAFS are interesting. The large size of Uranium atoms typically improves convergence of XAFSs calculations, so FEFF calculations often work well for L-edge XAFS spectra with 17 keV x-rays. On the other hand, K-edge XAFS of U compounds is often not useful due to the large core-hole broadening of U which limits the XAFS to short near neighbor distances, and the large > 100 keV K-edge energy is not available at many synchrotron sources. I'll be interested to hear what source you used to measure the XAFS. Thanks. With best wishes, John On Sat, May 21, 2022 at 10:13 AM Matt Newville <newville(a)cars.uchicago.edu> wrote: > Hi Juejing, > > Sorry for the trouble. It's hard to guess from the screenshots alone - > if only we had a Project file you could send (soon, soon). > > One thing I see is it looks like the Feff calculation you're using was > done at the U K-edge. Is that correct? Is the data U K-edge too? > > I don't know if that would completely explain the difference, and > Mike's suggestion of looking at the coordination number is a good idea. > > XAS Viewer writes a "feffit script" in your user folder > (C:\Users\jiuju\larch\xas_viewer\feffit_script.lar). Compared to the > GUI form, that's a little bit cryptic and formal, but it is also what > the program is really doing. If the suggestions above don't help > clarify the problem, can you post that? > > > > On Fri, May 20, 2022 at 7:35 PM <juejing.liu(a)gmail.com> wrote: > >> Hi, >> >> >> >> I am recently trying to use Larch to fit XAS spectra of uranium >> compounds (e.g., UO2, using an existing CIF file). I did not achieve >> a good fit and the amplitude of the model is way lower than the data. >> Then I tried to plot the uranium oxygen 1st path with all 8 atoms a >> sigma2=0.001 by using the plot model function. The resulting >> scattering peak is still far lower than it should be (images below). Did I do something strange with the program? >> >> >> >> The Larch version I used was 0.9.59. I can send the cif file and the >> UO2 data I used if necessary. >> >> >> >> Best, >> >> >> >> Juejing >> >> >> >> >> >> >> >> >> >> *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 >> >> >> >> >> _______________________________________________ >> 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 >> > > > > --Matt > _______________________________________________ > 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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Using Larch to analyze uranium compounds
by juejing.liu＠gmail.com 21 May '22

21 May '22

Hi, I am recently trying to use Larch to fit XAS spectra of uranium compounds (e.g., UO2, using an existing CIF file). I did not achieve a good fit and the amplitude of the model is way lower than the data. Then I tried to plot the uranium oxygen 1st path with all 8 atoms a sigma2=0.001 by using the plot model function. The resulting scattering peak is still far lower than it should be (images below). Did I do something strange with the program? The Larch version I used was 0.9.59. I can send the cif file and the UO2 data I used if necessary. Best, Juejing 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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Error Larch installation
by Christian Wittee Lopes 17 May '22

17 May '22

Dear Matt and members of the XAFS community. I'm trying to install Larch and after the installation process, I'm not able to run the program. It doesn't open. I am trying the Binary Installer File for Windows (64 bit). The error I get when running Larch GUI can be seen in the attachment. Am I doing something wrong? [image: image.png] Thank you in advance. Christian Wittee -- Christian Wittee Lopes Visiting Researcher - ANP/FINEP - PRH 50.1 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) chriswittee(a)gmail.com LinkedIn <https://www.linkedin.com/in/christian-wittee-lopes-561855219/> | ORCID <https://orcid.org/my-orcid?orcid=0000-0001-8420-1958> | Lattes <http://lattes.cnpq.br/4953371870936050>

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structure for reference Mn foil
by Hu, Yang (HIU) 17 May '22

17 May '22

Dear IFEFFIT members, I have been trying to obtain the S02 value from metal reference foils measured at the beamline. However, I constantly got a very low S02 value, such as 0.2 or 0.3 using Mn alpha or gamma cif file (first shell of 12 Mn). Only Mn-beta (4 subshell * 3 Mn) could give a S02 in the range 0.8 ~ 1, depending on whether I constrained sigam2 for all the 12 Mn or whether I fixed the CN for each subshell. But the uncertainty is very high. I also fitted the MnO measured together leaving S02 variable, and it resulted in a S02 close to 1. So I am guessing I didn't use the correct structure file for Mn foil . I appreciate if someone could help on this! Best regards, Yang Hu

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1. structure for reference Mn foil (Hu, Yang (HIU))
by Pierre Lecante 13 May '22

13 May '22

Dear Yang Hu, Your experience rings à bell in my mind: several times we got weird data from Co and Fe NPs, with S02 close to 0.2, much smaller than expected for a simple size effect. The point is that PDF studies were consistent with the so called Co Epsilon structure... based on the Mn beta phase, very disordered. By the way, I'd be very interested to check hypothesis on my side : I'd be very glad if you could provide me à data set. Sincerely, Pierre Lecante Le 13 mai 2022 19:00:01 GMT+02:00, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : >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. structure for reference Mn foil (Hu, Yang (HIU)) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 12 May 2022 18:29:19 +0000 >From: "Hu, Yang (HIU)" <yang.hu(a)kit.edu> >To: "Ifeffit(a)millenia.cars.aps.anl.gov" > <Ifeffit(a)millenia.cars.aps.anl.gov> >Subject: [Ifeffit] structure for reference Mn foil >Message-ID: <999901d0ad3743f59182feca823a08bd(a)kit.edu> >Content-Type: text/plain; charset="us-ascii" > >Dear IFEFFIT members, > > > >I have been trying to obtain the S02 value from metal reference foils >measured at the beamline. > > > >However, I constantly got a very low S02 value, such as 0.2 or 0.3 using Mn >alpha or gamma cif file (first shell of 12 Mn). Only Mn-beta (4 subshell * 3 >Mn) could give a S02 in the range 0.8 ~ 1, depending on whether I >constrained sigam2 for all the 12 Mn or whether I fixed the CN for each >subshell. But the uncertainty is very high. > > > >I also fitted the MnO measured together leaving S02 variable, and it >resulted in a S02 close to 1. So I am guessing I didn't use the correct >structure file for Mn foil . > > > >I appreciate if someone could help on this! > > > >Best regards, > >Yang Hu > > > > > >

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Larch 0.9.59, problems with PCA
by Mangold, Stefan (IPS) 10 May '22

10 May '22

Dear all, on 2 computers (Mac, Intel and ARM, newest version operating system) the PCA does not work. If I press "Build Model with selected groups“ on both computers and several different datasets, I only get „training model“ and nothing else happens. Absolutely nothing else changes within this tab inside XAS viewer. Best regards Stefan Mangold

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Question about an EXAFS analysis of C60-Cu/SiO2
by 王茂林 05 May '22

05 May '22

Dear IFEFFIT members, Recently I have read a paper <ambient-pressure synthesis of ethylene glycol catalyzed by C60-buffered Cu/SiO2> (https://www.science.org/doi/10.1126/science.abm9257) I have a question about the EXAFS analysis: the wavelet transform of C60-Cu/SiO2 (Figure S15B) has 2 peaks at (k, R) = (1.4, 2.2) and (3.8, 1.5), the author assigned them to Cu-C and Cu-O, respectively. And they think Cu-C is derived from d-\pi interactions between Cu and C60. However, Cu-C and Cu-O paths can hardly be separated since the f(k) and \phi(k) are nearly identical for C and O. Besides, the Cu-C distance is ~2 angstrom (according to the ref. 30: S.-Z. Zhan et al., J. Am. Chem. Soc. 2020, 142, 5943-5947.), why it can have a peak at R = 2.2 angstrom? (with Cu-O R = 1.5 angstrom) Thanks you advance for you time! Best regards, Maolin Wang

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