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

Standardized Spectra
by Kyle Draim 08 Aug '22

08 Aug '22

Hello! I don't have any X-Ray data to analyze in your app, I'm just seeking a visual display of each element's standardized/accepted X-Ray spectra (instead of a table of numbers). So far, I've downloaded the application, but I'm stuck on how to find this information. I would greatly appreciate it if you would be willing to provide the necessary steps to accessing this information or if you would be willing to direct me to the right source for that info. Thanks, Kyle

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xraylarch
by Paul Fons 06 Aug '22

06 Aug '22

Hi. Due to the difficulties of getting demeter to work on the Apple M1 machines, I have started to use xraylarch and so far I like the interface as well as the possibility of scripting later on. I had a couple of observations and a question regarding xraylarch usage that I hope could be addressed here. First, one can load multiple spectra into the (feff) fitting window. It seems, however, that which paths are selected are universal (the selected paths are used for all exafs spectra). Does this mean that multiple edge fitting is not possible. If multiple edge fitting is possible, how is it done? In the fitting window, one can have several spectra loaded and one can select all or some of the spectra to be fit. The interface seems like it was designed for multiple edge fitting, but is it? Second, it is strange that whenever a parameter is changed that the fitting variable settings (fixed, vary, constrain) are reset. For complex fits, this generates a lot of unnecessary clicking (and the corresponding mistake possibilities) Third, when one reads in several different feff calculations, one would, in principle, like to have a different value of e0 (the origin of energy offset) for each feff calculation. By default when a feff calculation is read in the variable e0 is defined. When one defines alternative energy offset variables for the different feff calculations and deletes the original e0 value, something strange happens. Accessing the “Edit Parameters” window results in e0 reappearing (even though it has been manually deleted previously). Is this a feature? The same thing may happen for other “automatic” variables as well. Four. This is really a feature request. When a variable is unused (lets say some additional paths are introduced in the fitting process and a new fit without them is attempted), the choices in the parameter list are (fix, vary, and constrain). There is no option to “skip” like in Artemis. Obviously, one can choose fix, but in doing so the unused variable shows up in the fit result summary and is somewhat confusing. It would be subjectively better to have the option to “skip” a variable and not have it show up in the fit summary. Just some initial thoughts...

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VC and V(CO)6 data to share
by Ismael Graff 06 Aug '22

06 Aug '22

Dear XAFS enthusiasts, would anyone have XAFS data of crystalline vanadium carbide (VC) and vanadium hexacarbonyl (V(CO)6) to share? In the case of V(CO)6 I´m having great trouble of finding any published measurement! I found papers for Cr(CO)6, but not V(CO)6. Bibliographical references are also welcome. All the best, Ismael. -- ************************************ * Ismael Graff * * * * Universidade Federal do Paraná * * Departamento de Física, CP 19044 * * 81531-980, Curitiba, Brazil. * * Tel (office): +55 41 3361 3093 * * Tel (Lab): +55 41 3361 3427 * * Fax: +55 41 3361 3418 * * http://fisica.ufpr.br/graff * * * * "DOCENDO DISCIMUS" * ************************************

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Re: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine)
by Mosselmans, Fred (DLSLtd,RAL,SCI) 04 Aug '22

04 Aug '22

Dear Abdallah, It is often quite reasonable to fix two paths debye waller factors to be the same if they are the same atom at similar distances. However there is a slight problem with what you are trying to do. Because EXAFS is a sum of sine waves the minimum distance it can resolve between two paths of the same atom type is Pi/2*Kmax where kmax is the maximum k value in your data. Hence if you are trying to fit separate paths of the same atom type 0.06 A apart you need data out to about 26 k. I think and no one has ever told me this is completely Ok the only way to get two distances from such an analysis is to assert that the difference between the path is a fixed value and thus refine the two paths with the same delta R (and probably the same debye wller factor) this in my experience works in some cases Best regards Fred Mosselmans -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 03 August 2022 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 234, Issue 2 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. Exafs spectra Fitting of WO3 nanoparticles (Abdallah Nassereddine) ---------------------------------------------------------------------- Message: 1 Date: Wed, 03 Aug 2022 14:40:44 +0200 From: Abdallah Nassereddine <abdallah.nassereddine(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Exafs spectra Fitting of WO3 nanoparticles Message-ID: <ddfc8c51f227c914d472d4115733b956(a)esrf.fr> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear all, Good morning, I try to Fit EXAFS spectra of a sample composed of supported tungsten oxide ( WO3/ZSM-5) nanoparticles obtained by operando studies under gas (CH4, He) at 750 ?C. First, and after several trials, I analyzed the WO3 reference spectrum obtained at room temperature and I succeeded in determining the amplitude (S0) by using the monoclinic structure WO3 cif file. Then, I used the value of this amplitude obtained to be able to fit the structural parameters (coordination number N, Debye-waller Factor, Interatomic distance) of WO3/ZSM-5 nanoparticles under gas, but I can't. the best result I got was by selecting the first two shells (at 1.858 and 1.919 Angstrom) of the monoclinic structure. However, with all the optimizations, the Debye-waller factor obtained for the second W-O shell (1.919 Angstrom) is always negative, and if I don't take this shell into account, I completely lose my Fit. Have any of you ever worked on this type of sample and might have an idea that would help me improve my Fit? Thank you in advance, Best regards, Abdallah Nassereddine

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Exafs spectra Fitting of WO3 nanoparticles
by Abdallah Nassereddine 03 Aug '22

03 Aug '22

Dear all, Good morning, I try to Fit EXAFS spectra of a sample composed of supported tungsten oxide ( WO3/ZSM-5) nanoparticles obtained by operando studies under gas (CH4, He) at 750 °C. First, and after several trials, I analyzed the WO3 reference spectrum obtained at room temperature and I succeeded in determining the amplitude (S0) by using the monoclinic structure WO3 cif file. Then, I used the value of this amplitude obtained to be able to fit the structural parameters (coordination number N, Debye-waller Factor, Interatomic distance) of WO3/ZSM-5 nanoparticles under gas, but I can't. the best result I got was by selecting the first two shells (at 1.858 and 1.919 Angstrom) of the monoclinic structure. However, with all the optimizations, the Debye-waller factor obtained for the second W-O shell (1.919 Angstrom) is always negative, and if I don't take this shell into account, I completely lose my Fit. Have any of you ever worked on this type of sample and might have an idea that would help me improve my Fit? Thank you in advance, Best regards, Abdallah Nassereddine

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Synchrotron geochemist position at DOE-National Energy Technology Laboratory
by Mengling Stuckman 02 Aug '22

02 Aug '22

Dear ifeffit members, Recently we are interested in hiring a synchrotron geochemist for our critical mineral sustainability program at NETL. U.S. citizens are strongly preferred. Here is the specific job posting. https://careers.leidos.com/jobs/9878648-synchrotron-geochemist Feel free to pass along this information to your coworkers or postdocs 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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Athena: the R factor for normalized mu(E)
by Jon-Petter Gustafsson 13 Jul '22

13 Jul '22

Hello all, I have been a frequent user of Athena for many years, mostly for interpreting P K-edge XANES spectra. Until last week I thought that the R factor in Athena was always defined as: sum( [data_i - fit_i]^2 ) ------------------------------- sum( data_i^2 ] This is also the definition given in the online manual, and it has been stated by me and by other colleagues in a number of papers dealing with P K-edge XANES. But well, this is not true when dealing with normalized XANES spectra! I realized this when I played around with a number of my old LC fits in Excel. While the chi-square value (or maybe more precisely, the sum of squared residuals) was reproduced perfectly, I always got "R factors" (i.e. with the above definition) between 2 and 3 times lower than what Athena gives. After that I consulted the Demeter programming documentation (https://bruceravel.github.io/demeter/pods/Demeter/LCF.pm.html) to find that, for normalized mu(E), "Demeter thus scales the R-factor to make it somewhat closer to 10^-2". However, the equation stated on this page actually reproduces the R factor even more poorly, and therefore I won't reiterate it here. After inspecting the Perl code, and trying out different alternatives in Excel, I now believe that the following equation provides a more accurate definition of the R factor (correct me if I'm wrong!): sum( [data_i - fit_i]^2 ) ------------------------------- sum( [data_i - avg data]^2 ) where "avg data" is the arithmetic mean of the data in the LC fitting range. It would be great if others could confirm this. As far as I understand, this won't affect the interpretations that any of us have made over the years, it only affects the understanding of what the R factor actually is... Kind regards, Jon Petter Jon Petter Gustafsson, Professor in Soil Chemistry Department of Soil and Environment Swedish University of Agricultural Sciences (SLU) Box 7014 750 07 Uppsala, Sweden Phone: 018-671284; e-mail: jon-petter.gustafsson(a)slu.se<mailto:jon-petter.gustafsson@slu.se> --- N?r du skickar e-post till SLU s? inneb?r detta att SLU behandlar dina personuppgifter. F?r att l?sa mer om hur detta g?r till, klicka h?r <https://www.slu.se/om-slu/kontakta-slu/personuppgifter/> E-mailing SLU will result in SLU processing your personal data. For more information on how this is done, click here <https://www.slu.se/en/about-slu/contact-slu/personal-data/>

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Literature question---FEFF-based wavelet
by Xinyu Luo 29 Jun '22

29 Jun '22

Hi everyone, I'm a graduate student interested in using wt-EXAFS to analyze LDH compounds. I've surfed the ESRF website, tried Continuous Cauchy and Morlet as mother wavelets, and am aware of their limitations. I'm inspired by previous work by Funke et al. [J. Synchrotron Radiat. 2007, 14 (5), 426–432.], that customizing the mother wavelet can strengthen the sensitivity to the path of interest. I have some questions as follows. 1)Can the FEFF-Morlet wavelet be manipulated through parameters like the Morlet or Cauchy wavelet to reach the desired Heisenberg box? 2)How to practically execute the as-mentioned four steps to construct the FEFF-Morlet wavelet? Could you suggest some software toolkit to start, perhaps Matlab? 3)I'm also curious about the 2D contour generated by FEFF-Morlet which didn't show up in the paper. Will the overview wt figure gain better general resolution simply by choosing an appropriate mother wavelet? Regards Xinyu

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data plotting
by Ofierska Weronika Lucja 28 Jun '22

28 Jun '22

Dear all, I am a new user of Athena and encountered some issues with data plotting. While plotting the uXAS data for Fe K pre-edge the quality of plotting is somehow less sharp compared to the actual data I plotted using other graphical tool (see below) [cid:4465cab9-2ae8-49e7-8253-e54ac3d22bb7] vs what I get from Athena [cid:4db817c1-78d0-4ac8-b094-12d37d055466] As you can see the resolution of the pre-edge in Athena is so poor I cannot resolve the Fe2+/Fe3+ ratio as the peak for Fe3+ is not visible. (I plotted Bruce's data from lepidocrocite to see if it's a common problem and it seems that his data look much better than mine). During my time on synchrotron we actually spent a lot of time to resolve best resolution on the pre edge, so it's not a acquisition problem. Does anyone have any idea how to fix this? I am attaching the project file and txt file (plot FluoRT2 column) with the original data. Thank you for your help, Weronika Ofierska

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new opening for high resolution X-ray spectroscopic studies of spent nuclear fuel
by Vitova, Tonya (INE) 15 Jun '22

15 Jun '22

Dear all, Please see this new job opportunity: https://www.pse.kit.edu/english/karriere/joboffer.php?id=155626 I hope that many of you will apply! Best regards, Tonya -----Ursprüngliche Nachricht----- Von: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Im Auftrag von ifeffit-request(a)millenia.cars.aps.anl.gov Gesendet: Dienstag, 31. Mai 2022 19:00 An: ifeffit(a)millenia.cars.aps.anl.gov Betreff: Ifeffit Digest, Vol 231, Issue 22 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: Larch 0.9.61 and 60 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 May 2022 07:10:28 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch 0.9.61 and 60 Message-ID: <CA+7ESbpx-dFvXkNkL0EFXPPxsi8d3oO4vO3T3xTWeVKYNKXNzA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Kathy, Thanks and sorry for the trouble. I think I can reproduce this: changing the definitions of Path Parameters is being ignored. I have a theory of what is going wrong, but I'll have to investigate this a bit... On Tue, May 31, 2022 at 6:12 AM Kathy Dardenne <kathy.dardenne(a)kit.edu> wrote: > Hello, > > > > I was trying to use Larch 0.9.59 to fit EXAFS Data. There was no > possibility to save work in progress but it was possible to do fit, > change name of the variable used and define the expression for > amplitude (default defined as ?n*s02? in Larch where n is taken from the feff calculation). > > I have 6 slightly different Cf-O distances in my model structure and > took only one path, changing the amplitude definition ?1.0 * s02? by ?NO * s02? > . this worked perfectly. > > > > However in Larch 60 and 61 where, thanks a lot!!!, we can now save our > work, it is not possible any more to change anything in the path > parameter (neither name or expression). The added variable is not any > more varied and not taken into account. Independently of the amplitude > definition s02 get the same value as default definition and new > variables stay by start value having no influence on the fit. > > > > I join some screenshot as well ?Path parameters? and ?Fit script?. > Looking at the Path parameter I saw that the amplitude is still by > default definition so no wonder that it acts without taking into account changes. > This is the same for name changes. > > > > Am I the only one having trouble now? I worked till now with artemis, > ifeffit and previously feffit soI do not have a big experience with Larch. > The old feffit based versions stop all by Pu (Z=94) and I need Z=98 so > I changed to Larch but need to get used to. > > I am using Larch in anaconda3 on a Win10 Computer. > > > > Thanks a lot for your help. > > > > Kind regards > > > > Kathy > _______________________________________________ > 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 Newville <newville at cars.uchicago.edu> 630-327-7411

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Larch 0.9.61 and 60
by Kathy Dardenne 31 May '22

31 May '22

Hello, I was trying to use Larch 0.9.59 to fit EXAFS Data. There was no possibility to save work in progress but it was possible to do fit, change name of the variable used and define the expression for amplitude (default defined as "n*s02" in Larch where n is taken from the feff calculation). I have 6 slightly different Cf-O distances in my model structure and took only one path, changing the amplitude definition "1.0 * s02" by "NO * s02" . this worked perfectly. However in Larch 60 and 61 where, thanks a lot!!!, we can now save our work, it is not possible any more to change anything in the path parameter (neither name or expression). The added variable is not any more varied and not taken into account. Independently of the amplitude definition s02 get the same value as default definition and new variables stay by start value having no influence on the fit. I join some screenshot as well "Path parameters" and "Fit script". Looking at the Path parameter I saw that the amplitude is still by default definition so no wonder that it acts without taking into account changes. This is the same for name changes. Am I the only one having trouble now? I worked till now with artemis, ifeffit and previously feffit soI do not have a big experience with Larch. The old feffit based versions stop all by Pu (Z=94) and I need Z=98 so I changed to Larch but need to get used to. I am using Larch in anaconda3 on a Win10 Computer. Thanks a lot for your help. Kind regards Kathy

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PostDoc position at BM23/ID24 beamlines of ESRF
by Kirill LOMACHENKO 30 May '22

30 May '22

Dear all, we are looking for an outstanding postdoc to do research in chemistry at BM23 and ID24 XAS beamlines of the ESRF. The prioritized fields are catalysis and electrochemistry. We expect a postdoc to run their own research exploiting their collaboration network. The ideal candidate would be a link between our cutting-edge XAS facilities and leading academic groups in the field. More details and the Apply button are here: https://esrf.gestmax.eu/1592/1/post-doc-id24-bm23/en_US Thank you for spreading the news! All the best, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Larch 0.9.61
by Matt Newville 27 May '22

27 May '22

Hi Folks, It's only been a few days, but there were some fairly important bugs and misfeatures found with Larch 0.9.60. Rather than wait, these have mostly been fixed (details at https://github.com/xraypy/xraylarch/releases/tag/0.9.61) You can either update the code yourself with `pip install --upgrade xraylarch`, with the binary installer, or by allowing XAS Viewer to run its updater. Bug reports, comments, and suggestions are always welcome. --Matt

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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 06 May '22

06 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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2022 APS/IIT XAFS Summer School
by Matt Newville 24 Apr '22

24 Apr '22

Hi Folks, The APS/IIT XAFS Summer School will be July 24-29, 2022 at the Illinois Institute of Technology. The school will be in-person but limited to 40 students due to continuing concerns about COVID. See the attached flyer for details. For even more information, and to apply, please email bunker(a)iit.edu with the subject line “2022 XAFS School”. --Matt Newville

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XAFS 2022 reminders
by Matt Newville 21 Apr '22

21 Apr '22

Hi Folks, Another reminder for XAFS 2022: The abstract deadline has been extended to Monday, April 25th, but with a deadline of midnight Sydney time: https://xafs2022.org And, nominations for the IXAS awards are due May 1: https://xrayabsorption.org/ixas-awards-2022/ Cheers, --Matt

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