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

Help for checking my EXAFS fitting
by cbmeherrem＠gmail.com 10 Dec '25

10 Dec '25

Hello, I am a graduate student working on Ge and Sn K-edge XAS measurements. I have performed some EXAFS fitting in Artemis, but I am not fully confident that my analysis is correct since my sample is a bit complex. I was wondering if anyone with expertise in EXAFS fitting might be willing to look over my results. I would be happy to email my fitting files and analyzed data if someone is available to provide guidance. Thank you very much for your time and help. Best Maharram

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Data for Mn metal L-edge XAS
by Ismael Graff 15 Nov '25

15 Nov '25

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Strange low-r peak in Pt foil EXAFS
by FAN Dongxiao 03 Nov '25

03 Nov '25

Dear All, My target is the L3-edge of Pt foil and Pt-contained high-entropy alloy. In the Pt foil L-edge FT-EXAFS (k range: 3-20 A-1), there is a strange peak lower than the first near neighboring peak. This low-r peak makes confused because I did not found in other metal foil spectra. Also this peak cannot be reduced by increasing the Rbkg value. When I decrease the k range, this strange peak disappears with phase shift. In the Pt-contained high-entropy alloy, this strange peak becomes more pronounced than the 1st NN. Can anyone can give me help interpret this strange peak? Best regards, Fan ******************* JASRI, Sping8 *******************

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Shifting FDMNES spectra for comparison between multi-site and single-site runs
by oliel1995＠gmail.com 08 Oct '25

08 Oct '25

Hello everyone, I’m running FDMNES calculations, and I have the following situation: Run A: Multi-site calculation with 3 non-equivalent positions. FDMNES internally applies epsii shifts, and I merge the per-site spectra — the merged spectrum is correct internally, meaning the relative positions between sites are preserved. Run B: Single-site calculation with 1 non-equivalent position. My goal is to compare the merged spectrum from Run A with the single-site spectrum from Run B. The challenge: because FDMNES aligns energies internally per run, the merged spectrum from Run A is not correctly referenced to the same absolute energy scale as Run B. My question: What is the recommended way to shift the merged multi-site spectrum from Run A so that it can be meaningfully compared with a completely different single-site calculation? Is it acceptable to use the position of a peak B, WL, etc, for a rigid shift, and are there best practices for doing this while preserving the internal relative positions of the merged spectrum? Thank you! Sincerely, Olga Olga Filimonova Post-doc researcher - ID26 European Synchrotron Radiation Facility (ESRF), Grenoble, France

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Symposium on Data-Driven Approaches in X-ray Absorption Spectroscopy
by Clark, Adam Hugh 08 Oct '25

08 Oct '25

Dear Colleagues, The upcoming Symposium on Data-Driven Approaches in X-ray Absorption Spectroscopy, is presently accepting abstracts for oral presentations and registration is open. The symposium aims at bringing together researchers in the field of x-ray absorption spectroscopy, machine learning, and computational modelling. This symposium will focus on recent developments in data-driven and machine learning techniques for the interpretation of XANES and EXAFS spectra, enabling new insights into materials structure and dynamics from large complex operando/in situ datasets. The program will feature four themed sessions: 1. Data-Driven Decomposition and Spectral Extraction 2. Machine Learning for XANES Prediction and Analysis 3. Advanced Approaches to EXAFS Analysis 4. Bridging Simulations and Experiments with Machine Learning Date: 5th-6th January 2026 Location: ETH Zurich Hönggerberg campus, Switzerland Abstract submission deadline: 15th October 2025 Symposium Webpage: https://urldefense.us/v3/__https://indico.psi.ch/event/dataxas2026__;!!G_uC… We warmly invite your participation in this symposium and look forward to your contributions and discussions. __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/219 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41563104151 E-Mail: adam.clark(a)psi.ch

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Larch 2025.3.0
by Matthew Newville 19 Sep '25

19 Sep '25

Hi Folks, A new version of Larch and the Larix GUI are now available for download and for automated update. The last message about Larch 2025.2.0 was in late May, though there were updates pushed on in late July too. Since then, there have been many updates and improvements, especially to the Larix GUI. A more complete list of changes is at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/tag… (and see https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/tag… too), but a few of the most obvious changes include: * The “List of Groups/Files” in Larix and many related “List of Groups” windows have a richer set of options with the Right Mouse Button. All these actions also now have "keyboard shortcuts" or "accelerators" (Ctrl- / Alt- keys) that do most actions to move and select groups. This allows much faster and easier manipulation of the list of datasets. * Configuring lotting options such as linewidths, colors, themes, and so forth is easier and better. The "plot" tab is "Edit Preferences" now has (only) a "Save Plot Configuration" to save the configuration of the current Plot Window #1 (to the file ".larch/wxmplot.yaml"). From the Plot Window, you can configure these settings (themes, colors, etc) for any plot. When you are happy with those, saving them from the Larix Preferences window will save those settings for future sessions. * Saving and Loading Session Files is more robust, and saving will happen in the background, without hanging the main window. * The main Larix window now has a Title (ie, “Top Window Bar”) that shows the name of the “Current Session File”. You can change that with “Save Session As”. The Plot Windows (or most of them anyway) will have Titles that show this Session File name and the name of the Analysis Panel or Data Task window that generated the plot. If you are running 2 Larix sessions, this makes it much easier to tell what windows go together. * On startup, you may be prompted to open recently automatically saved Session files for Sessions that did not exist cleanly. There has long been a list of “autosaved sessions” that you can import, but this will tell you if any session did not close well. * 2025.2.0 introduces a Generic XY Data Analysis Panel, for non-XAS data. You can now choose any X, Y arrays for a group as the XY data, and overplot several groups of scaled or unscaled datasets. And the Curve Fit Panel allows pretty generic curve-fitting for X, Y data. There have been many bug fixes and other improvements, too. As always, Mauro Rovezzi and Shelly Kelly and her group at the APS deserve a lot of credit for either making or inspiring these changes. There have also been bug reports and pull requests from a growing number of people. The GitHub repository is really the best place for this, but thanks to everyone. Let us know if you have any questions, comments, or suggestions. --Matt

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Issue with Athena – XANES Data Cannot Be Plotted in k
by biswajit.mishra＠vsb.cz 14 Sep '25

14 Sep '25

Dear Prof., I am facing an issue while processing my XAS data in Athena. When I load my dataset (Pt foil.dat), the software shows the message: “XANES data cannot be plotted in k” and it does not generate any plots at all. From what I understand, this usually occurs if the software does not recognize the correct element or edge. However, even after checking the energy range and parameters, the problem persists. I noticed that in my session Athena automatically set the element to W (74, Tungsten, L2-edge) instead of Pt (78, L3-edge). I am not sure if this mismatch is causing the issue, but I have been unable to correct it successfully. Could you please advise me on how to resolve this problem? I have attached a screenshot of the error message for your reference. Thank you for your help. Best regards, Biswajit

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XAS spectra for K4[Fe(CN)6] and K3[Fe(CN)6]
by Charmaine Nkala 08 Sep '25

08 Sep '25

Dear all, I am looking for Fe K-edge XAS spectra for K4[Fe(CN)6] and K3[Fe(CN)6] that I can use as standards for linear combination fitting. If anyone has the data and they don't mind sharing, I would be grateful. I have checked the databases https://urldefense.us/v3/__https://ixdb.jxafs.org/__;!!G_uCfscf7eWS!foQ6c2e… and https://urldefense.us/v3/__https://xasdb.lightsource.ca/__;!!G_uCfscf7eWS!f… as previously suggested in past requests, to no avail. Thank you, in advance, for your assistance. Kind regards, Charmaine

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post-doc position in the field of X-ray and UV Photoelectron Spectroscopy at University of Nova Gorica, Slovenia
by iztok.arcon＠guest.arnes.si 05 Sep '25

05 Sep '25

Dear all, The University of Nova Gorica (Slovenia) is offering a position of assistant with PhD (postdoctoral associate) in the field of X-ray and UV photoelectron spectroscopy. Details for the applications are published on: https://ung.si/en/news/news/6929/assistant-with-phd-postdoctoral-associate-… Inquiries regarding the research work should be addressed to Prof. Giovanni De Ninno: giovanni.de.ninno(a)ung.si . Deadline for the applications is 18. 9. 2025 regards Iztok Arčon

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Elemental concentrations in XRFMap_Viewer
by Tian, Tony 05 Sep '25

05 Sep '25

Good afternoon, Thanks for the platform to address X-ray related questions. I was using XRFMap_Viewer in the Larch package to look at some uXRF data of my soil samples, and the main element of interest is Fe, and to some extent Mn too. I went through the steps to choose them (Ar was auto detected), calculate model, then fit model. Under the Composition tab, concentrations were given as in the screenshot below. The dropdown units has 3 options (ng/mm^2, wt % and ppm), but when i switch among them, none of the values changed. From a bit research online, I seem to understand there are two approaches to get absolute elemental concentrations. One is by measuring reference standards and establishing calibration curves, and the other is by fundamental parameters which is built-in in Larch (or XRFMap_Viewer in my case?). We didn't run any standards at the time. Could anyone please shed some light on how [Fe] in weight % can be computed in a built-in manner? Thank you. [cid:75a2d0c6-35d4-4136-b519-73fde6e623ad] [cid:4a98ae3b-96c2-4348-b138-4312b63ceafd] Best regards, Tony

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Symposium on Data-Driven Approaches in X-ray Absorption Spectroscopy
by Clark, Adam Hugh 04 Sep '25

04 Sep '25

Dear Colleagues, We are delighted to announce the upcoming Symposium on Data-Driven Approaches in X-ray Absorption Spectroscopy, which aims at bringing together researchers in the field of x-ray absorption spectroscopy, machine learning, and computational modelling. This symposium will focus on recent developments in data-driven and machine learning techniques for the interpretation of XANES and EXAFS spectra, enabling new insights into materials structure and dynamics from large complex operando/in situ datasets. The program will feature four themed sessions: * Data-Driven Decomposition and Spectral Extraction * Machine Learning for XANES Prediction and Analysis * Advanced Approaches to EXAFS Analysis * Bridging Simulations and Experiments with Machine Learning Date: 5th-6th January 2026 Location: ETH Zurich Hönggerberg campus, Switzerland Abstract submission deadline: 15th October 2025 Symposium Webpage: https://urldefense.us/v3/__https://indico.psi.ch/event/dataxas2026__;!!G_uC… We warmly invite your participation in this symposium and look forward to your contributions and discussions.

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Re: Issue with AtomS reporting CIF file created in Diamond
by I. D. 30 Aug '25

30 Aug '25

Dear All, I am experiencing a problem with AtomS reporting a CIF file generated in Diamond. Please find the CIF file attached. Diamond correctly displays the coordination of each gallium atom in this structure (space group Pna2₁): - Ga1 has tetrahedral coordination, - Ga2 has octahedral coordination, - Ga3 has pentahedral coordination, - Ga4 has tetrahedral coordination. However, when I load the CIF file into AtomS, only Ga4 shows the correct coordination. The other three Ga atoms are all reported with coordination 6 instead of 4, 6, and 5, respectively. Could you please advise on how to resolve this issue? Thank you in advance for your help. Best regards, Iraida PS: A similar problem occurs if the *.cif file is generated by the Vesta program.

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network outage to mailing list and related sites: August 25 and possibly 26
by Matt Newville 21 Aug '25

21 Aug '25

Hi Folks, The APS will be doing network maintenance and upgrades for several sectors at the APS. They have told us to expect no network access on Monday, August 25th, possibly going into the 26th. That will include the server running this mailing list (both mail delivery and web configuration) as well as all web pages at millennia.cars.aps.anl.gov and seescience.org (so, including larixite.seescience.org and xraydb.seescience.org) I do not have specific times, but guess the outage will start between 7 and 9 AM Chicago time on the 25th. I hope that we can all manage a day or two in late August without these resources ;). --Matt

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Variation in pre-edge intensity with replicate scans without change in EXAFS
by Rachel Pepper 21 Aug '25

21 Aug '25

Hi everyone, I've got some XAS data at the Cr K edge for Cr-doped alumina (i.e. ruby) powder samples (Cr 0.1-1 atomic%) where we are seeing a reduction in one of the pre-edge peaks with replicate scans. There are three sets of samples; each made by a different synthetic method. We did do the repeat scans on the same spot on the samples and noted this change after the data was collected, which means that the change might be a result of beam damage. However, the results are odd because: 1. The reduction in intensity is consistent across different Cr concentrations for samples made by the same method, but is not observed for all preparation methods 2. The XAFS does not show the same systematic variation with replicate scans which suggests that this change in the pre edge is not due to a structural change 3. The edge position doesn't change with repeat scans 4. We have compositional data for these samples, and there are no significant impurities 5. I've worked up the XAFS data in Artemis and there doesn't seem to be significant differences in the structures of the samples prepared by the three different methods. For all methods, it looks like there is a second Cr atom in the second coordination shell, which is also supported by luminescence data. I've looked online and found a computational study where intensity differences in ruby samples may be related to electron spin (doi: 10.1238/Physica.Topical.115a00191, doi: 10.1039/b926499j), but I'm not sure if this is a sensible explanation - I'm still quite new to this technique. Has anyone come across anything similar, or does anyone know why we might have seen this in our samples? I've attached some images of the pre-edge and XAFS regions for the scans to illustrate what I'm asking about. Thank you, Rachel

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Demeter won't start in Windows 11
by Shi, Jueli 19 Aug '25

19 Aug '25

Hi Everyone, I'm experiencing an issue with Demeter (v0.9.26) after upgrading from Windows 10 to Windows 11. On Windows 10 it worked without problems, but now it won't start properly. When I click the desktop icon (or run it from the Start menu), the window briefly appears and then crashes. I've tried rebooting, running as Administrator, and reinstalling, but the issue persists. Has anyone else run into this on Windows 11? Thanks in advances, Jueli Shi Postdoc Research Associate Pacific Northwest National Laboratory Richland, WA 99352 USA Tel: 509-375-2284 Jueli.Shi(a)pnnl.gov

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Re: Help installing Demeter on a Mac
by Fowler, Joseph W. (Fed) 07 Aug '25

07 Aug '25

Dear Matt, Many thanks for opining on Mac installations of x-ray code. Much more, many thanks for building a really nice suite of useful tools for x-ray physics. (Congratulations on the new major version of Larch!) I am the official MacPorts “maintainer” of Ifeffit and the Demeter suite and have been for roughly a decade. For several years, I was able to keep the port alive, albeit barely. For roughly the last 4-5 years, I have been unsuccessful building Ifeffit under the MacPorts project; without it, Demeter can’t be used. Given that the package is unmaintained and pulled from GitHub, I will plan to work with MacPorts to remove the demeter and ifeffit packages, or mark them as permanently moribund, or whatever they favor. Perhaps that will help clarify for people that installing these tools on Macs is no longer possible in 2025. Hi Kyle, Yep, it has been well-established that trying to build and run Demeter on macOS is very hard, and the results will be fragile. If you got advice in the past 5 years that was something other than "don't bother", then I would ZjQcmQRYFpfptBannerStart Best wishes, Joe Fowler NIST Quantum Sensors Division, Boulder Colorado ZjQcmQRYFpfptBannerEnd From: Matthew Newville <matt.newville(a)gmail.com> on behalf of Matt Newville <newville(a)cars.uchicago.edu> Date: Wednesday, August 6, 2025 at 2:56 PM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: Kluherz, Tk <Tk.Kluherz(a)nrel.gov> Subject: [Ifeffit] Re: Help installing Demeter on a Mac Hi Kyle, Yep, it has been well-established that trying to build and run Demeter on macOS is very hard, and the results will be fragile. If you got advice in the past 5 years that was something other than "don't bother", then I would say you were misled. Larch installs without any trouble, and Larix runs just fine on macOS. Yep, there are a few things that Larix does not do that Demeter does, and there are many things that Larix does that Demeter does not. Larch and Larix are actively developed. If some feature is not working well for you, we have plenty of mechanisms for asking for help, getting feedback, and contributing. There have been 5 releases of Larch in the past 12 months. Most installations of Demeter use only the Fortran Ifeffit library. This has not been supported for more than 10 years. It has many known bugs that will not ever be fixed. I recently removed the repository from GitHub, as some people were still trying to use and build that code. This needs to stop. These are open-source software, written by volunteers. You are free to use any version or modification of these you want – that is one of the points of open-source software. But you cannot expect support for very old software, especially when the developers are clearly stating that it is not supported. Please stop asking about installing Demeter on macOS. It is not going to be supported. --Matt

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Re: Help installing Demeter on a Mac
by Matt Newville 06 Aug '25

06 Aug '25

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Re: Help installing Demeter on a Mac
by Kluherz, Tk 05 Aug '25

05 Aug '25

Following up on this much later: I think I have tracked down the initial issue, which unfortunately has only revealed other problems. Looking in /opt/local/bin, the commands appear to be links: lrwxr-xr-x 1 root admin 43 Jul 30 15:45 athena -> /opt/local/libexec/perl5.34/sitebin/dathena lrwxr-xr-x 1 root admin 44 Jul 30 15:45 artemis -> /opt/local/libexec/perl5.34/sitebin/dartemis lrwxr-xr-x 1 root admin 47 Jul 30 15:45 hephaestus -> /opt/local/libexec/perl5.34/sitebin/dhephaestus The sitebin folder does not exist in perl15.34, so this seems to be the reason why I’m getting ‘command not found’ when I try to run athena. Poking around, it seems that dathena, dartemis, and dehepaestus do exist in /opt/local/libexec/perl5.34/ But when I try to run them, I get several errors: ./dathena Can't load '/opt/local/lib/perl5/vendor_perl/5.34/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle' for module Ifeffit: dlopen(/opt/local/lib/perl5/vendor_perl/5.34/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle, 0x0001): Library not loaded: @rpath/libgfortran.5.dylib Referenced from: <39AD3897-F60B-30DA-B626-3DEF435072F2> /opt/local/lib/perl5/vendor_perl/5.34/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle Reason: no LC_RPATH's found at /opt/local/lib/perl5/5.34/darwin-thread-multi-2level/DynaLoader.pm line 197. at (eval 21) line 1. Compilation failed in require at (eval 21) line 1. BEGIN failed--compilation aborted at (eval 21) line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/vendor_perl/5.34/darwin-thread-multi-2level/Demeter.pm line 70. Compilation failed in require at /opt/local/lib/perl5/vendor_perl/5.34/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at /opt/local/lib/perl5/vendor_perl/5.34/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24. Compilation failed in require at ./dathena line 31. BEGIN failed--compilation aborted at ./dathena line 31. It seems there are larger installation problems. This is as far as I’ve gotten, as IT was able to setup a Windows remote machine for me and install Demeter on there instead. I have not yet tried the directions Matt linked from George Sterbinsky, so those may be a working option. I’d also like to take a look at Larch sometime, but want to get these data processed before venturing into those woods. Thanks again for your help. My apologies for disappearing on this issue, EXAFS work ended up being shelved and I didn’t receive email notice of your responses so wasn’t aware of them until I went looking in the mailing list. -- Kyle Kluherz Postdoc | MCCS National Renewable Energy Laboratory (NREL) 15013 Denver West Parkway | Golden, CO 80401 303-384-7747 kkluherz(a)nrel.gov<mailto:kkluherz@nrel.gov> | https://urldefense.us/v3/__http://www.nrel.gov__;!!G_uCfscf7eWS!ayhMNEBuDrh… <https://urldefense.us/v3/__http://www.nrel.gov__;!!G_uCfscf7eWS!ayhMNEBuDrh… >

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Problems with linear combination fitting S-XANES data in Athena
by Muretta, Julie 28 Jul '25

28 Jul '25

Hello, First of all, thank you all so very much for offering this platform to address XAS data processing!! It is wonderful to know it is available. I am having a problem using Athena "Linear Combination Fitting" with x-ray fluorescence data from SSRL. Last year, we collected sulfur K-edge XANES data at SSRL, beamline 4-3 and processed them using SixPack (averaging 5 sweeps and normalization) and then used Athena to conduct linear combination fitting of the XANES region. It worked great! This year's data are presenting a problem when I get to the LCF step, however. When I import the sample data .mu file into Athena and plot it by pressing the orange "E" button, the normalized spectrum looks like it should (albeit noisy and sometimes not the best data, but that is not Athena's fault). When I attempt to apply the Linear Combination Fitting algorithm, fitting a number of spectra from reference samples also collected last year and this year, Athena inverts the sample.mu spectrum (between -1 and 0 rather than 0 and 1). It does not invert old or new reference sample spectra. When I try this with old data, using old and new reference sample spectra, I do not have this problem. With the inverted sample spectrum, it often does not find a fit, but sometimes it does. Attached is an example Athena project file, the .mu file, and a plot of the output of a test fit, for your reference. I am hoping someone can please help me figure out why this is happening. I cannot see anything wrong, based on my limited experience, but hopefully it is something I have done wrong that can be easily corrected. Thank you in advance, Julie Julie Muretta, Ph.D. Materials Testing Laboratory Manager Center for Advanced Materials Processing (CAMP) (406) 496-4808 | jmuretta(a)mtech.edu [Montana Technological University]<https://urldefense.us/v3/__https://www.mtech.edu/__;!!G_uCfscf7eWS!cA8TPa7r… >

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Postdoctoral position opening
by Anatoly Frenkel 18 Jun '25

18 Jun '25

We will have an opening (pending final funding approval) for a Postdoctoral Researcher in my group — the *Structure and Dynamics of Applied Nanomaterials* at Stony Brook University. We are seeking a highly motivated scientist to explore the mechanisms of novel electromechanical materials, focusing on systems that exhibit non-classical electrostriction. This research builds on our recent work: 🔹 https://urldefense.us/v3/__https://pubs.acs.org/doi/full/10.1021/jacs.5c003… 🔹 https://urldefense.us/v3/__https://www.nature.com/articles/s41467-023-43032… The successful candidate will: ✅ Lead synchrotron-based experimental efforts ✅ Study the effects of stress, electric fields, and temperature on these materials ✅ Collaborate with international teams ✅ Leverage unique access to both Stony Brook University and Brookhaven National Laboratory Required: 🔹 Proven expertise in X-ray absorption spectroscopy (XAS) 🔹 Strong publication record Note: We are considering only candidates currently in the U.S. who are authorized to work. 📩 Interested or know someone who might be? Please reach out to me at anatoly.frenkel(a)stonybrook.edu. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor and Deputy Chair Department of Materials Science and Chemical Engineering Affiliate Professor, Department of Chemistry * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… -------------------------------------------------------------------

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Larch for XES processing
by Morrell, Colin T. 15 Jun '25

15 Jun '25

Hello, I am new to the technique of XES and have been working out a way to analyze some XES spectra. I have used Larch in the past for XAS analysis and found a few places that indicated that larch is also capable of processing XES data in the LarchGUI application. I have been working to install a version or find how to do this and have not been successful. Have XES support been removed from the larch applications? Any help or clarification is greatly appreciated! Thank you in advance. Sincerely, Colin Morrell PhD Candidate | See Group Division of Chemistry & Chemical Engineering California Institute of Technology

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XRFMap_viewer tricolor map legend
by Tian, Tony 07 Jun '25

07 Jun '25

Good afternoon, I was able to make a tricolor map with Larch's XRFMap_viewer like below, [cid:010cee66-2afd-4b58-8065-f70e947a2810] but couldn't have a pie-shaped diagram legend like this displayed like in a lot of XRF publications. Could you give some advice on how to do it? Thank you. [cid:95e76dd6-42ad-45f2-9498-8a664a065d64] Best regards, Tony

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FEFF does not generate feff.inp from cif
by 정은석 07 Jun '25

07 Jun '25

Hello~ all I opened the cif file in CIF Browser. I couldn't make feff.inp in this Browser. In a previous version, feff.inp was generated. However, it isn't now. What is the problem? I installed xraylarch in anaconda virtual system as following: (base) C:\>conda update --all (base) C:\>conda create --name xraylarch (base) C:\>conda activate xraylarch (xraylarch) C:\>conda install -c conda-forge python=3.9.10 (xraylarch) C:\>pip install torch (xraylarch) C:\>conda install -y -c conda-forge wxPython pymatgen scipy h5py matplotlib (xraylarch) C:\>conda install -y -c conda-forge openbabel tomopy (xraylarch) C:\>pip install epicsapps (xraylarch) C:\>pip install xraylarch (xraylarch) C:\>larch -m I have been using Window 10 system [image: image.png] Best regards, Eun-Suk Jeong

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Question about Air sensitive sample holder
by Helen Chen 05 Jun '25

05 Jun '25

Hello, Our group (Jerry Seidler) just started a project involving doing VTC and HERFD on Yb doped CrX3 material. They are thin small crystal sheets and are very air sensitive. We have tried encapsulated them between a layer of laptop tape and film, but after 12hr we see degradation due to air leaks. I am looking for some advice on air sensitive sample holder. What are some typical methods you use to deal with air sensitivity, especially for samples in thin sheets geometry? Thank you

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Influit Energy - Materials Scientist - X-ray Characterization Specialist
by Carlo Segre 03 Jun '25

03 Jun '25

Influit Energy is a dynamic and rapidly expanding company, developing energy storage solutions through cutting-edge research in battery technology, nanomaterials, and materials science. Please see the job posting at Influit Eneergy - Materials Scientist Position <https://urldefense.us/v3/__https://jobs.gusto.com/postings/influit-energy-i… > -- Carlo U. Segre, CTO Influit Energy, LLC 2312 W. Warren Blvd. Chicago, IL 60612

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Larch 2025.2.0
by Matt Newville 27 May '25

27 May '25

Hi Folks, Larch 2025.2.0 has been released, with many fixes and improvements in the past few months, especially for the Larix GUI application. When running Larix, you should be prompted to run the "Update Larch" program. Some of the changes for this release include: - The Plotting section for the XAS Normalization panel has changed to give fewer "main plotting options", but then additional options for pre-edge lines, derivatives, etc. - The Plotting section for the EXAFS panel has also changed. Here, the choices for what to plot are now organized by "Space": Energy, k (including filtered or q), and R. Because there are many choices for making 2 plots at a time, the options can be saved and recalled later (including in later sessions). - There are several improvements for reading and showing non-XAS or "XY data". - There is an initial working version of a generic Curve Fitting Panel for XY and XAS data. This is similar to the Pre-edge Peak Fitting Panel, but it does not require the removal of a baseline first. - There is now an "XAS Mode" selection when importing data from plain Column Files. Currently, the choices are "Unknown", "Transmission", "Fluorescence", "HERFD", and "Calculation". The intent is to allow adjusting normalization and analysis parameters based on this Mode. Currently, only "Calculation" actually adjusts the normalization parameters. - Reading in XAS calculations from Feff (xmu.dat) or FDMNES with "Mode=Calculation" gives better pre-edge (using only the first point) and normalization. There are many more bug fixes and improvements detailed at See https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/tag… . There are plenty of people to thank for these fixes, but special thanks again goes to Mauro Rovezzi and Shelly Kelly. --Matt PS: We have missed a few recent Developers+Interested Users meetings. I think we should get back to having these, but maybe at a different pace. If anybody would like to discuss development or features in more detail, let me know.

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Cancellation of the 19th International XAFS conference in 2025 in Chicago
by Matthew Newville 15 Apr '25

15 Apr '25

Hi All, Some of you may not have heard this yet. The International X-ray Absorption Society and the Conference organizers have canceled the XAFS19 Conference scheduled for July 14-19, 2025. From Professor Asakura, Chair of the IXAS: Dear all involved with XAFS, As you may know, the 19th International XAFS conference (XAFS 19) was scheduled to occur in Chicago from the 14th to the 19th of July 2025. After considering the many uncertainties with hosting an international conference in the US given the current political climate, the organizer of the 19-XAFS conference proposed its postponement. The IXAS EC voted on the subject and unanimously voted to cancel the 19-XAFS in Chicago in 2025. We appreciate your kind understanding. We will now call for a bid to host the conference next year, XAFS 2026, and we will decide on the new venue and communicate the decision to the community as soon as possible. Please contact the IXAS chair, Kiyotaka Asakura (kytkaskr(a)fc.ritsumei.ac.jp<mailto:kytkaskr@fc.ritsumei.ac.jp>), if you are interested in organizing the XAFS 2026. Thanks. Kiyotaka Asakura IXAS Chair Carlo Segre Chair of the 19-XAFS Also See XAFS19 homepage https://urldefense.us/v3/__https://www.icdd.com/xafs19/__;!!G_uCfscf7eWS!dg…

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XAS spectra for Na2CoP2O7, Li2CoP2O7, NaCoPO4 and LiCoPO4
by Carlos Triana Estupinan 15 Apr '25

15 Apr '25

Dear Colleagues, I was curious if anyone has XAS spectra for Na2CoP2O7, Li2CoP2O7, NaCoPO4 and LiCoPO4 that you would not mind sharing. Thanks and Best Regards, -- ______________________________________ Phd. - Lic.Phil. - Msc. & Bsc. in Sciences Physics Senior Researcher, University of Zurich Department of Chemistry Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Email: carlos.triana(a)chem.uzh.ch Phone: +41 44 63 54 646 Movil: +41 076 814 41 60 -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web https://urldefense.us/v3/__http://www.unal.edu.co__;!!G_uCfscf7eWS!eoeeN3SW… <https://urldefense.us/v3/__http://www.unal.edu.co/__;!!G_uCfscf7eWS!eoeeN3S… >.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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A warning about feff8 vs feff6
by Joshua J. Kas 11 Apr '25

11 Apr '25

Dear ifeffit community, While doing some fitting of theoretically produced data, we noticed that there are some differences between feff6 and feff8, even when all settings are the same as far as we can tell. This was expected for some parameters such as the E0 shift, since the approximation has changed from feff6 to feff8. However, there is also a difference in the scattering amplitudes. In particular, for the Pt case that we are looking at, the nearest neighbor scattering amplitudes from feff8,9, and 10 are roughly 11/12 the size of the scattering amplitudes from feff6. This likely has something to do with a difference in the prescription to create the muffin-tin potentials, but we haven't tracked down the difference completely. In any case, as found by Bruce Ravel <https://urldefense.us/v3/__http://bruceravel.github.io/SCFtests/scf.html__;… >, differences in physical parameters between feff6 and feff8 are within errors of each other when each code is used consistently. This message is mainly meant to warn people not to mix the two codes when doing analysis. For example, an s02 extracted by fitting data with feff6 cannot be used with a feff8 analysis. -- Joshua Kas (He/Him/His) Research Assistant Professor University of Washington

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CLS Introduction to X-ray absorption spectroscopy and microprobe Worksop
by Amani Ebrahim 10 Apr '25

10 Apr '25

Dear Ifeffit community, The CLS is organizing a 2-day workshop/ summer school for new commers to XAS, with a specific focus on topics such as food, soil and environmental science (see following link<https://urldefense.us/v3/__https://event.fourwaves.com/cls-xas-workshop/pag… >). Please help disseminate amongst your network. Deadline to apply is May 15. For details on the workshop, please visit: Intro to XAS and microprobe workshop<https://urldefense.us/v3/__https://event.fourwaves.com/cls-xas-workshop/pag… > Thank you from the workshop organizers ----------------------------------------------- Amani M. Ebrahim, PhD (She/Her) Associate Scientist | Canadian Light Source Ph: 306-657-3659 | C: 306-227-7228 https://urldefense.us/v3/__https://bioxas-spectroscopy.lightsource.ca/__;!!… lightsource.ca<https://urldefense.us/v3/__https://www.lightsource.ca/__;!!G_uCfscf7eWS!c8d… > | @canlightsource [AE4A24CF] [5A8E16B5][12A76F8B][601FFCD1][8CA6807][EDA296AD][CF6D0A43] We acknowledge we are on Treaty Six territory and the traditional homeland of the Métis. We pay our respects to the First Nations and Métis ancestors of this place and reaffirm our relationship with one another.

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Delete me
by Richard Brand 01 Apr '25

01 Apr '25

Von meinem iPad gesendet New iPhone +49 159 06238965 New eMail brand.richard(a)web.de

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XAFS19 Abstract Submissions open
by Carlo Segre 17 Mar '25

17 Mar '25

Hello All, The abstract submission page on the XAFS19 Conference web site will be open later this afternoon. You will be able to request a poster or oral presentation. The Program Committee will make the final decisions on which format your work will be presented. For those of you who need an invitation letter for a Visa, please email xafsconference2025(a)gmail.com to request one with your abstract number. For the XAFS19<https://urldefense.us/v3/__https://www.icdd.com/xafs19/__;!!G_uCfscf7eWS!Zj… > organizing committee, Carlo -- Carlo Segre, Duchossois Professor of Physics Illinois Institute of Technology

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PostDoc position as Beamline Scientist at KIT Light Source
by Zimina, Anna (IKFT) 14 Mar '25

14 Mar '25

Dear all, Postdoc position for the challenging job at KIT Light Source synchtrotron as beamline scientist at the X-ray absorption spectroscopy beamline is open in our group at IKFT/KIT: https://www.pse.kit.edu/english/karriere/joboffer.php?id=164965 Curious? Find out more here: https://www.ikft.kit.edu/english/234.php Please forward the advertisement further. Thank you in advance, Anna Zimina ____________________________________________________________________________ __________ Karlsruhe Institute of Technology (KIT) Institute of Catalysis Research and Technology (IKFT) Dr. Anna Zimina Catalysis at KIT Light Source group Hermann-von-Helmholtz-Platz 1 Building 345 Office 304 76344 Eggenstein-Leopoldshafen Phone: +49 721 608 28673 Fax: +49 721 608 26789 E-Mail <mailto:anna.zimina@kit.edu> anna.zimina(a)kit.edu

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XANES reference Spectra of V2O5 and VO2
by Dooshaye Moonshiram 14 Mar '25

14 Mar '25

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Athena - LCF component export error
by miranda.vu＠lightsource.ca 10 Mar '25

10 Mar '25

Hi, I am having an issue with the export of LCF data in Athena version 0.9.26. When I export the .lcf of files, it will re-order the components without properly re-ordering the associated data columns. The data and components will plot correctly in Athena before exporting. Is this something that can be fixed? Or if not would it be possible for me to get version 0.9.24 if you still have a copy of it? Please let me know if there is any additional information that I can provide. Thanks, Miranda

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International XAFS Conference 19 - Chicago July 14-18, 2025
by Carlo Segre 05 Mar '25

05 Mar '25

Hello IFEFFIT Mailing List, I am pleased to let you know that the website and registration pages for the XAFS19 conference to be held on the Illinois Tech Main Campus in Chicago, Illinois, July 14-18 is now available. The links to the registration for participants and exhibitors are both live and we are able to take registration. Members of the International XAFS Society can take advantage of the discount on the full participant registration fee with a promotion code that will be available shortly from the Society. The Abstract submission will open early next week and I will send an additional announcement out at that time. Please bear with us as the web site is still a work in progress. Housing information as well as more information regarding invited speakers is forthcoming. The link to the main conference web site is https://urldefense.us/v3/__https://www.icdd.com/xafs19/__;!!G_uCfscf7eWS!cy… . Please feel free to disseminate this announcement. For any questions, please email the conference at <xafsconference2025(a)gmail.com>. This email will be used for individual correspondence. If you have corrections about the web site, please feel free to email me at <segre(a)iit.edu>. Carlo Segre for the XAFS19 Local Organizing Committee -- Carlo Segre, Duchossois Professor of Physics Illinois Institute of Technology

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Water-free binder advice
by Paul Aronstein 01 Mar '25

01 Mar '25

Hello, I'm looking for some advice on binder alternatives for preparing either pellets or packed powder samples in a dry glovebox. Please also note if the binder requires preparation (i.e. desiccated prior to use, etc) or if there are other considerations. Thank you, -Paul

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Question about Ti edge
by Benito Melas 01 Mar '25

01 Mar '25

Hi all, I was following this article about Li2TiS3 https://urldefense.us/v3/__https://pubs.acs.org/doi/full/10.1021/acs.inorgc… and found this Ti edge XANES figure [image: image.png] The authors claim The peak position for LTS-213 is approximately 4970 eV, which agrees well > with that for rutile TiO2 with a valence of titanium species in the 4+ > oxidation state. Should we use the pre-edge to determine the oxidation state? Is it reliable, or should we use E₀ and compare it with references of well-known oxidation states? > In addition, TiS2, in which titanium is also in the 4+ oxidation state, > shows pre-edge peaks at 4968–4971 eV. (21) Considering the titanium > oxidation state in the raw materials, the stability of the titanium > species, and the XANES results, the oxidation state of the titanium species > in LTS-213 is likely to be 4+. The second conclusion is even more unclear. Would you help me see if I am missing something in my understanding of oxidation states using XANES? Best, B.

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Re: Question about Ti edge
by Benito Melas 28 Feb '25

28 Feb '25

Hi Matt, Thank you for the explanation. In this case, comparing oxides provides only a rough approximation of the oxidation states. Using both oxides and sulfides would incorporate the contribution of covalency and lead to inaccuracies. What about utilizing the pre-edge mixing oxides and sulfides? I have a concept that is more related to the symmetry of the site, although this understanding also originates from oxides. Best regards, On Fri, Feb 28, 2025 at 11:54 PM matt.newville(a)gmail.com < matt.newville(a)gmail.com> wrote: > Hi Benito, > > > > The energy of the sharp rise (ie, the energy of the empty metal 4p states) > is a simple measure of the “charge state” or “oxidation state” of a > metal. To be clear, for a particular ligand type (say, oxygen), the > energy of 4p states, and so also the energy of the main rise in mu(E), will > change systematically with energy. But if you change the ligand, and the > covalency/ionicity of the bond, that will also move the energy of the > metal’s 4p states. Metal sulfides are much more covalent than metal > sulfides, and many are semi-metallic. If I understand correctly, titanium > disulfide is used because it is electrically conductive. > > > > OTOH, titanium dioxide will have a band gap of a couple of eV. That “band > gap” is strongly correlated with the edge shift. > > > > Again, the energy of the “main edge” is just not a simple measure of > “oxidation state”, especially if the ligand is not oxygen. > > Using the term “oxidation state” for a sulfide is not going to give you > much insight. > > > > --Matt > > > > > > *From: *Benito Melas <metal.cnea(a)gmail.com> > *Date: *Friday, February 28, 2025 at 7:58 AM > *To: *matt.newville(a)gmail.com <matt.newville(a)gmail.com> > *Subject: *Re: [Ifeffit] Question about Ti edge > > Hi Matt, > As you mentioned, "for the transition metals, there will usually be a > sharp rise in mu(E) at the energy." > In the case of LTS, however, this sharp rise occurs at lower energies than > in TiO2, which raises concerns regarding the claim that both compounds > exhibit the same oxidation state. > Thank you for your continued dedication to enlightening our community. > Best regards, > > > > > > > > On Fri, Feb 28, 2025 at 3:46 AM matt.newville(a)gmail.com < > matt.newville(a)gmail.com> wrote: > > Hi Benito, > > > > > The authors claim > > >> The peak position for LTS-213 is approximately 4970 eV, which agrees > well with that for rutile TiO2 with a valence of titanium species in the 4+ > oxidation state. > > > > > Should we use the pre-edge to determine the oxidation state? Is it > reliable, or should we use E₀ and compare it with references of well-known > oxidation states? > > > > Many people use pre-edge peaks of transition metals for reliable analysis > of metal oxidation states. > > > > E0 is sort of poorly defined term. For the transition metals, there will > usually be a sharp rise in mu(E) at the energy of the metal’s own 4p > electrons – the “main edge”, though this can sometimes be tricky to > identify precisely, and sometimes has structure (as TiO2 does – slightly > different for its different forms). > > > > >> In addition, TiS2, in which titanium is also in the 4+ oxidation state, > shows pre-edge peaks at 4968–4971 eV. (21) Considering the titanium > oxidation state > > >> in the raw materials, the stability of the titanium species, and the > XANES results, the oxidation state of the titanium species in LTS-213 is > likely to be 4+. > > > The second conclusion is even more unclear. > > What confuses me there is “TiS2 is in the 4+ *oxidation* state”. > Titanium disulfide is not oxidized at all - it is bound to sulfur. Its > charge state could be 4+, and many chemists use “oxidation” to mean the > transfer of charge to and from a metal, whether this is done by oxygen or > not. For XANES, the ligand species matters. K-edge XANES shows the > energies of the unfilled p states at the center of the Ti atom, which will > be very different for Ti-S (more covalent) and Ti-O (more ionic) bonds. > > --Matt > > > > > > *From: *Benito Melas via Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > *Date: *Thursday, February 27, 2025 at 7:28 AM > *To: *ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov > > > *Cc: *Benito Melas <metal.cnea(a)gmail.com> > *Subject: *[Ifeffit] Question about Ti edge > > Hi all, I was following this article about Li2TiS3 https: //pubs. acs. > org/doi/full/10. 1021/acs. inorgchem. 4c03864 and found this Ti edge > XANES figure The authors claim The peak position for LTS-213 is > approximately 4970 eV, which agrees well with > > ZjQcmQRYFpfptBannerStart > > *This Message Is From an External Sender * > > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > > Hi all, > > I was following this article about Li2TiS3 > > > https://urldefense.us/v3/__https://pubs.acs.org/doi/full/10.1021/acs.inorgc… > <https://urldefense.us/v3/__https:/pubs.acs.org/doi/full/10.1021/acs.inorgch…> > > > and found this Ti edge XANES figure > > > The authors claim > > > > The peak position for LTS-213 is approximately 4970 eV, which agrees well > with that for rutile TiO2 with a valence of titanium species in the 4+ > oxidation state. > > > > Should we use the pre-edge to determine the oxidation state? Is it > reliable, or should we use E₀ and compare it with references of well-known > oxidation states? > > > > In addition, TiS2, in which titanium is also in the 4+ oxidation state, > shows pre-edge peaks at 4968–4971 eV. (21) Considering the titanium > oxidation state in the raw materials, the stability of the titanium > species, and the XANES results, the oxidation state of the titanium species > in LTS-213 is likely to be 4+. > > > > The second conclusion is even more unclear. > > Would you help me see if I am missing something in my understanding of > oxidation states using XANES? > > > > Best, B. > > > >

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Diatomic distance on each EXAFS of both elements
by "Qiang Chang (常强)" 27 Feb '25

27 Feb '25

3 2

Re: Water-free binder advice
by Michele Piana 27 Feb '25

27 Feb '25

1 0

Not being able to generate FEFF paths from CIF
by cameron.mollazadeh＠colorado.edu 25 Feb '25

25 Feb '25

Hi! I have been trying to generate a FEFF path from a CIF I have however it hasn't worked. I tried pre-generating the inp file as well but it just stalls out and doesn't go anywhere. I have talked to some people In my lab who use the software as well and they also have encountered the same problems. It had worked once in the past for me but now is longer working. I have tried changing the unit cell and everything, however nothing is seeming to work. Best, Cameron

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Error saving Feffit results in Filtered X(k)
by DANILO OLIVEIRA DE SOUZA 21 Feb '25

21 Feb '25

Dear Matt, Firstly, I must congratulate you for your effort in making Larch such a nice, user-friendly, intuitive tool for XAS analysis. Cheers to you and all the collaborators. And thank you for making it available for the whole community. I would like just to report a (small) issue concerning saving Feffit results using Larix. After an EXAFS fitting, I tried successfully save the graphs in every option available, i.e., k-weighted chi(k), chi(R), Real[Chi(R)] and Filtered X(k). Everything works pretty well, except the last one, where an error can be observed on the prompt: File "C:\...\Python\Python311\site-packages\larch\wxxas\feffit_panel.py", line 2211, in onSaveFit ydata = getattr(ds0.data, yname)[:nx] * xarr**kw ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ValueError: operands could not be broadcast together with shapes (259,) (326,)" I do not know if it happens just on my version and I know it is a minor issue, since having the window used on back-FT we can plot it easily. In any case, I am just reporting the situation for your knowledge. Cheers, Danilo OLIVEIRA DE SOUZA

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Request for proposals to host International XAFS Conference 2028
by Bare, Simon R 15 Feb '25

15 Feb '25

International XAFS Conference 2028 Proposals to host the 2028 International XAFS Conference are now solicited and accepted. Proposal guidelines are given below, but if you have questions, please contact the IXAS Chair. Proposal Deadline: June 1, 2025 Proposal Presentations (videoconference): June 1 to July 1, 2025 Announcement of 2028 venue: During the 2025 XAFS Conference in Chicago https://urldefense.us/v3/__https://xrayabsorption.org/ixas-conference-selec… Send your proposal by email to the IXAS Chair: Asakura Kiyotaka kytkaskr(a)fc.ritsumei.ac.jp<mailto:kytkaskr@fc.ritsumei.ac.jp> Proposal Guidelines The proposal submitted for the conference can be made by email to the Chair by email and should include the following information. 1. Description of Proposed Conference Venue The conference proposal should include a description of the details about the venue for the conference (based on the 600 participants, the average number of recently held conferences), including: * One conference room for plenary sessions, accommodating 600 or more attendees. * Additional space for at least 200 posters, poster presenters, and sufficient room for attendees to view and discuss posters. * Additional conference rooms for parallel sessions which can accommodate at least 200 attendees each. Close proximity of rooms is to be secured for parallel sessions. * Projection and PA systems appropriate for a scientific conference in all conference session rooms. * One or more small meeting rooms for IXAS-EC, IUCr Commission on XAFS, and related executive meetings, which accommodates at least 30 attendees. * The main conference rooms are preferred to be climate-controlled. * Compliance with local regulations for disability access. 2. Description of Organization The conference proposal should name expected members of the conference organization including Chair(s). The conference organizers should form appropriate committees with different functions such as Local Committee, Program Committee, and International Advisory Committee, and the proposal should name some of the expected members of these committees. Please include: * CV and profile of the conference chair(s) * Letter(s) of commitment for host institution(s) and any other supporting institutions. * Proposed List of Local Committee members fully committed to the organization of the conference. * Proposed List of Program Committee members representing all relevant fields and topics. * Proposed list of Fundraising Committee. * Proposed List of an International Advisory Committee formed by the IXAS-EC members and other distinguished scientists selected by Conference Organizers taking into account regional and scientific balance. * Plan for circulating conference information to XAFS communities (Web site etc.). 3. Scope and Proposed Scientific Program The conference proposal should describe the scope of the scientific program for the conference, including * expected number of parallel sessions. * fields or special topics to be highlighted * plans for any satellite meetings (scope, locations, and expected number of attendants). * list of supporting organizations (institutes and academic societies). * expected plans for an exhibition. * expected tours of nearby scientific facilities. 4. Description of Infrastructure and Logistical Plan The conference proposal should provide a list of sufficient accommodations close to the conference venue, with a range of prices and an approximate number of rooms available. Transportation options between the conference venue and accommodation sites, restaurants, regional attraction sites, social events sites, etc. should also be given, as well as a description of transportation between airports or train stations and conference venue. 5. Preliminary Budget Draft Please include projections of the total cost, income breakdown, supports from institutes and other organizations, and start-up plan. Expected ranges for registration fees should be given. Also provide any expected details about support for young scientists, scientists from developing countries, and so forth. 6. Plans for Publication Conference Organizers should circulate the full conference program to all registered attendees prior to the conference. Conference Organizers are responsible for publishing Conference Proceedings with guidance and assistance from the IXAS. It is recommended that the proceedings are published in Radiation Physics and Chemistry as first choice or J Synchrotron Radiation as second choice. Simon R Bare Distinguished Scientist Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory and Adjunct Professor Chemical Engineering University of California, Davis srbare(a)slac.stanford.edu<mailto:srbare@slac.stanford.edu> Ph: 650-926-2629 https://urldefense.us/v3/__https://web.slac.stanford.edu/coaccess/__;!!G_uC… [cid:image001.jpg@01DB7FBD.A7741230][cid:image002.png@01DB7FBD.A7741230]

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Artemis: Rejects first shell fitting
by avijay＠ethz.ch 14 Feb '25

14 Feb '25

Hello all, I am trying to fit my data using Artemis for a reference foil sample. However, the fit seems to get worse when I include the scattering paths at lowest R (i.e. the first shell scattering, with the highest rank). Does it make physical sense to not include this in the fitting? Is it acceptable to try and fit only a certain range of the |X(R)| vs R for the foil reference - in order to estimate the amplitude reduction factor for subsequent fitting of the real samples? Any insight/advice is much appreciated. Thank you. Best, A

5 5

Constraining phase composition
by Olena Zavorotynska 09 Feb '25

09 Feb '25

Hello, I have been fitting in Artemis three phases to my samples, that I denote x, y, and 1-(x+y). It often happens that x and y get unreasonable or negative values. How do I constrain x, y to be positive, and x+y < 1? On a side note, I have simple metallic lattices, and fitting two samples at the same time so have enough independent points. Best regards Olena Zavorotynska Sent from my Galaxy

2 1

Correcting for over absorption
by cameron.mollazadeh＠colorado.edu 06 Feb '25

06 Feb '25

Hi Matthew, I was re-reading the larch documentation as my data is suffering for over absorption and was wondering how I can go about implementing the correction factor. I am primarily using the data for EXAFS analysis and was also wondering if this technique is still questionable for EXAFS. Thank you! Cameron

2 1

Re: [EXT] Ifeffit Digest, Vol 276, Issue 2
by Christopher Chantler 05 Feb '25

05 Feb '25

Hi Cameron See Trevorah R et al. regarding correction for absorption and self-absorption; Yes it is probably still suitable for EXAFS analysis subject to other criteria and constraints. Also see Schalken M et al. for the comparison of transmission EXAFS (largely without self-absorption) versus angle-dependent fluorescence EXAFS (which almost always has self-absorption and absorption in an angle-dependent manner) and how to extract the data. Note that fluorescence data has a functional which is not directly that of a transmission or absorption measurement. Best wishes Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Member, CIT, CCN; Former Chair, International Union of Crystallography Commission on XAFS International Radiation Physics Society, Former President School of Physics, University of Melbourne, Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<mailto:chantler@unimelb.edu.au> chantler(a)me.com<https://urldefense.us/v3/__https://owa.unimelb.edu.au/owa/redir.aspx?C=c7Bo… > https://urldefense.us/v3/__https://www.ph.unimelb.edu.au/*chantler/opticsho… <https://urldefense.us/v3/__http://www.ph.unimelb.edu.au/*chantler/home.html… > https://urldefense.us/v3/__https://www.ph.unimelb.edu.au/*chantler/opticsho… ________________________________ From: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, 5 February 2025 5:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [EXT] Ifeffit Digest, Vol 276, Issue 2 External email: Please exercise caution Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe 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. Correcting for over absorption (cameron.mollazadeh(a)colorado.edu) 2. In reference to the prior overabsorption (Cameron Mollazadeh) ---------------------------------------------------------------------- Message: 1 Date: Mon, 03 Feb 2025 21:59:27 -0000 From: cameron.mollazadeh(a)colorado.edu Subject: [Ifeffit] Correcting for over absorption To: ifeffit(a)millenia.cars.aps.anl.gov Message-ID: <173861996743.2557830.8195040248000522658(a)millenia.cars.aps.anl.gov> Content-Type: text/plain; charset="utf-8" Hi Matthew, I was re-reading the larch documentation as my data is suffering for over absorption and was wondering how I can go about implementing the correction factor. I am primarily using the data for EXAFS analysis and was also wondering if this technique is still questionable for EXAFS. Thank you! Cameron ------------------------------ Message: 2 Date: Mon, 3 Feb 2025 22:01:09 +0000 From: Cameron Mollazadeh <Cameron.Mollazadeh(a)colorado.edu> Subject: [Ifeffit] In reference to the prior overabsorption To: Cameron Mollazadeh via Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <SN6PR03MB4592175B3E3C1276F36D33F9F1F52(a)SN6PR03MB4592.nam prd03.prod.outlook.com> Content-Type: multipart/related; boundary="_004_SN6PR03MB459217 5B3E3C1276F36D33F9F1F52SN6PR03MB4592namp_"; type="multipart/alternative" Here is a photo of the “normalized” spectra [cid:image001.png@01DB764C.751787B0] Best, Cameron Mollazadeh PhD Student | Toney Group | CU Boulder

2 1

In reference to the prior overabsorption
by Cameron Mollazadeh 03 Feb '25

03 Feb '25

Here is a photo of the “normalized” spectra [cid:image001.png@01DB764C.751787B0] Best, Cameron Mollazadeh PhD Student | Toney Group | CU Boulder

1 0

Athena .dat file
by Raspante, Fabio 01 Feb '25

01 Feb '25

Hi, I worked on some data and I aligned them properly before to do any comparison. I also checked the alignment by plotting all the data together. After that I exported the data to have a file usable on Origin (the .dat format) but the problem is that after plotting the data on Origin, they are not aligned anymore. Specifically one group of data is not aligned to the others. Do you know what could be the problem? And how can I solve it? Many thanks, Fabio

2 1

Looking for a beamline scientist-KIT Light Source, Germany
by Vitova, Tonya (INE) 31 Jan '25

31 Jan '25

Dear all, We are looking for a beamline scientist with a focus on our X-ray emission spectrometer at the ACT station, CAT-ACT beamline at the KIT Light Source, Germany. Please note that the position is initially for two years; however, we are strongly committed to extending it and offering a long-term perspective. https://www.pse.kit.edu/english/karriere/joboffer.php?id=164749 Unlike a classical user operation, the beamline scientist will support our own projects and collaborative projects. Thank you for applying or forwarding the opening to suitable candidates. All the best, Tonya Vitova -----Original Message----- From: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Freitag, 31. Januar 2025 07:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 275, Issue 6 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe 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. Help with constrains (Otal Eugenio) 2. Re: Help with constrains (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 30 Jan 2025 18:48:18 +0900 From: Otal Eugenio <eugenio_otal(a)shinshu-u.ac.jp> Subject: [Ifeffit] Help with constrains To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <CAEzOxfgjTtpfBg6bYP87pmTiQ2=otSfBVc3NAD8PNwx+z1wAUQ(a)mail.gmail.com> Content-Type: multipart/alternative; boundary="00000000000088cc25062ce95500" Hi all, I am experiencing an issue with CN and sigma2, which are correlated. My CN value is too high, and I would like to reduce it to see if I can improve the fit. I have three questions: 1. Are constraints a viable option? If not, could you clarify the alternatives? 2. The examples I found are in Python, but I am using the GUI. How should I correctly define a constraint? GPT suggested the following: max(4, 12 * exp(-sigma2_O232 / 0.02)), is it correct? 3. I attempted to apply this constraint, but now I cannot delete it. Restarting Larch for each value is not a practical solution. How can I modidy the constraint efficiently? Thank you for your help! Best regards,

1 0

Help with constrains
by Otal Eugenio 31 Jan '25

31 Jan '25

Hi all, I am experiencing an issue with CN and sigma2, which are correlated. My CN value is too high, and I would like to reduce it to see if I can improve the fit. I have three questions: 1. Are constraints a viable option? If not, could you clarify the alternatives? 2. The examples I found are in Python, but I am using the GUI. How should I correctly define a constraint? GPT suggested the following: max(4, 12 * exp(-sigma2_O232 / 0.02)), is it correct? 3. I attempted to apply this constraint, but now I cannot delete it. Restarting Larch for each value is not a practical solution. How can I modidy the constraint efficiently? Thank you for your help! Best regards,

2 1

Re: Larch 2025.1.1
by Cameron Mollazadeh 15 Jan '25

15 Jan '25

Hi Matt, I saw the feedback you requested for Larch and was wondering if we could have both of those options 1 and 2. Thank you! 1. Should we have a monthly Zoom meeting (maybe alternating time of day) as “Office Hours” ? 2. Should we send a survey of user needs and desires for features, recommendations, etc? (for reference) Best, Cameron

1 0

XRFMap Viewer not opening - India Reddell
by India Reddell 15 Jan '25

15 Jan '25

Good afternoon, I was hoping to get some help accessing the XRFMap viewer on my computer. I downloaded Larch for Windows from the binary installer and was able to get the folder with all the software onto my computer. However, when I try to open the XRFMap viewer the only thing that pops up is a terminal with a error message. [image: Screenshot 2025-01-10 121622.png] Then it closes and nothing happens. Would y'all happen to know what's going on and how I can fix it? I am trying to fix up the maps I have collected from NSLS-II. Thank you! Best, -- *India Reddell* Environmental Engineering | U4 Texas A&M University

3 3

Larch 2025.1.1
by Matthew Newville 14 Jan '25

14 Jan '25

Hi Folks, Larch version 2025.1.1 has been released. This fixes a serious issue for generating Feff data files, and a few other issues too. It had been more than a year since fresh binary installers were made, so those have been updated too. As always, suggestions and feedback are welcome. Since this is the first release of the year, and since we have an XAFS Conference and Q2XAFS meeting coming up this summer in Chicago (July 14-20), I encourage people to think about what they would like to see for these and other tools for XAFS and related work. And also: think about coming to the conference ;). For those interested, we’ll restart monthly meetings to discuss the development of these tools later this month (probably January 24, probably 9 AM Chicago time). This is not development-only, but often about feature requests, complaints about the GUIs, and ideas. If you are interested, let me know, and I’ll happily add you to the invite list for that Zoom call. We would like to hear feedback on: 1. Should we have a monthly Zoom meeting (maybe alternating time of day) as “Office Hours” ? 2. Should we send a survey of user needs and desires for features, recommendations, etc? If you have opinions on any of these topics, let me know either here or by direct email. --Matt

2 3

Larch version 2025.1.1 deglitching seems not to work
by Mangold, Stefan (IPS) 13 Jan '25

13 Jan '25

Dear all I have just installed the newest version on my Mac. I tried to deglitch some of my data and can nicely remove the glitch from the data in the visualization. if I try to save the data, it just saves the data unchanged. Tried this several times and restarted larix several times. there is also still a bug in the loading dialog. If I try to load my data in transmission I choose „log“ and „Ioni1“ and „Ioni2“. If I load again files the software remembers correctly the "Ioni1“ and „Ioni2“, but „-log“ is selected. (Spec-like files) best regards Stefan

2 1

Problem installing Demeter
by Amy Shober 12 Jan '25

12 Jan '25

Hi all, I had to have my IT folks completely wipe my computer. They updated me to Windows 11 enterprise edition. I previously had Demeter installed so that I could use Athena. We were able to download the Demeter Version 0.9.26 installation package. However, it did not actually install the programs on my computer. And in the folder DemeterPerl, the only application I can launch is "unisn000". I see an icon for Demeter (ICO file) but when I click it, I only see a little thumbnail image. I'm guessing this is an icon file. Can someone help? Amy -- Amy L. Shober, Ph.D. Professor and Extension Specialist - Nutrient Management and Environmental Quality *Associate Chair - Department of Plant and Soil Sciences* 531 South College Avenue 152 Townsend Hall University of Delaware Newark, DE 19716 Phone: (302) 831-2146 Fax: (302) 831-0605 Email: ashober(a)udel.edu Website: https://urldefense.us/v3/__http://sites.udel.edu/canr-nmeq/__;!!G_uCfscf7eW…

2 1

FEFF running but not displaying paths
by Cameron Mollazadeh 10 Jan '25

10 Jan '25

Hello, I recently had downloaded Larch on my new MacBook and had a good amount of technical difficulties, however after downloading a few extra packages it downloaded successfully (or so I thought). The packages were needed as there is a difference between previous macs as they used intel processors not apple processors. I had previously used an intel-based Mac and had no problem with FEFF however now when I run FEFF on my new computer I get one path result and nothing else displays (shown below). Any help would be greatly appreciated! [cid:image001.png@01DB62B5.FA5A34E0] Thank you

2 1

Larch version 2024.12.0
by Matthew Newville 20 Dec '24

20 Dec '24

Hi Folks, Larch version 2024.12.0 is now released and ready for download. After many years of version "0.9.something", Mauro convinced me that we should use a date-based version string. This version has many small fixes, with the most important being: - Athena Projects saved by Larch/Larix are now again readable by Athena. - the CIF/XRD/ CIF->Feff conversion code has been moved to a separate project, larixite, where it can be managed separately, and used by Larch/Larix. As usual, much of the work here is from Mauro Rovezzi, and with bug reports and fixes from many people. Hoping everyone has a good winter break, but if analyzing XAS data was on your list of things to get done for the New Year, I hope this helps. Cheers, --Matt

1 0

XAFS 2025 conference question
by Daria Boglaienko 19 Dec '24

19 Dec '24

Hello I'm wondering about the XAFS conference next year in Chicago. I didn't find the details and deadlines on the IXAS website. Please, let me know! Thank you Daria ________________________________ From: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Thursday, December 12, 2024 10:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 271, Issue 2 Note: This message originated from outside the FIU Faculty/Staff email system. Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe 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: noise in chi(k) (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 12 Dec 2024 13:04:03 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> Subject: [Ifeffit] Re: Larch: noise in chi(k) To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: Kirill LOMACHENKO <lomachenko(a)esrf.fr> Message-ID: <75404126-CD49-3148-AC0A-9CC90FBA62ED(a)hxcore.ol> Content-Type: text/html; charset="utf-8" A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 32641 bytes Desc: not available ------------------------------ Subject: Digest Footer ifeffit mailing list: https://urldefense.com/v3/__https://millenia.cars.aps.anl.gov/mailman3/list… to unsubscribe, send mail to ifeffit-leave(a)millenia.cars.aps.anl.gov ------------------------------ End of Ifeffit Digest, Vol 271, Issue 2 ***************************************

2 1

Re: Larch: noise in chi(k)
by Matt Newville 12 Dec '24

12 Dec '24

1 0

Fundamentals of XAS. 2025 Data Analysis tutorial at NSLS-II
by istavitski＠bnl.gov 10 Dec '24

10 Dec '24

XAS course: "The Fundamentals of X-ray Absorption Spectroscopy (XAS) 2025 Data Analysis: A hands-on tutorial" will be held onsite at the National Synchrotron Light Source II (NSLS-II) at Brookhaven National Laboratory from March 11-13, 2025 is now accepting applications: https://lnkd.in/ge3KfeUX Application deadline is December 18, 2024

1 0

Larch: noise in chi(k) - another try
by Kirill LOMACHENKO 09 Dec '24

09 Dec '24

3 4

INCREASE NOVP Error
by Anis Attiaoui 04 Dec '24

04 Dec '24

Dear Matt and Community, I am having a problem related to a specific .inp file when I am trying to generate the inp file from its corresponding cif with feff8. I am attaching the .cif and feff.inp. The error I am getting is the following: '' Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters : ipot, Norman radius, Muffin tin radius, Overlap 0 1.49498E+00 1.39776E+00 1.15000E+00 1 1.20678E+00 8.53844E-01 1.15000E+00 2 1.56883E+00 1.42805E+00 1.15000E+00 tell authors to INCREASE NOVP '' I did try to run the same cif using ARTEMIS and it worked wo any issues using the feff6L instead of version 8. Thus, I tried to use the new Larixite ciff2feffinp module and use the feff6L instead of version 8 but I noticed this is not installed yet. I also found that a similar issue has previously been documented but I didn't find any clear answers in there. https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/feff/feffusers… Any suggestions will be tremendously appreciated. Thank you very much. Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!d… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

2 1

Larch: noise in chi(k)
by Kirill LOMACHENKO 22 Nov '24

22 Nov '24

1 0

Re-Installing Larch for Windows
by Daria Boglaienko 18 Nov '24

18 Nov '24

Hello, I'm sorry if I missed information related to troubleshooting of larch installation. My earlier larch version stopped loading and I uninstalled it in order to install the latest one. After doing that I can't find XAS viewer. No folder containing it was created after installation (unlike before). I went to “Scripts” in "xraylarch", found larch exe and many other exe files but they don’t load (open and crash). I uninstalled and installed it around 4 times. I also uninstalled anaconda and python for potential conflict, after that Larch installation went without errors, but still … the same issue. Please, let me know. Thank you in advance! Daria

4 4

Generating feff.inp from .cif file issues
by Anis Attiaoui 15 Nov '24

15 Nov '24

Dear Ifeffit Community, I am struggling to generate the feff.inp file using the following .cif file (attached). I am using py-Larch for this project. I tried using these 2 functions: from larch.xrd.cif2feff import cif2feffinp and from larch.xrd.structure2feff import structure2feffinp. For some reason both of them, they cannot seem to read the cif cluster file (attached). The snippet of the code I am using is : inp_file = cif2feffinp(cif_file, 'Sn', edge='K', absorber_site=1, version8=False) I am trying to generating inp_file using feff6. I keep getting the error output of inp_file: "# could not read CIF file". I am wondering if this is because the .cif file is bad or there is sthg else going on. Any suggestions will be tremendously helpful. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!a… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

4 6

XANES-Linear Combination Fitting (LCF) Au standard sample
by liyy15＠outlook.com 09 Nov '24

09 Nov '24

Hi, All I am recently learning to use XAS to characterize some Au mixture solution samples. I would like to study the chemical valence by XANES. Unfortunately, I have only gotten Au foil data. Could I use the standard data from literature like [AuCl4]-, [AuCl2]-, Au hydroxide etc? Best regards, Yu

1 0

demo data for XAFS tutorial
by Yohei Uemura 30 Oct '24

30 Oct '24

Dear Matt, I'm wondering if the demo data for the Larch tutorials is still available. https://urldefense.us/v3/__https://youtu.be/5mYRqpAWK-o?si=MS7_aqBiYF_cQTtf… My colleague wants to learn how to use Larch from the tutorial, but the link to the demo data is expired. 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 ================================================

2 2

larixite: a WebAtoms-like app for converting crystallographic information into XAS input files
by Matthew Newville 30 Oct '24

30 Oct '24

Hi Folks, As some of you have noticed, the WebAtoms application stopped working on millenia.cars.aps.anl.gov a month or so ago. We now have a start of an alternative at https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/larixite__;!!G… This uses PyMatGen to convert CIF files into Feff.inp files. This includes a simple searchable interface to data collected from the American Mineralogist Crystal Structure Database (https://urldefense.us/v3/__https://rruff.geo.arizona.edu/AMS/amcsd.php__;!!… ) of published mineral structures that has been included in xraylarch for some time. You can upload a CIF file – and most should work. We expect to be able to add inputs for FDMNES soon, and we’re looking into formats for other calculations (say, Ocean) as well. On a practical note, we thought it would be best to pull this code out of the main Larch repository and start a fresh project just for “working with crystallographic information and atomic clusters to generate inputs for XAS calculations”. This code is now under https://urldefense.us/v3/__https://github.com/xraypy/larixite__;!!G_uCfscf7… (and does not rely on the larger xraylarch package). At some point soon we plan to remove this code from xraylarch itself and use this project for that functionality. This is all sort of new, so suggestions on any part of this and bug reports are most welcome. --Matt

3 3

MD EXAFS comparison with Experimental EXAFS
by awade9＠bu.edu 25 Oct '24

25 Oct '24

Hello, I'm trying to compare my experimental EXAFS data for a molten salt (NaF-ZrF4) sample (extracted through Athena), with EXAFS obtained through running FEFF iteratively on multiple atomic configuration files obtained through MD to get an average EXAFS out. This has been performed before by Pauvert et al. (https://doi.org/10.1021/jp203137h) for a similar salt as well as others for different materials. In our comparison, there seems to be a phase shift in MD EXAFS (to higher k) compared to experimental EXAFS and I would like to know if that's normal. I've read that there is an energy shift when we use FEFF and this might be affecting the MD EXAFS here but all the comparisons I've come across in literature overlay quite well... Thank you. Best, Anubhav

2 1

SIXPACK Background Removal not reading averaged data file from SamView
by Muretta, Julie 21 Oct '24

21 Oct '24

Hello, I have been using SIXPACK to process my S K-edge XANES data from SSRL beamline 4-3. I am using SamView to average 5 scans (to improve S/N) for each sample. Then I save the averaged file (.avg) and open in the SIXPACK Background Removal application for normalization. All data sets seem to be working great with this method except one. This one opens fine in SamView, but Background Removal cannot open the averaged file. Here is the error message: *** read_data: error opening file *** C:\sixpack/test.inp pre_edge: no energy array? pre_edge: no energy array? I have saved the averaged file as a .txt file to look at it (.avg and .txt files attached), and I see an energy array. How can I open and use this in SIXPACK Background Removal? Thank you in advance, Julie Muretta

1 0

Query regarding smoothing data
by Muskan Verma 19 Oct '24

19 Oct '24

Good morning professor Would you help me in this question. I am doing XANES analysis of N-K edge of some irradiated sample. There is a lot of noise in the data. I want to smooth the data. Which method should I prefer and how many number of data points should be taken to get a good peak to get a good fit? Kind regards

1 0

Problem with fit data export
by Otal Eugenio 17 Oct '24

17 Oct '24

Dear all, I was exporting the filtered data and found Larch is not exporting the filtered data. No new files were found in the folder I was saving the files. I found a victory in doing it from the plotting window after fitting, File > Export data. I exported the chi(k) with chi(q), chi(k) with the fit and chi(q) with the fit. All included bellow. The signal in chi(k) with its fit and chi(q) with its fit, both match well. The fit shown chi(k) and chi(q) has different aspects. Am I wrong or the fit should look the same in both cases? Is there any compensation for the window used? Do I need to change something in the configuration to export it properly? Best regards [image: image.png] [image: image.png] [image: image.png] (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Research Initiative for Supra Materials, Shinshu University 4-17-1 Wakasato, Nagano city. 380-8553, Japan eugenio_otal(a)shinshu-u.ac.jp ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯

2 2

Retrieving errors (uncertainties) for sigma2 = eins(temperature, thetae) in Artemis
by albeiro.henaow＠gmail.com 11 Oct '24

11 Oct '24

I am modeling the Debye-Waller factor by using the Einstein model in Artemis, where the Einstein temperature (thetae) is a guess parameter and sigma2 is a defined parameter as eins(temperature, thetae). Although, after running the fit, the error for the estimation of thetae is given by the fit report, the error for the corresponding defined sigma2 is missing. I am working on some models to reduce the errors in the estimation of the Debye-Waller factor, so it's an important value for my research. I tried to propagate the errors by using the equation in the ref paper (E. Sevillano, H. Meuth, and J. J. Rehr. Extended x-ray absorption fine structure Debye-Waller factors. I. Monatomic crystals. Phys. Rev. B, 20:4908–4911, Dec 1979. doi:10.1103/PhysRevB.20.4908.) However, I cannot obtain the same value of sigma2 when I substitute thetae into the equation from the paper compared to the value reported in the fit. Can anyone help clarify the equation (or script) used in Artemis? Thank you! Wilson Henao

2 1

Can't get access to WebAtoms via http://millenia.cars.aps.anl.gov/webatoms/
by Mangold, Stefan (IPS) 30 Sep '24

30 Sep '24

Dear all, I have a problem to open WebAtoms via http://millenia.cars.aps.anl.gov/webatoms/ <http://millenia.cars.aps.anl.gov/webatoms/>, is there another server available ? best regards Stefan Mangold

3 4

Help request
by Khadidja Elkobra Benzahra Belkacem 13 Sep '24

13 Sep '24

Good morning professor, Would you please help me in this question. I have EXAFS data of an unknown new structure, the CIF file wasn't provided to me neither the samples of 3 different doping (the ones which the EXAFS data belong) . Is it possible to refine the coordination number of each scattering path without having any information about the standard value of S02 of this specific material measured in the same experimental condition , or even without having the exact CIF file of this alloy with 3 different doping ratios. Kind regards -- *Fai crescere le giovani ricercatrici e i giovani ricercatori*** *con il 5 per mille alla Sapienza* Scrivi il codice fiscale dell'Università *80209930587 **Cinque per mille <https://urldefense.us/v3/__https://www.uniroma1.it/it/node/23149__;!!G_uCfs… >*

1 0

Question about rare noise in Pb spectra at high k
by Otal Eugenio 13 Sep '24

13 Sep '24

Dear all, I measured Na2Ti3O7 with Pb replacing Na. I measured the L3 edge in transmission mode. Mainly all samples have noise at k>8 but two of them show the "same noise". Pb0375 replaces 18% of Na by Pb while Pb1000 replaces 50%. I would like to know if this is a signal to pay attention or just cut it off. I am planning to measure at low temperatures in the next call. Any suggestion is welcome. I also attach the csv of the samples and PbO2 std. Best regards. [image: image.png] (^ㅇᆽㅇ^)(=˃ᆺ˂=)(=🝦 ༝ 🝦=) Eugenio H. OTAL Assistant Professor Research Initiative for Supra Materials, Shinshu University 4-17-1 Wakasato, Nagano city. 380-8553, Japan eugenio_otal(a)shinshu-u.ac.jp ¯\_(ツ)_/¯ ¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯ ¯\_(ツ)_/¯

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updates to this mailing list
by Matthew Newville 11 Sep '24

11 Sep '24

Hi Folks, We needed to upgrade the operating system on the machine running this mailing list late last week. That went well, but part of that process involved upgrading the "mailman" software used for this mailing list to the latest version. That upgrade was long overdue (the web pages looked 20 years old because they were) but was also fairly involved. Fortunately, we have great support in our group, and the new mailing list should be running smoothly (if you get this email, that is). A consequence of this change is that many of the links for the mailing list have changed. With recent changes in Argonne National Lab policies, URLs in emails get mangled to have "https://urldefense.us/v3/__https://urldefense.us/v3__;!!G_uCfscf7eWS!e6kk3J… " prefixes. So I apologize for the ugly and long following links: The Main page for this list is at https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/mailman3/lists… If you had a password for the older list, this did not get moved over. If you want to change your setting, you can just use "Forgot Password" to sign in. The Archives are now at https://urldefense.us/v3/__https://millenia.cars.aps.anl.gov/archives/list/… This is a completely new archive format, but the translation (of about ~10,500 messages) worked reasonably well. Existing links to any older message should redirect to the "top level archiive": we did not try map old message links to new ones or fix any broken links. In addition, the archives at https://urldefense.us/v3/__https://www.mail-archive.com/ifeffit@millenia.ca… should also still works. If you have any questions, please let me know. --Matt

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Save the date: SCC short course at BNL, Nov. 6-8, 2024
by Anatoly Frenkel 21 Aug '24

21 Aug '24

Hello, As a follow up on my previous "save the date" message, the dates of the Synchrotron Catalysis Consortium short course have been finalized (they changed from the previous dates in an attempt to resolve the conflict with other meetings). The final dates are: Nov. 6 (Wed) through Nov. 8 (Fri), 2024. The course will be held at Brookhaven National Laboratory. The course is in the final stage of approvals - after we have it officially approved I will send another update with the course agenda and registration details. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) *Stony Brook University* Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… ------------------------------------------------------------------- On Fri, May 3, 2024 at 10:58 AM Anatoly Frenkel < anatoly.frenkel(a)stonybrook.edu> wrote: > Dear subscribers: > > Please pass it along to your group members who may be interested in this > opportunity. > In continuation of the annual tradition at the Synchrotron Catalysis > Consortium (SCC) at Brookhaven National Laboratory to organize and run XAFS > short courses there since 2005, we are planning a first specialized course > targeting catalysis and electrocatalysis researchers. The course will > follow a successful model of our XAFS courses: the lectures (on the topics > ranging from in situ/operando characterization and multimodal > instrumentation to data analysis) and software demonstrations on the first > two days, followed by the hands-on data analysis session on the last day. > The program is being finalized, and we are in the process of getting the > necessary approvals from BNL and DOE. In the meantime, please, mark your > calendars and contact me if you have any questions. > > Anatoly > ******** > On sabbatical leave at Weizmann Institute of Science, Israel > ******** > ------------------------------------------------------------------- > Anatoly I. Frenkel > Professor > Department of Materials Science and Chemical Engineering (primary > appointment) > Department of Chemistry (affiliate appointment) > *Stony Brook University* > Stony Brook, NY 11794 > Email: anatoly.frenkel(a)stonybrook.edu > <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… > Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL > https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… > > Joint Appointment: > Senior Chemist > Chemistry Division, *Brookhaven National Laboratory* > Upton, NY 11973 > Email: frenkel(a)bnl.gov > https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… > ------------------------------------------------------------------- > Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… -------------------------------------------------------------------

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Athena .lcf export file
by Miranda Vu 09 Aug '24

09 Aug '24

Hello, I think I may have found an issue in Athena regarding the LCF file export. I have been analyzing data using the LCF section of Athena. Everything looks good on the plot within Athena, but my exported file has my weighted components incorrectly labelled. For example, I have the weighted components in Athena correctly displayed here: [cid:image002.jpg@01DAEA68.340F5790] And an Excel plot of the .lcf export file here where the 3 standards are incorrectly labelled: [cid:image004.png@01DAEA68.340F5790] Has anybody else noticed this or found a solution? I have tried closing and re-opening the file, starting up new athena files, and re-ordering the standards with no luck. Thanks, Miranda

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Looking for Nb K-edge spectrum of Nb2O5
by Jiyun Hong 09 Aug '24

09 Aug '24

Dear all, I'm looking for a XAS spectrum of Nb2O5 at Nb K-edge to use as a bulk standard in XANES analysis. If possible, would anyone on the mailing list be willing to share their data with me? Thank you for your help, Jiyun

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Problem with XRF mapviewer post-update
by Sarah Bowie 02 Aug '24

02 Aug '24

Hi all, Apologies if this has already been asked elsewhere. I have previously been using XRF mapviewer with no issues on my MacBook pro (fully updated). Larch recently prompted me to update to the newest version, and following this, XRF mapviewer seems to be unable to open (tries and then immediately closes without any window ever opening). Oddly, all other programs in the Larch folder still work as normal. I've tried removing Larch, redownloading and reinstalling, and still have the same issue. Any suggestions would be much appreciated - I'm definitely regretting the update currently! I was also curious if there's somewhere I could just download an older Larch version? Thanks in advance, Sarah Bowie PhD student School of Environment, Geography and Geoscience University of Portsmouth, UK

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Periodic boundary condition when generating .inp file and scattering paths in GeSn_Larch
by Anis Attiaoui 29 Jul '24

29 Jul '24

Dear All, While generating the .inp file (attached) of a GeSn DFT structure from a .cif file (attached), I noticed some anomalies in the feff path calculation. In this specific case, we should expect Sn to have 4 nearest neighbors in the first shell. However, when the absorbing (Sn) atom is located on the edge of the supercell, the number of nearest neighbors is reduced to 2, which is non-physical. The DFT structure was generated with periodic boundary conditions (PBC). My question is the following: Is it possible to incorporate the PBC in the feff calculation process to generate the right scattering paths, especially for atoms absorbers located on the edge of the supercell? I wanted to know if there are any option in larch to deal with this specific case. I am attaching the .cif and the current .inp files that I obtained of GeSn structure. Thank you so much for your help. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!e… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

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How to model the photoexcited charge transfer on FEFF calculation?
by FAN Dongxiao 27 Jul '24

27 Jul '24

Hello, everyone, I am doing the time-resolved XAFS, pump-pulse technique. Sample is Cu2Ti2O5, the absorber is Cu, the scatter is Ti. With photoexcitation, the one electron is excited from Cu site and transfer to neighbor Ti site. My question is how to model this photoexcited charge transfer on the FEFF software? I have tried as below: First method, To separate the absorber Cu and neighbor scattering Ti with other Cu and Ti ions, I create a cluster and modify the POTENTIALS and ION card: POTENTIALS 0 29 Cu (absorber, charge +1) 1 29 Cu 2 22 Ti 3 8 O 4 22 Ti (neighbor scatter, charge -1) ION 0 -1 ION 4 1 The results shows the chi.dat file is same for with or without ION card. Second method, Use the same cluster as the first method and the use the CONFIG card to model the charge transfer: CONFIG card 2 0 Cu Ar 3d 4 6 4s 0 4p 0 #(lost on electron from 4s) 4 Ti Ar 3d 2 0 4s 2 4p 1 #(receive on electron to 4p) But this method gives error before the run. Can some body tell where I am wrong? Best regards, Fan

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Larch 0.9.80
by Matthew Newville 18 Jul '24

18 Jul '24

Hi Folks, I have released Larch version 0.9.80. It's been a few months since the last announced release, and there have been a few important bug fixes and changes, especially to the Larix GUI. A list of changes is at https://urldefense.us/v3/__https://github.com/xraypy/xraylarch/releases/tag… . If you run Larix, you should be prompted to update. The most obvious changes in this GUI are a) the re-organization of the main menus, and b) that the different Analysis Tabs can now be re-arranged or even removed (and added back when needed). This is so that we can add more Analysis Tabs for different kinds of data processing and different kinds of data. At this point, Larix is still heavily focused on XANES and EXAFS, but we would like to be able to expand this, and still use much of the infrastructure of the GUI. I think I have addressed all the issues raised over the past couple of months and found several more in testing myself. Comments, suggestions, or bug reports are always welcome. --Matt

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Modeling a spinel structure with fractional occupancy
by matthew marcus 12 Jul '24

12 Jul '24

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Re: [Ifeffit] Modeling a spinel structure with fractional occupancy
by Robert Gordon 12 Jul '24

12 Jul '24

"Does anyone have a good idea or tool with which to do this? " Ummm...6 different metal shells at once! https://urldefense.us/v3/__https://www.amazon.ca/Generic-Pack-Sided-Dice-Bo… 10-sided happy Friday, folks! cheers, -R. On 2024-07-12 11:10 a.m., matthew marcus wrote: > A colleague want to fit EXAFS on a NiAl2O4-based material (I don't > have the details). As shown in the attached CIF, Ni (the central atom) > is distributed 60-40 between the 1 and 2 sites, and Al 20-80. I > imagine that to model this, I'll need > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > A colleague want to fit EXAFS on a NiAl2O4-based material (I don't have > the details). As shown in the attached CIF, Ni (the central atom) is > distributed 60-40 between the 1 and 2 sites, and Al 20-80. I imagine > that to model this, I'll need to somehow generate feff.inp files, one > centered around Ni1 and one Ni2, each with neighboring atoms randomly > chosen according to the site occupancies. Does anyone have a good idea > or tool with which to do this? I'd rather not have to write a program > to do that, but will if it's necessary. > mam

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problem Generating feffNNNN.dat with Larch in python
by Anis Attiaoui 12 Jul '24

12 Jul '24

Dear All, I am trying to generate the path files of a DFT structure using larch in python. I will briefly describe the methodology I am following in hope it might help shed some light to the problem I am facing. I start from a .cif file of the relaxed DFT structure of 64-atoms GeSn. Then, I try to evaluate all the possible .inp file of the corresponding absorbing atoms (Sn and Ge). I am attaching the .inp file of one site0 for Sn ( tested it through Artemis and it works fine). Then I try to call the FeffRunner module to extract the corresponding feffNNNN.dat path files that will be used to build the EXAFS spectra. It is in this step that I am facing an issue. It seems that FeffRunner is working but it doesn't generate the corresponding feffNNNN.dat path files. (I am attaching an image of what is produced when I run the FeffRunner module). Below is the python script I used to generate the .inp file as well as the paths via Larch. " from larch.xafs import FeffRunner from larch.xrd.struct2xas import Struct2XAS # read .cif DFT data with ase DFT_path = '/home/ml-dell/Documents/Simulation/exafs/DFT/' cif_file = f'{DFT_path}CIF-00010-T300K.xyz' mat_obj = Struct2XAS(file = cif_file, abs_atom="Ge") for site in range(mat_obj.nabs_sites): mat_obj.set_abs_site(site) #to get information on the coordination environment around absorber atom mat_obj.get_coord_envs_info() mat_obj.get_coord_envs() # use feff to generate .inp mytemplate = None mypath = DFT_path mat_obj.make_input_feff(radius=9.0, template=mytemplate, parent_path=mypath) # now we can run feff to generate the paths via larch feff_inp = f"{mat_obj.outdir}/feff.inp" session = Interpreter() sim = FeffRunner(feff_inp,_larch=session) sim.run() " I will be thankful for any suggestions on how to fix this issue. Best regards, Dr. Anis Attiaoui, Stanford University, GLAM Dept. Material Science and Engineering, McCullough Building, 476 Lomita Mall, Stanford California, USA, 94305 Office/shipping: McC-203 Tel: +1(650)485-0501 Web: https://urldefense.us/v3/__https://mcintyre.stanford.edu__;!!G_uCfscf7eWS!c… <https://urldefense.us/v3/__https://mcintyre.stanford.edu/__;!!G_uCfscf7eWS!… >

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XAS beamline scientist position open at NSLS II
by Stavitski, Eli 10 Jul '24

10 Jul '24

Dear all, Beamline scientist position is now open at the Inner Shell Spectroscopy beamline at the National Synchrotron Light Source II. ISS beamline is an XAS and high energy resolution spectroscopy beamline with a lot of research opportunities and vibrant user community. Apply at https://urldefense.us/v3/__https://jobs.bnl.gov/job/upton/beamline-scientis… https://urldefense.us/v3/__https://jobs.bnl.gov/job/upton/beamline-scientis… POSITION DESCRIPTION The NSLS-II is seeking am experienced scientist to support the user program, operations and new developments at the Inner Shell Spectroscopy (ISS) beamline, working closely with the ISS team and Hard X-ray Scattering and Spectroscopy program staff. The selected candidate will participate in internal and external scientific and technical collaborations that leverage the unique capabilities of ISS and NSLS-II. Brookhaven National Laboratory and the Energy and Photon Sciences Directorate are committed to your success. We offer a supportive work environment and the resources necessary for you to succeed. Essential Duties and Responsibilities: Supports the user program at the ISS beamline. Develops and operates beamline equipment to enhance the beamline productivity and impact Collaborates with NSLS-II and BNL staff, and external users to advance scientific and technical research and development. Contributes to the design, implementation, and maintenance of in-situ/operando capabilities at the beamline and Operates and develops high energy resolution spectrometers. Supports and develops beamline software infrastructure to enable experiments with real-time data analysis and modeling capabilities. Assists with preparation of funding proposals and beamline progress reports . Required Knowledge, Skills, and Abilities: PhD. in physics, materials science, chemistry or related field, and at least 2 years of postdoctoral experience. Ability to work effectively in a team environment with a diverse group of scientists, engineers, technical staff, and users. Proven track record of using synchrotron X-ray spectroscopy including high energy resolution techniques Demonstrated experience using Python (or similar high-level, general-purpose programming language) for data visualization/reduction/analysis. Experience with XAS data analysis. Excellent written and oral communication skills. Preferred Knowledge, Skills, and Abilities: Demonstrated personal interest in research, methodology and instrumentation development aligned with the scientific mission of the NSLS-II. Experience with collaborative code development using version control platforms. Prior experience in the design, installation, commissioning, and/or operation of synchrotron beamline components. Experience in quantum chemistry-based XAS data analysis Experience in high throughput measurements and data analysis. Experience in supporting users at a user facility. Other Information: Brookhaven Laboratory is committed to providing fair, equitable and competitive compensation. This is a multi-level role and the full salary range for this position is $101200 - $184000 / year. You will be placed at the level and salary commensurate with your experience. Salary offers will be commensurate with the final candidate’s qualification, education and experience and considered with the internal peer group. Brookhaven employees are subject to restrictions related to participation in Foreign Government Talent Recruitment Programs, as defined and detailed in United States Department of Energy Order 486.1A. You will be asked to disclose any such participation at the time of hire for review by Brookhaven. The full text of the Order may be found at: https://urldefense.us/v3/__https://www.directives.doe.gov/directives-docume… [Image] Eli Stavitski Scientist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist. Phone: 631-344-8641 Email: istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 [NSLS-II ISS]<https://urldefense.us/v3/__https://www.bnl.gov/nsls2/beamlines/beamline.php… >[Title: LinkedIn - Description: image of LinkedIn icon]<https://urldefense.us/v3/__https://www.linkedin.com/in/eli-stavitski-a033a7… >[Google, scholar Icon in SuperTiny]<https://urldefense.us/v3/__https://scholar.google.com/citations?user=cVxErO… >

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Ni standard spectra
by Qiang 08 Jul '24

08 Jul '24

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Upcoming Q2XAFS, Data Formats, and request for data files
by Matthew Newville 07 Jul '24

07 Jul '24

Hi Folks, As some of you may have heard, there will be a virtual Q2XAFS (Quality and Quantity for X-ray Absorption Fine Structure) symposium series this summer, with presentations from Working Groups defined and formed at the 2023 Q2XAFS meeting in Melbourne last August. Details for this summer’s series are at https://urldefense.us/v3/__https://sites.google.com/view/q2xafs/home__;!!G_… , including a registration form. I will be giving the first of the presentations, on July 26 (0600 Seattle, 1400 London, 2200 Tokyo), describing the work of a Working Group on Data Formats and Metadata. Our Working Group has made good progress on defining a NeXuS/HDF5 definition for XAS data which is compatible with XDI and fits the typical NeXuS/HDF5 requirements. We have started working on tools to convert between XDI, NeXuS/HDF5, and even to help convert “raw” beamline data into this format, to make it easy to convert raw beamline data into these two formats for uploading to databases, data portals, supplemental information, etc. We have a pretty good collection of “real-world, as-collected” XAS data (see https://urldefense.us/v3/__https://github.com/XraySpectroscopy/pynxxas/tree… ) that we are working with as test cases. Please let us know if the data you get from your facility is in some other format (including binary files such as HDF5, or even into some database or “document store”). That is, if Larix or Athena struggles to read your data files, please let us know. If you can, please send an example file (you can send it directly to me or use https://urldefense.us/v3/__https://github.com/XraySpectroscopy/pynxxas__;!!… ). Thanks, --Matt

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Re: [Ifeffit] High-r range EXAFS fitting by Larch
by Robert Gordon 06 Jul '24

06 Jul '24

Hi Fan, I tried simulating BaSnO3 in Feff and played with the NLeg card to see the influence of multiple scattering: Blue curve is Nleg = 2 (backscattering only); red is Nleg=3 (backscatter + triangular multiple-scattering) Calcs done with DEBYE 100 307, CRITERIA 0 0, RPATH 9.5 Multiple-scattering (focused) seems to be strongly contributing both below 4Ang and below 8Ang. It seems possible that multiple scattering around the nearest neighbours may be more significant than the backscattering from 8.14Ang away. I haven't tried playing with decreasing the cluster size but keeping RPATH at 9.5Ang to see if NN MS is the culprit, but this may give you some ideas of what to check. cheers, -R. On 2024-07-05 1:45 a.m., FAN Dongxiao wrote: > Dear All, I met a problem about the misfit of EXAFS at high-range > (around 8 angstrom). My target is the B site EXAFS of perovskite > structure (BaSnO3, a=b=c=4. 105 angstrom) I want to study the > displacement correlation between the Sn and the > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > > Dear All, > > I met a problem about the misfit of EXAFS at high-range (around 8 > angstrom). > > My target is the B site EXAFS of perovskite structure (BaSnO3, > a=b=c=4.105 angstrom) > > I want to study the displacement correlation between the Sn and the > neighboring Sn atoms. > > For the first, second, and third Sn neighboring shells, the fitting is > good, but the Sn-Sn4 is bad in both amplitude and phase. > > I try to include the third cumulant, not become better. > > Can anybody tell me what’s the problem? > > I suspect the high frequency background signal of k space to produce > non-structure contribution in the FT spectra. > > But the data is very clean, I think this should not be the problem. > > Best, > > Fan >

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Re: [Ifeffit] High-r range EXAFS fitting by Larch
by Robert Gordon 06 Jul '24

06 Jul '24

Hi Fan, I tried simulating BaSnO3 in Feff and played with the NLeg card to see the influence of multiple scattering: Blue curve is Nleg = 2 (backscattering only); red is Nleg=3 (backscatter + triangular multiple-scattering) Calcs done with DEBYE 100 307, CRITERIA 0 0, RPATH 9.5 Multiple-scattering (focused) seems to be strongly contributing both below 4Ang and below 8Ang. It seems possible that multiple scattering around the nearest neighbours may be more significant than the backscattering from 8.14Ang away. I haven't tried playing with decreasing the cluster size but keeping RPATH at 9.5Ang to see if NN MS is the culprit, but this may give you some ideas of what to check. cheers, -R. On 2024-07-05 1:45 a.m., FAN Dongxiao wrote: > Dear All, I met a problem about the misfit of EXAFS at high-range > (around 8 angstrom). My target is the B site EXAFS of perovskite > structure (BaSnO3, a=b=c=4. 105 angstrom) I want to study the > displacement correlation between the Sn and the > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > > Dear All, > > I met a problem about the misfit of EXAFS at high-range (around 8 > angstrom). > > My target is the B site EXAFS of perovskite structure (BaSnO3, > a=b=c=4.105 angstrom) > > I want to study the displacement correlation between the Sn and the > neighboring Sn atoms. > > For the first, second, and third Sn neighboring shells, the fitting is > good, but the Sn-Sn4 is bad in both amplitude and phase. > > I try to include the third cumulant, not become better. > > Can anybody tell me what’s the problem? > > I suspect the high frequency background signal of k space to produce > non-structure contribution in the FT spectra. > > But the data is very clean, I think this should not be the problem. > > Best, > > Fan >

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Re: [Ifeffit] High-r range EXAFS fitting by Larch
by Robert Gordon 06 Jul '24

06 Jul '24

Hi Fan, I tried simulating BaSnO3 in Feff and played with the NLeg card to see the influence of multiple scattering: Blue curve is Nleg = 2 (backscattering only); red is Nleg=3 (backscatter + triangular multiple-scattering) Calcs done with DEBYE 100 307, CRITERIA 0 0, RPATH 9.5 Multiple-scattering (focused) seems to be strongly contributing both below 4Ang and below 8Ang. It seems possible that multiple scattering around the nearest neighbours may be more significant than the backscattering from 8.14Ang away. I haven't tried playing with decreasing the cluster size but keeping RPATH at 9.5Ang to see if NN MS is the culprit, but this may give you some ideas of what to check. cheers, -R. On 2024-07-05 1:45 a.m., FAN Dongxiao wrote: > Dear All, I met a problem about the misfit of EXAFS at high-range > (around 8 angstrom). My target is the B site EXAFS of perovskite > structure (BaSnO3, a=b=c=4. 105 angstrom) I want to study the > displacement correlation between the Sn and the > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > > Dear All, > > I met a problem about the misfit of EXAFS at high-range (around 8 > angstrom). > > My target is the B site EXAFS of perovskite structure (BaSnO3, > a=b=c=4.105 angstrom) > > I want to study the displacement correlation between the Sn and the > neighboring Sn atoms. > > For the first, second, and third Sn neighboring shells, the fitting is > good, but the Sn-Sn4 is bad in both amplitude and phase. > > I try to include the third cumulant, not become better. > > Can anybody tell me what’s the problem? > > I suspect the high frequency background signal of k space to produce > non-structure contribution in the FT spectra. > > But the data is very clean, I think this should not be the problem. > > Best, > > Fan >

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High-r range EXAFS fitting by Larch
by FAN Dongxiao 05 Jul '24

05 Jul '24

Dear All, I met a problem about the misfit of EXAFS at high-range (around 8 angstrom). My target is the B site EXAFS of perovskite structure (BaSnO3, a=b=c=4.105 angstrom) I want to study the displacement correlation between the Sn and the neighboring Sn atoms. For the first, second, and third Sn neighboring shells, the fitting is good, but the Sn-Sn4 is bad in both amplitude and phase. I try to include the third cumulant, not become better. Can anybody tell me what's the problem? I suspect the high frequency background signal of k space to produce non-structure contribution in the FT spectra. But the data is very clean, I think this should not be the problem. Best, Fan

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Re: [Ifeffit] Creating a structure from EXAFS fitting
by Robert Gordon 27 Jun '24

27 Jun '24

Hi Lisa, Starting from a similar crystal structure could work. Alternatively, building a basic "crystal" structure using symmetry P1 and just putting the atoms where you want them would be feasible - tedious if you have a lot of atoms, easier if you know you have higher symmetry. e.g. Test Symmetry P1 * i.e. no symmetry a = 10 b = 10 c = 10 *Angstroms, easy to scale alpha = 90 beta = 90 gamma = 90 * so metrically cubic Central atom 0.000 0.000 0.000 * at origin, could always displace by 1/2 lattice constants to keep all in the unit cell 1st NNa 0.220 0.000 0.000 * 1st nns at 2.2 Angstroms away 1stNNb 0.000 0.220 0.000 1stNNc 0.000 0.000 0.220 1stNNd -0.220 0.000 0.000 etc... I've used this for modelling molecules, surfaces (with deposited films) as well as 3D crystals. It is a bit of brute force, but should work in any crystal visualization program... cheers, -R. On 2024-06-27 8:47 a.m., Lisa Langlois wrote: > Hello XAFS friends. I would like to know how to create a structure > model for a molecule that was measured with EXAFS, then modeled using > the typical strategies? - So, in the end you have some distances and > bond angles from the central atom > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > Hello XAFS friends. > I would like to know how to create a structure model for a molecule > that was measured with EXAFS, then modeled using the typical > strategies? - So, in the end you have some distances and bond angles > from the central atom to the first, and maybe second neighbor. > I was thinking that you start from a similar crystal structure and > then adapt that model using the numbers you got from EXAFS fitting, > using for example the Vesta program. > Best wishes, > Lisa. > > > > > Lisa Langlois, PhD > Beamline scientist > Rm 144 > Phone: +1 225-578-9341 > LSU-CAMD > 6980 Jefferson Hwy, Baton Rouge, LA 70806 > https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!adSZ4… > <https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!ZSSym…> > >

1 0

Creating a structure from EXAFS fitting
by Lisa Langlois 27 Jun '24

27 Jun '24

Hello XAFS friends. I would like to know how to create a structure model for a molecule that was measured with EXAFS, then modeled using the typical strategies? - So, in the end you have some distances and bond angles from the central atom to the first, and maybe second neighbor. I was thinking that you start from a similar crystal structure and then adapt that model using the numbers you got from EXAFS fitting, using for example the Vesta program. Best wishes, Lisa. Lisa Langlois, PhD Beamline scientist Rm 144 Phone: +1 225-578-9341 LSU-CAMD 6980 Jefferson Hwy, Baton Rouge, LA 70806 https://urldefense.us/v3/__https://www.lsu.edu/camd/__;!!G_uCfscf7eWS!ZSSym…

1 0

Al and Si references
by Amine EL MESSBAHI 10 Jun '24

10 Jun '24

Hi, Where can I find some Al and Si K-edge normalized data? Thank you, Amine El Messbahi email: amineelmessbahi(a)outlook.com

2 1

alpha and σ2 values for EXAFS data fitting in Artemis came negative
by Arpita Nandy 04 Jun '24

04 Jun '24

Hello Everyone, During one of the data fittings in Artemis, alpha and σ2 came negative!!! What is/are the reason/s behind it? The corresponding file is attached... Regards, Arpita Nandy, PhD student Saha Institute of Nuclear Physics, India

1 0

Issue about plotting simulated EXAFS in Larix
by AowenLi 24 May '24

24 May '24

Dear Matt, I am trying to simulate a theoretical EXAFS with a DFT calculated CIF file via Larix. I performed a FEFF calculation on the CIF file and imported a path to the FEFF fitting panel. However, I didn't get any results when I clicked on the "Plot Current Model" bottom. I get the following error message: TypeError: unsopported format string passed to NoneType.__format__. Could you please help me? Thank you in advance. Best regards, Aowen

2 2

Request for Assistance with Data Import Error of Athena 0.9.26
by Cai, Rui 19 May '24

19 May '24

To whom it may concern, Here's Rui, a PhD student at Georgia Tech. I am writing this email to seek your assistance regarding an import warning I encountered while importing SSRL XAS data collected by uXAS server into Athena 0.9.26, as the Screenshot_Import Warning shows. According to the response from the Ifeffit mailing list, I clicked on all buttons in "Plugin registry", as the Screenshot_Plugin registry shows, and tried to import the same data again. However, there was still the same import warning with the another Athena warning. The data caused error has been attached. I would greatly appreciate it if you could provide guidance on how to resolve this matter. Thank you for your attention to this matter. I look forward to your prompt response. Best regards, Rui Cai

4 3

Choice of E0 in the presence of a huge pre-peak
by Jan-Benedikt Weiss 14 May '24

14 May '24

4 3

Re: [Ifeffit] Trouble downloading Demeter for mac
by Fowler, Joseph W. (Assoc) 09 May '24

09 May '24

Dear Christopher, I have bad news for you. I’m the official MacPorts maintainer of Demeter, and I have not been able to overcome the problems you’re seeing. I’ve seen them too over the last 1-2 years. The ifeffit package has unaddressed problems that have become fatal. I believe they correspond to small incompatibilities with the latest compilers. Over time, code that used to be allowed eventually became deprecated with a warning, and is now an error. As Matt helpfully explained (thanks, Matt!), ifeffit is basically replaced by Larch, and no one wants to update ifeffit to fix problems of that sort. Unfortunately, Demeter, Artemis, and Athena do still depend on ifeffit, and there’s no clear path to integrate that front end with the physics back end of Larch. Or at least, I discussed this a few years ago with the Demeter and Larch authors, and they didn’t see one. If indeed Larch can replace (99% of) the functionality that used to be in the Demeter and ifeffit ports in the MacPorts project, then I am inclined to remove those ports entirely from MacPorts. Otherwise, they are just sitting there, broken. By the way, I have created a `py-xraylarch` port. You could use it, although I don’t particularly recommend that. I’d suggest you use its usual installation options (such as `pip install xraylarch`). Honestly, the pip-based installation is getting so capable these days that I question why we even need MacPorts to package up any python code at all. (Should I ask that in public?) Why not use the MacPorts port? Because I’m the maintainer but not an actual user—I don’t regularly update upstream versions or make it work with the latest Python because of all its dependencies that first have to be updated. For instance, last summer I tried to make a Python 3.11 version, but I was stymied by the lack of Python 3.11 releases by some dependency. I lost interest and haven’t checked in months whether that was resolved. On the other hand, you (obviously) already installed MacPorts, so it’s at least an option if the pip method gives you trouble. Best wishes, Joe Fowler NIST Boulder Labs p.s. Here’s a politically charged question. Has this mailing list’s name falling out of sync with its range of topics, given that ifeffit is finished? On May 9, 2024, at 10:51 AM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.us/v3/__https://gcc02.safelinks.protection.outlook.com/?… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… > or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@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. Trouble downloading Demeter for mac (Christopher Reitwiesner) 2. Re: Trouble downloading Demeter for mac (Matt Newville) From: Christopher Reitwiesner <christopher.reitwiesner(a)uconn.edu<mailto:christopher.reitwiesner@uconn.edu>> Subject: [Ifeffit] Trouble downloading Demeter for mac Date: May 8, 2024 at 1:37:46 PM MDT To: ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> This Message Is From an External Sender This message came from outside your organization. Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… <https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw…> if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner From: Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> Subject: Re: [Ifeffit] Trouble downloading Demeter for mac Date: May 9, 2024 at 10:51:01 AM MDT To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> This Message Is From an External Sender This message came from outside your organization. Hi Christopher, Installing Demeter on macOS has always been painful. The MacPorts solution can work sometimes, but it does require some expertise to use MacPorts and to think about the software as something that needs to be compiled and built. Some of the packages needed (especially "ifeffit" and "wxPerl") are just not very well supported. At this point, I cannot recommend using the old ifeffit - it has too many known issues that will not be fixed. I know that using a virtual Windows interface like Parallels works for some people. But, if you are just getting started, I highly recommend installing Larch, either using the installer at https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.… <https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.…>(you'll have to go into Privacy & Security and allow the installer from "an untrusted source" to run. Also, it might say that it has less than a minute to go for about 5 minutes ;) ), or by downloading and running the GetLarch script at https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.… <https://urldefense.us/v3/__https://xraypy.github.io/xraylarch/installation.…> and running that from a Terminal. With this installed, the Larix App (in the Larch folder on your Desktop: also, the first launch might take a minute) will run and do basically everything that Athena and Artemis do. There are some differences, and there may be a missing feature or two, but many things are better. In general, comments, complaints, and suggestions are welcome. We aim for "highly compatible and familiar" with Demeter and "better than" the underlying ifeffit library. And, it does install and run on macOS. It turns out that most of the development and testing happens on macOS. Cheers, --Matt On Wed, May 8, 2024 at 2:54 PM Christopher Reitwiesner <christopher.reitwiesner(a)uconn.edu<mailto:christopher.reitwiesner@uconn.edu>> wrote: This Message Is From an External Sender This message came from outside your organization. Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… <https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw…> if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf…> Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options… <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options…> -- --Matt Newville <newville at cars.uchicago.edu<https://urldefense.us/v3/__http://cars.uchicago.edu__;!!G_uCfscf7eWS!fZTlh9…>> 630-327-7411 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinf… Unsubscribe: https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options…

1 0

Trouble downloading Demeter for mac
by Christopher Reitwiesner 09 May '24

09 May '24

Hello! I am an undergraduate researcher looking to utilize Demeter. Unfortunately I only have access to a mac. I followed the instructions on the github page. Downloading MacPorts went fine, so did installing Command Line Developer Tools. However when trying to install demeter from Terminal, I eventually run into this error message: Building ifeffit Error: Failed to build ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ifeffit/ifeffit/main.log for details. Error: Follow https://urldefense.us/v3/__https://guide.macports.org/*project.tickets__;Iw… if you believe there is a bug. Error: Processing of port demeter failed I am at a loss on where to go from here and was wondering if someone could point me in the right direction. Thank you for your time! Christopher Reitwiesner

2 1

Save the date: SCC short course at BNL, Oct. 29-31, 2024
by Anatoly Frenkel 03 May '24

03 May '24

Dear subscribers: Please pass it along to your group members who may be interested in this opportunity. In continuation of the annual tradition at the Synchrotron Catalysis Consortium (SCC) at Brookhaven National Laboratory to organize and run XAFS short courses there since 2005, we are planning a first specialized course targeting catalysis and electrocatalysis researchers. The course will follow a successful model of our XAFS courses: the lectures (on the topics ranging from in situ/operando characterization and multimodal instrumentation to data analysis) and software demonstrations on the first two days, followed by the hands-on data analysis session on the last day. The program is being finalized, and we are in the process of getting the necessary approvals from BNL and DOE. In the meantime, please, mark your calendars and contact me if you have any questions. Anatoly ******** On sabbatical leave at Weizmann Institute of Science, Israel ******** ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://urldefense.us/v3/__https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adz… > https://urldefense.us/v3/__http://you.stonybrook.edu/frenkel__;!!G_uCfscf7e… Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL https://urldefense.us/v3/__http://you.stonybrook.edu/scc2__;!!G_uCfscf7eWS!… Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973 Email: frenkel(a)bnl.gov https://urldefense.us/v3/__https://www.bnl.gov/staff/frenkel__;!!G_uCfscf7e… -------------------------------------------------------------------

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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

2 1

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.

3 4

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

4 3

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

1 0

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

1 0

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

2 1

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!

3 2

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

2 1

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

1 0

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

25 Mar '24

1 0

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 ================================================

2 1

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

1 0

[IFEFFIT] Polarized FEFF calculation
by Soyoung Kim 11 Mar '24

11 Mar '24

Dear XAFS community, I have a series of Ru K-edge data on a single-crystal RuO2 sample measured at different incident X-ray angles. Because of the linear polarization of X-rays, the EXAFS of this single-crystal sample depends on the X-ray angle. I am trying to fit the four EXAFS spectra simultaneously with one set of parameters to extract the deltaR and MSRD parameters of this sample. For oriented samples, N for a certain single scattering path is supposed to be proportional to 3*cos^2(θ), where θ is the angle btwn the X-ray's e-vector and the absorber-scatterer vector. Instead of manually calculating the 3cos^2(θ) for all of the scattering paths in RuO2 (there are 7 single and 3 multiple scattering paths that need to be included to achieve a good fit with a reference RuO2 powder sample), I decided to use the polarization card in my FEFF input. For example, for one of the X-ray angles, the e-field vector would be (1, 0, 0), so I added the line "POLARIZATION 1 0 0" in the FEFF input file. Running this input file gave me a list of paths that had different importance values for each path compared to the non-polarized (isotropic) calculation. *Since "importance" is the relative magnitude of each path's scattering contribution (integration of the chi(k)), I thought that it would be proportional to 3cos^2(θ).* That is, for path i from a FEFF calculation for angle a, the "importance" (abbreviated as "Imp") of that path would be: Imp(a)_i = C(a) * Imp(iso)_i * 3cos^2(θ_i) where C(a) is a constant for each angle that accounts for the fact that importance values are relative (because it is scaled so that the first path in the list has an importance of 100). Now, I wanted to check whether the polarized FEFF calculations really follow this relationship underlined above. So, I tried manually calculating the values of 3cos^2(θ) for two of the paths from the same polarized FEFF calculation, then plug them into the above equation to get C(a). But, as the table below shows, the C(a) values are not the same. FEFF 1 has a disagreement that is small enough to ignore, but the disgareement of C(a) values for The disagreement is small enough to ignore for FEFF 1, but for FEFF 2 and 3 the disagreements are quite large. [image: image.png] *FEFF 1, 2, 3 designate individual polarized FEFF calculations. FEFF 1 was with polarization vector = (1, 0, 0). FEFF 2 and 3 were with polarization vector = (0.85, 1.13, 0). For this polarization, the two Ru sites gave different lists of paths. I do think the qualitative trend of the "importance" values in the polarized FEFF calculations is correct, and I can get a bad but not-disastrous fit from simultaneously fitting the data from different angles. However, the above analysis makes me wonder whether the "importance" values from polarized FEFF are truly proportional to 3cos^2(θ), and whether my fitting models for different angles, which I derived from the polarized FEFF calculations, are correct. An alternative would be to manually calculate 3cos^2(θ) for all the paths, but I'm not sure how to calculate it for multiple scattering paths. One note, I am running the FEFF calculation with Larix to get the importance values (labeled as "amp ratio" in the list.dat file, in the FEFF output folder). I wonder if the default settings for getting these amp ratios are not accurate enough for my purposes. It would be nice if I could just pull out the 3cos^2(θ) terms from the FEFF calculations... Anyways, thank you very much for reading this rather lengthy question. Hope it makes sense, and I would appreciate any help regarding this. Best, Soyoung

3 5

Meaning of ldosNN
by jaskirat brar 05 Mar '24

05 Mar '24

Dear list I have a question regarding DOS calculations using feff. (I am using feff8.2) I have calculated the DOS of V-doped Ni, with Ni as the central atom and Ni and V as neighboring atoms. The potential indexes are 0 - Ni 1 - Ni 2 - V I have obtained ldos00.dat, ldos01.dat, and ldos02.dat files corresponding to the l-projected DOS for the NNth potential index. I am not clear about the meaning of ldosNN. Does it correspond to the DOS of the central atom modified by the presence of the potential index NN? If yes, does ldos02 contain the effect of both potentials 01 and 02 or that of just 02? If this is not the case, what does ldosNN mean? Kindly provide your comments to clarify this. Thanks in advance. Jaskirat Brar FMP Lab, South Campus IIT Mandi, H.P., India

4 10

Re: [Ifeffit] Ifeffit Digest, Vol 252, Issue 21
by Ryuichi Shimogawa 21 Feb '24

21 Feb '24

1 0

test/validation sample for air-sensitive sample cells?
by Gerald T. Seidler 21 Feb '24

21 Feb '24

Dear XAFS community, We've been developing air-sensitive sample cells for several of our XAFS experiments, but we don't have a good way of characterizing how well they actually reject air and water. Does anyone have recommendations for easily available 3d transition metal compounds that have a 'reasonable' amount of air sensitivity for purposes of sample call validation? Any suggestions for other methods to validate performance? We would grind the sample and form a pellet with a degassed binder, in a glovebox or glovebag. With thanks, Jerry -- *Gerald Seidler* *Professor, Physics Department* *University of Washington* *https://urldefense.us/v3/__http://faculty.washington.edu/seidler/index.html__;!!G_uCfscf7eWS!bc8I7gtiYjYV5xc8tbm1xHCOWp8emLi4nZo7rvTjsDdGw3JMBVgas9avdYSiT995CKzLi-eu2GCc0RfkE-Cz2uX2VeU-3A$ <https://urldefense.us/v3/__http://faculty.washington.edu/seidler/index.html… >* *seidler(a)uw.edu <seidler(a)uw.edu>*

4 3

Larix.desktop on Arch Linux AttributeError: 'list' object has no attribute 'shape'
by Chris Vijeu 19 Feb '24

19 Feb '24

Hello, So I recently installed Larch on two different machines running two different distributions of Arch (Manjaro and EndeavourOS). When I am starting Larix.desktop from the terminal and open a .xlsx data file with two columns (energy and intensity), I get the following error: Traceback (most recent call last): File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 1162, in onReadDialog self.onRead(path) File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 1187, in onRead self.show_subframe('readfile', ColumnDataFileFrame, filename=path, File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 1114, in show_subframe self.subframes[name] = frameclass(self, **opts) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxlib/columnframe.py", line 870, in __init__ self.set_energy_units() File "/home/chris/xraylarch/lib/python3.11/site-packages/larch/wxlib/columnframe.py", line 1208, in set_energy_units ncol, npts = workgroup.data.shape ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape' I haven't modified any of the respective files at all. This is what the programme came as. Chris Cristian Vijeu, Postgraduate PhD Student, Materials for Energy and Electronics Division of Natural Sciences

2 1

Fe K-edge maghemite (gamma-Fe2O3)
by Christian Wittee Lopes 17 Feb '24

17 Feb '24

Dear XAFS community, Does anyone have a Fe K-edge XAS spectrum of maghemite (gamma-Fe2O3) sample or standard? Thank you in advance. Best, Christian Wittee Lopes -- Christian Wittee Lopes Professor Adjunto *Departamento de Química - Setor de Ciências Exatas* Universidade Federal do Paraná (UFPR) *Curitiba - Paraná* *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>*

5 5

XAS data on U-oxychloride standards
by Nirmalendu Patra 15 Feb '24

15 Feb '24

Dear All, Can anyone share the XAS data collected at U L3-edge on various Uranium Oxychloride standards. ? Thank you. Kind regards, *Nirmalendu Patra*

1 0

Problem with cif files using Larch
by Otal Eugenio 15 Feb '24

15 Feb '24

Dear all. I am trying to generate the path for fitting Mn and Ni K edge at LiMn1.5Ni0.5O2 using cif files from ICSD. I receive this error: *Elements: ['Li', 'Mn', 'Ni', 'O']Sites: [2.08337619 6.16682619 6.08352381] Li:0.980Traceback (most recent calls last): File "C:\Users\Me\xraylarch_2023_10\Lib\site-packages\larch\wxlib\cif_browser.py", line 447, in onShowCIF sites = ['%d' % (i+1) for i in range(len(sites))] ^^^^^^^^^^TypeError: object of type 'PeriodicSite' has no len()* I also attached the cif. Any hint to go forward? 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 ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯

3 3

Ir standards
by Ольга Филимонова 13 Feb '24

13 Feb '24

Hello! Does everyone have standards of metallic Ir, IrO2 etc.? (L3-edge, both XANES and EXAFS would work). Thank you! Sincerely, Olga -- Olga Filimonova Post-doc researcher - BM28 - XMaS Office: 30-1-24 Extension: 2436 European Synchrotron Radiation Facility (ESRF), Grenoble, France

2 1

weak scattering from second-nearest neighbors for single atom catalysts
by Qiang 08 Feb '24

08 Feb '24

Hi everyone, I would like to have a discussion about the common EXAFS for single atom catalysts. It is usually observed that there is only one strong peak around 1.5A in EXAFS, and it is attributed to the nearest neighbors of O or N. Take an example of Pt1/CeO2 catalyst. Pt single atom is coordinated with a few oxygens, i.e., PtOx. These oxygens constitute the first shell of Pt. It is supposed that these O should also attach to the metal element of the support (Ce here). So there is also Pt-O-Ce structure. Why it doesnot have strong scattering peak in EXAFS? Is it that because the Pt-O-Ce formed is not ordered, or it is actually not a bond just some weak contact? Thank you very much. Qiang

3 2

Larch version up problem
by 정은석 07 Feb '24

07 Feb '24

Hello~ I used Larch 0.9.71. until now. However, I would like to update larch and I reinstall anaconda and larch. I installed Larch 0.9.74. as following installation guide I didn't have any problems during the installation process. However, I faced problems during feffit fitting. Before, I used feffit fitting in larch 0.9.71., and then I hadn't had any problems. I only changed larch as new version. What am I doing? When I run feffit fitting, I have debugs as the below: ------------------------------------------------------------------------------------------------------------------------- File "c:\Users\Administrator\Desktop\RL\feffit_error_test\test-feffit.py", line 51, in <module> out = feffit(pars, dset) ^^^^^^^^^^^^^^^^^^ File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 645, in feffit ds.prepare_fit(params=params, other_hashkeys=dset_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 374, in prepare_fit self._generate_hashkey(other_hashkeys=other_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 291, in _generate_hashkey dat = [self.data.ek0, self.data.e0, self.data.rbkg] ^^^^^^^^^^^^^ AttributeError: 'Group' object has no attribute 'ek0' ---------------------------------------------------------------------------------------------------------------------- -- Best regards, Ph. D. Eun-Suk Jeong X-ray absorption fine structure(EXAFS+XANES) Mobile:+82-10-4628-9896

2 8

Larch version up problem in Python, Window 10
by 정은석 03 Feb '24

03 Feb '24

Hello~ I have used Larch 0.9.71. until now. However, I would like to update larch and I reinstall anaconda and larch. I installed Larch 0.9.74. as following installation guide I didn't have any problems during the installation process. However, I faced problems during feffit fitting. Before, I used feffit fitting in larch 0.9.71., and then I hadn't had any problems. I changed larch as new version. What am I doing? When I run feffit fitting in python, I have debugs as the below: ------------------------------------------------------------------------------------------------------------------------- File "c:\Users\Administrator\Desktop\RL\feffit_error_test\test-feffit.py", line 51, in <module> out = feffit(pars, dset) ^^^^^^^^^^^^^^^^^^ File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 645, in feffit ds.prepare_fit(params=params, other_hashkeys=dset_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 374, in prepare_fit self._generate_hashkey(other_hashkeys=other_hashkeys) File "C:\ProgramData\anaconda3\envs\xraylarch\Lib\site-packages\larch\xafs\feffit.py", line 291, in _generate_hashkey dat = [self.data.ek0, self.data.e0, self.data.rbkg] ^^^^^^^^^^^^^ AttributeError: 'Group' object has no attribute 'ek0' ---------------------------------------------------------------------------------------------------------------------- The data(EXAFS(k)), which are inputted for feffit, have two column, k and chi. As you know, it doesn't have ek0. -- Best regards, Ph. D. Eun-Suk Jeong X-ray absorption fine structure(EXAFS+XANES) Mobile:+82-10-4628-9896

1 0

Query: abnormal FT-EXAFS peak at ~1.1A
by Huaming 30 Jan '24

30 Jan '24

Hello! I faced an issue with fitting of FT-EXAFS data (Rh@zeolite) with Artemis. There is one distinct peak located at ~1.1 angstron. The intensity is comparable to the nearby peak of Rh-O scattering. I wonder the peak (~1.1A) is a real peak or just noise. Raw data is enclosed. Another question is why S02 can be negative in data fitting with Artemis. Cheers, Huaming

1 0

Query: Demeter
by Robbie Taylor 24 Jan '24

24 Jan '24

Good Afternoon, Hope you are well! Please could you advise when Demeter was last updated? And if it is still in active development / regularly bug fixed? Best wishes, Robbie Taylor (he/him) | Software Officer - Vendor Management | IT & Digital | Manchester Metropolitan University 8th Floor | Bridgewater House | Whitworth Street | Manchester, M1 6LT | United Kingdom |[cid:image001.jpg@01DA4A1A.9404F950] [cid:image002.jpg@01DA4A1A.9404F950] Before acting on this email or opening any attachments you should read the Manchester Metropolitan University's email disclaimer available on its website at mmu.ac.uk/emaildisclaimer<http://www.mmu.ac.uk/emaildisclaimer> "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

3 2

bug in Athena
by Alexander Zherebker 24 Jan '24

24 Jan '24

Hello! I faced an issue with 0.9.26 Athena. Doing LCF the option for weights doesn't really work so I keep getting negative components. Cheers, Alex

2 1

Question about mixed second coordination shell
by Otal Eugenio 18 Jan '24

18 Jan '24

Dear all, Happy New Year! I am dealing with the fitting of NaMn0.3Fe0.4Ni0.3O2 second shell. I have Mn, Ni, and Fe at 2.9772Å and Na at 3.1859Å, showing only one shell. If I use any of the transition metals (dZ <5) for fitting the second coordination shell. fitting is fine, but when I introduce the Na path, the fitting has no sense, CN_Na grows and also its error. Even including Na, I have Nvary = 10 and Ninp = 13.98, so I am getting out of ideas and nothing helpful in the ifeffit Archive until now. Is there any strategy for dealing with mixed second coordination shells? I am attaching the file exported from Larch and the cif file. 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 ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯

4 7

Inquiry About Demeter's Capabilities in Simulating Spectra from Structures
by 徐微 17 Jan '24

17 Jan '24

Dear IFEFFIT Team, I hope this message finds you well. I am writing to inquire about the capabilities of the Demeter software suite, specifically regarding its ability to simulate spectra from given structural data. I am particularly interested in understanding whether Demeter can be used to generate X-ray absorption spectra based on detailed structural information. This functionality would be extremely valuable for my work. Could you please provide information on whether Demeter includes this feature? Additionally, if there are any relevant guidelines or documentation on how to use Demeter for this purpose, I would greatly appreciate if you could point me in the right direction. Thank you for your time and assistance. I look forward to your response. Best regards, XUwei

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 250, Issue 5
by Ryan Parmenter 18 Dec '23

18 Dec '23

Hi Matt, Thank you for your detailed response. Given my limited expertise in this area, I'm currently grappling with the intricacies of Python scripts, and I wouldn't typically enter the Larch buffer. I recognise that this is a current limitation on my part and am actively addressing it by attending Python workshops to enhance my understanding soon. When I input print(peakresult.result.fit_report()), the Larch command doesn't yield any values. Additionally, the box at the bottom of the GUI, where the command can be entered, transitions from'>Larch' to '...>' in red text. However, the fit statistic report can be exported/saved through the pre-edge results. Following this, the 'uvars' commands yield the area of the sum of the two Gaussians - thanks! :) Regarding your suggestion for improving the software's functionality, including a "peaks_area" parameter within the fit variables window may be valuable. I am currently comparing the areas among 15 datasets and having a 'peaks_area' parameter would facilitate the straightforward extraction and comparison of these values. Interestingly, another user expressed interest in this feature and reached out to me via email. I may have additional suggestions, but I will note them down during the next round of fits. Best regards, Ryan -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, December 15, 2023 6:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 250, Issue 5 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: Larix Pre-edge Statistics (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 14 Dec 2023 20:29:38 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larix Pre-edge Statistics Message-ID: <CA+7ESboeUMm6iH9JmEfie9AuajYwDBvtYp8GrtLBSCegdkM=Fg(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi Ryan, Yeah, this could be a little richer. For clarity, the "amplitude" Parameters will be the area of each peak. Well, it's the amplitude factor for the unit-normalized lineshape (Gaussian, Lorentzian, Voigt, etc), so it will be the area under that curve from -Inf to Inf. Those Infinities probably have small effects, here anyway ;). As you say, the centroid of multiple peaks is given, but not the total area under the sum of non-background peaks. That would not be too hard to add. But it might also fall into the category of "the sorts of calculations we should allow the user to do after a fit" without having to bake them all in. That is, if you open a Larch buffer after a pre-edge peak fit, you could get the most recent best-fit Parameters from lmfit with: pars = peakresult.result.params But also, you can get "uvars" as uvars = peakresult.result.uvars which is a dictionary of name:"ufloat" values for all Parameters (variables and "constrained values"). These "ufloat" values come from the `uncertainties` package and include uncertainties that know about the correlations between the Parameters. You can use these for simple calculations that will propagate the uncertainties (including correlations). As an example, if I do a pre-edge peak fit, with 2 Gaussian peaks (plus Line+Lorentzian for the background), I might get a good fit and a resulting report (from the larch buffer, do `print(peakresult.result.fit_report()`) that looks like this: [[Model]] (((Model(lorentzian, prefix='bpeak_') + Model(linear, prefix='bpoly_')) + Model(gaussian, prefix='gauss1_')) + Model(gaussian, prefix='gauss2_')) [[Fit Statistics]] # fitting method = leastsq # function evals = 355 # data points = 162 # variables = 11 chi-square = 4.5237e-04 reduced chi-square = 2.9958e-06 Akaike info crit = -2049.75462 Bayesian info crit = -2015.79106 R-squared = 0.99953048 [[Variables]] bpeak_amplitude: 1.82988250 +/- 0.04372160 (2.39%) (init = 2.462209) bpeak_center: 7118.44625 +/- 0.02812082 (0.00%) (init = 7120.091) bpeak_sigma: 1.36103880 +/- 0.01273292 (0.94%) (init = 2.121656) bpeak_fwhm: 2.72207761 +/- 0.02546583 (0.94%) == '2.0000000*bpeak_sigma' bpeak_height: 0.42795967 +/- 0.00701416 (1.64%) == '0.3183099*bpeak_amplitude/max(1e-15, bpeak_sigma)' bpoly_intercept: -6.37404087 +/- 0.65831626 (10.33%) (init = 2.467005) bpoly_slope: 8.9825e-04 +/- 9.2664e-05 (10.32%) (init = -0.000347) gauss1_amplitude: 0.10390560 +/- 0.00363058 (3.49%) (init = 0.14991) gauss1_center: 7111.52424 +/- 0.02714092 (0.00%) (init = 7112.452) gauss1_sigma: 0.75932812 +/- 0.02151410 (2.83%) (init = 1.315216) gauss1_fwhm: 1.78808103 +/- 0.05066183 (2.83%) == '2.3548200*gauss1_sigma' gauss1_height: 0.05459081 +/- 7.8147e-04 (1.43%) == '0.3989423*gass1_amplitude/max(1e-15, gauss1_sigma)' gauss2_amplitude: 0.03945700 +/- 0.00329914 (8.36%) (init = 0.116005) gauss2_center: 7113.18957 +/- 0.04258439 (0.00%) (init = 7113.403) gauss2_sigma: 0.57985874 +/- 0.03338641 (5.76%) (init = 0.556759) gauss2_fwhm: 1.36546297 +/- 0.07861898 (5.76%) == '2.3548200*gauss2_sigma' gauss2_height: 0.02714638 +/- 0.00110204 (4.06%) == '0.3989423*gauss2_amplitude/max(1e-15, gauss2_sigma)' fit_centroid: 7111.98258 +/- 0.01448240 (0.00%) == '(gauss1_amplitude*gauss1_center +gauss2_amplitude*gauss2_center )/(gauss1_amplitude+gauss2_amplitude)' [[Correlations]] (unreported correlations are < 0.100) C(bpoly_intercept, bpoly_slope) = -1.0000 C(bpeak_amplitude, bpeak_center) = +0.9722 C(gauss1_amplitude, gauss1_sigma) = +0.9186 .... C(gauss1_amplitude, gauss2_amplitude) = -0.7900 So there are 2 "gaussN_amplitude" Parameters for the area under each Gaussian, with a strong negative correlation. If you do >>> uvars = peakresult.result.uvars >>> print(uvars['gauss1_amplitude'], uvars['gauss2_amplitude']) >>> print(uvars['gauss1_amplitude'] + uvars['gauss2_amplitude']) You'll get the area of the sum of the two Gaussians as 0.104+/-0.004 0.0395+/-0.0033 0.1434+/-0.0023 That is, one might expect the uncertainties in 'gauss1_amplitude' and 'gauss2_amplitude' should add in quadrature, but that would overestimate the uncertainty in the sum by almost ~2x because the parameters are highly (and negatively) correlated. The uncertainty in the reported peak heights and the centroid of the two peaks also takes the correlations into account. Such calculations are not too hard to do from the Larch buffer or Python script, but we might think about how that could be exposed more flexibly. I can be persuaded to just add a Parameter "peaks_area" = the sum of the amplitudes, which would then have this value and uncertainty. Any suggestions for what should be exposed here? Cheers, --Matt On Thu, Dec 14, 2023 at 10:47?AM Ryan Parmenter <rap35(a)kent.ac.uk> wrote: > > Hello, > > > > I successfully fitted Gaussian curves to my pre-edge peaks using Larix (XAS Viewer), yielding the centroid energy for indicating Fe oxidation state. The expected trends are observed, however, in reviewing articles, I noticed they report the area and integrated intensities of Gaussian curves, often automated with Peakfit software. Can Larix generate these values in its statistical report? If not, how can I calculate the area and integrated intensity using Larix's provided values, considering the absence of standard deviation? > > > > Thanks, > > Ryan > > > > _______________________________________________ > 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 ------------------------------ Subject: Digest Footer _______________________________________________ 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 ------------------------------ End of Ifeffit Digest, Vol 250, Issue 5 ***************************************

1 0

Larix Pre-edge Statistics
by Ryan Parmenter 15 Dec '23

15 Dec '23

Hello, I successfully fitted Gaussian curves to my pre-edge peaks using Larix (XAS Viewer), yielding the centroid energy for indicating Fe oxidation state. The expected trends are observed, however, in reviewing articles, I noticed they report the area and integrated intensities of Gaussian curves, often automated with Peakfit software. Can Larix generate these values in its statistical report? If not, how can I calculate the area and integrated intensity using Larix's provided values, considering the absence of standard deviation? Thanks, Ryan

2 1

Reviews of Modo Loan
by Vlog and Love birds 10 Dec '23

10 Dec '23

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Ref. XAS Data for Fe K-edge (Fe3C Iron Carbide)
by Esmael Balaghi 05 Dec '23

05 Dec '23

Dear All, Does anyone by chance have the Fe K-edge XAS data for Iron Carbide (Fe3C)? Best regards, Esmael

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O K-edge energy shift in feff8
by Otal Eugenio 05 Dec '23

05 Dec '23

Dear all, I am simulating O K-edge from LiNi0.5Mn1.5O4 with partial fluoride substitution. I am starting from a DFT simulated cif file with 30 different oxygen atoms, so I am simulating each Oxygen for a later average and comparing them with experimental results. I am using these flags: * O K edge energy = ##.## eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * ixc [ Vr Vi ] EXCHANGE 0 * r_scf [ l_scf n_scf ca ] SCF 6.50 * kmax [ delta_k delta_e ] XANES 4.0 0.05 0.3 * r_fms l_fms FMS 6.50 0 * emin emax eimag LDOS -30 20 0.1 RPATH 0.1 *EXAFS 20 POTENTIALS * IPOT Z Tag 0 8 O 1 8 O 2 25 Mn 3 28 Ni 4 3 Li 5 9 F ATOMS * x y z ipot tag distance site_info 0.00000 0.00000 0.00000 0 O 0.00000 * O_25 (...) I just finished some simulations and I found the energy limits are shifted in xmu.dat for the different oxygen sites, just in absolute (omega) and relative (e) energy. As I want to see the relative intensities in the pre-edge, I am worried about normalizing the energy before averaging all the spectra. Is this ok? Is there a way to normalize the energies or am I making any mistakes? I m attaching a plot of three 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 ¯\_(ツ)_/¯¯\_(ツ)_/¯ Who is John Galt? ¯\_(ツ)_/¯¯\_(ツ)_/¯

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Post-Doc at U Minnesota and ALS
by Matt Newville 30 Nov '23

30 Nov '23

Hi Folks, Brandy Toner at the University of Minnesota is looking to hire a post-doc to be stationed at the Advanced Light Source at Lawrence Berkeley National Lab for soft and tender X-ray science work for Earth and Environmental Science. For more information, see the attached PDF, and to apply for this position, visit https://hr.umn.edu/Jobs/Find-Job and access Job Opening ID 358786 --Matt Newville

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beamline scientist position at ALS
by Matt Newville 30 Nov '23

30 Nov '23

Hi Folks, Brandy Toner at the University of Minnesota is looking to hire a beamline scientist to be stationed at the Advanced Light Source at Lawrence Berkeley National Lab to support soft and tender X-ray science work for Earth and Environmental Science. For more information, see the attached PDF, and to apply for this position, visit https://hr.umn.edu/Jobs/Find-Job and access Job Opening ID 358826 --Matt Newville

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Matt Newville and my Friends
by foxseo2023 24 Nov '23

24 Nov '23

I hope this message finds you well and thriving in your endeavors. As a fellow Vietnamese student currently pursuing education in the United States, I can't help but feel a sense of pride and excitement about the prospect of inviting you to experience the beauty and charm of my homeland, Vietnam. Vietnam is a land of captivating landscapes, rich history, and warm hospitality. From the breathtaking Ha Long Bay with its emerald waters and limestone karsts to the vibrant city life of Ho Chi Minh City, our country offers a diverse range of experiences for every traveler. Picture yourself exploring the ancient town of Hoi An, with its lantern-lit streets and traditional architecture, or hiking through the terraced rice fields of Sapa, surrounded by lush greenery. Beyond the scenic landscapes, you will discover the heart and soul of Vietnam in its people. The kindness and friendliness of the Vietnamese people create an atmosphere of warmth that is truly unique. Whether you're savoring the delicious street food in Hanoi, engaging in conversations with locals, or witnessing the traditional water puppetry shows, you'll find yourself immersed in a culture that values community and connection. Vietnam is not just a destination; it's an experience that will leave a lasting impression on your heart. I extend this invitation to you with the hope that you'll consider making Vietnam your next travel destination. Come and discover the hidden gems, the delectable cuisine, and the genuine smiles that await you in the heart of Southeast Asia. I look forward to the day when I can share the beauty of my homeland with you in person. Until then, safe travels and may your curiosity lead you to the wonders of Vietnam. Best regardshttps://vking.vn/kien-truc/biet-thu-tan-co-dien/

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Health Sciences/Specialized Reference
by Mahiyan Molla 23 Nov '23

23 Nov '23

Hello, I was speaking with someone today who is curious about the possibility of more specialized reference assistance in the cooperative. Does anyone have any health sciences libraries participating in cooperative virtual reference? Do you feel there's sufficient support within the cooperative for a health sciences or hospital library to join? We're just trying to get a sense of what might be out there already or if this is something others have tried. All best, Mahiyan Mahiyan Molla Reference & Research Services Coordinator Research Peptides <https://researchpeptides.net/> 423 E 7th St <https://www.google.com/maps/place/423+E+7th+St,+Los+Angeles,+CA+90014,+USA/…> Los Angeles, CA 90014 <https://www.google.com/maps/place/423+E+7th+St,+Los+Angeles,+CA+90014,+USA/…>

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beamline scientist position at NSLS-II beamline XFM
by Matt Newville 22 Nov '23

22 Nov '23

Hi Folks, The University of Chicago is looking to hire a beamline scientist to be stationed at the NSLS-II XFM (4-BM) beamline. Details are at: https://uchicago.wd5.myworkdayjobs.com/en-US/External/details/Research-Prof… --Matt Newville

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Help with Larch install on MacOSX 14 (Sonoma)
by Sandeep Haripuria 19 Nov '23

19 Nov '23

Hi Matt, I’m trying to install Larch on MacOSX 14 (Sonoma) using the 64 bit binary installer (new install, new laptop). It created the xraylarch folder in my home folder, and installed the python library there. However, it did not create a Larch folder on the desktop (or anywhere else I can find). I tried the command from the terminal console ($HOME/xraylarch/bin/larch -m) but get the message of no such file or directory. Not sure what to do next… Hope all is well and thanks for your help, Sandeep Haripuria [ThePlattery.Com](https://theplattery.com/)

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Help with Larch install on MacOSX 14 (Sonoma)
by Peggy O'Day 17 Nov '23

17 Nov '23

Hi Matt, I’m trying to install Larch on MacOSX 14 (Sonoma) using the 64 bit binary installer (new install, new laptop). It created the xraylarch folder in my home folder, and installed the python library there. However, it did not create a Larch folder on the desktop (or anywhere else I can find). I tried the command from the terminal console ($HOME/xraylarch/bin/larch -m) but get the message of no such file or directory. Not sure what to do next… Hope all is well and thanks for your help, Peggy

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Errors when I try to export CSV file
by Yi Sang 12 Nov '23

12 Nov '23

Dear developer, I met an error when I try to export my XANES data as CSV file. Below is the error message: Traceback (most recent calls last): File "/Users/yisang/xraylarch/lib/python3.11/site-packages/larch/wxxas/xasgui.py", line 684, in onExportCSV groups2csv(savegroups, outfile, x=res.xarray, y=res.yarray, TypeError: groups2csv() got an unexpected keyword argument '_larch' How do you think I should resolve this problem? Thanks, Yi

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upcoming Webinar on Synchrotron for Earth and Environmental Science
by Matt Newville 09 Nov '23

09 Nov '23

Hi Folks, For the Earth and environmental scientists on the list, there will be a webinar introducing the newly formed "Synchrotron for Earth and Environmental Science" on Tuesday, November 14th, at 3 PM Chicago time, as presented by SEES Director Andy Campbell. If you are interested in learning more, you can sign up for the Zoom link for the webinar at: https://cars.uchicago.edu/sees/2023/09/27/sees-webinar-sees-the-light/ For a little more background: SEES (Synchrotron Earth and Environmental Science) is a new cooperative agreement with NSF to manage and enhance NSF Earth Science-supported beamline operations for Earth and environmental science research at four DOE synchrotron facilities: the Advanced Photon Source (APS), the Advanced Light Source (ALS), the National Synchrotron Light Source II (NSLS-II), and the Stanford Synchrotron Radiation Lightsource (SSRL). See https://cars.uchicago.edu/sees/ for more information. SEES will support many beamlines across the US for Earth and environmental science, including a few X-ray microprobe beamlines for XAS and other spectroscopy and imaging experiments such as the one I run at the APS. This new organization will also be the source of most of my support for the foreseeable future, with a healthy fraction of that explicitly earmarked for work on cyber-infrastructure, including the XAFS-related software discussed here. Cheers, --Matt

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Postdoc position at Argonne National Laboratory - X-ray characterization of low-temperature fuel cell and electrolyzers
by Myers, Deborah J. 30 Oct '23

30 Oct '23

https://argonne.wd1.myworkdayjobs.com/Argonne_Careers/job/Lemont-IL-USA/Pos…

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Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations
by Ava Rajh 18 Oct '23

18 Oct '23

Hello Matt! thank you for the response. In putting together all the project files for the minimal working example I tested a bunch more .cif files of various materials including different graphite file, and there was no difference in Larch and Athena in any of them (as long as the same FEFF version and input settings are used) as expected. Looking closely at the feff input file for the C.cif I was having trouble with, there were some differences which I haven't noticed when looking through them before. So as far as I am concerned, this was a user error on my part, as the generated input files weren't exactly the same. If I save the input feff file from Larch and use that in Artemis or the other way around, as you suggested, the results match exactly. The compared spectra in my previous message were calculated separately, exported and plotted together. thank you for very much for the help and kind regards, Ava > Message: 1 > Date: Mon, 16 Oct 2023 15:24:26 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Differences between Larch and Artemis when > performing FEFF calculations > Message-ID: > <CA+7ESbrWm5UoBYggLmi+-WZRU6mn4Y_-z1OBVg57pAu4rsXM7w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Ava, > > I think you'll have to give us more details about what you have done. > The > figures you show are all in R-space, so after at least some > processing... > So, yes, project files and/or scripts would be helpful. Yes, there > can be > subtle changes in the background subtraction (and in the normalization > process too) between Larch and Ifeffit/Athena/Artemis. > > By default, Artemis uses Feff 6.10 and Larch uses Feff 8. For the C K > edge, that could have a noticeable difference, especially in the > placing of > the k=0 value, though I do not know how big that effect would be for C > (graphite?). But also, Artemis and Larch can both read the inputs > from > the other calculations: it might be that this is what you have done to > make the plots, but that wasn't 100% clear to me. > > > > > On Mon, Oct 16, 2023 at 2:08?PM Ava Rajh <ava.rajh(a)ijs.si> wrote: > >> Dear all! >> >> I haven't been able to find a similar question/issue in the previous >> threads, so I hope someone can help me figure out what is going on. >> >> I am trying to fit a Carbon EXAFS spectra, using graphite as a model. >> I >> am first focusing on just the first two single scattering paths, so I >> calculated the theoretical paths with FEFF in Larch and tried using >> them >> to fit the spectra. I was consistently getting slightly lower >> distances >> than expected, but otherwise an OK fit. >> >> The issue is, I tried to compare the analysis with a colleague who is >> using Athena. At first glance the EXAFS spectra, using the exact same >> parameters, looked very similar (but not exactly the exactly the same, >> this I attributed to Larch using a different autobk procedure). I >> would >> have however expected the theoretical paths to match exactly, if they >> were calculated and plotted with the same parameters. But they were >> also >> slightly different. I then downloaded Athena and spent time trying to >> find where the differences come from. If I compare the first two >> calculated shells from Larch with the ones from Athena, with exactly >> the >> same set of test parameters (S02 = 1, E0 = 0, dr1 = 0, s2_1 = 0, dr2 = >> 0, s2_2 = 0), the resulting models do not match. I made sure the paths >> are calculated from the came .cif file in both cases, use FEFF6, have >> the same calculated reference distances, same FT... >> >> So, my main question is, am I missing something important in regards >> to >> calculations, why would the calculated paths be different and which >> one >> would be the "correct" one to use for the fit? And the other question >> would be about the fact that EXAFS spectra of experimental data look >> slightly different using Larch and Athena, am I right in disregarding >> this, or should I dig deeper and find the source of discrepancy? >> >> I am enclosing a plot of just the calculated first two shells from >> Athena and Larch (FT: kmin = 2, kmax = 7.5, Fittting in R space, kw = >> 3, kWindow = Hanning, dk = 1.0, Rmin = 0.6, Rmax = 2.1) along with the >> cif file I ended up using for testing the differences. If it would be >> helpful, I can also provide the project files and larch script I used >> for the dataset, but I am mainly interested in understanding the >> differences seen in the theoretical parts first. I tested this using >> Larch v 0.9.72 and Demeter 0.9.26 >> >> Thank you ver much for the help, and If I need to provide any >> additional >> info please let me know. >> kind regards, Ava >> >> -- >> Ava Rajh_______________________________________________

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EXAFS fitting - Reff command not recognized
by van der Veer, Siebe 17 Oct '23

17 Oct '23

Hi all, I'm having an issue where I want to use a * reff (also tried a*reff, a * Reff, a*Reff) as the expression for delta R, but instead of recognizing the command Reff, Larix now considers this a parameter it should fit, whereas in the past it would just use the value for Reff contained in the path in question. Is anyone else experiencing this issue as well and if so, how can I fix this? Best, -- *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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Differences between Larch and Artemis when performing FEFF calculations
by Ava Rajh 16 Oct '23

16 Oct '23

Dear all! I haven't been able to find a similar question/issue in the previous threads, so I hope someone can help me figure out what is going on. I am trying to fit a Carbon EXAFS spectra, using graphite as a model. I am first focusing on just the first two single scattering paths, so I calculated the theoretical paths with FEFF in Larch and tried using them to fit the spectra. I was consistently getting slightly lower distances than expected, but otherwise an OK fit. The issue is, I tried to compare the analysis with a colleague who is using Athena. At first glance the EXAFS spectra, using the exact same parameters, looked very similar (but not exactly the exactly the same, this I attributed to Larch using a different autobk procedure). I would have however expected the theoretical paths to match exactly, if they were calculated and plotted with the same parameters. But they were also slightly different. I then downloaded Athena and spent time trying to find where the differences come from. If I compare the first two calculated shells from Larch with the ones from Athena, with exactly the same set of test parameters (S02 = 1, E0 = 0, dr1 = 0, s2_1 = 0, dr2 = 0, s2_2 = 0), the resulting models do not match. I made sure the paths are calculated from the came .cif file in both cases, use FEFF6, have the same calculated reference distances, same FT... So, my main question is, am I missing something important in regards to calculations, why would the calculated paths be different and which one would be the "correct" one to use for the fit? And the other question would be about the fact that EXAFS spectra of experimental data look slightly different using Larch and Athena, am I right in disregarding this, or should I dig deeper and find the source of discrepancy? I am enclosing a plot of just the calculated first two shells from Athena and Larch (FT: kmin = 2, kmax = 7.5, Fittting in R space, kw = 3, kWindow = Hanning, dk = 1.0, Rmin = 0.6, Rmax = 2.1) along with the cif file I ended up using for testing the differences. If it would be helpful, I can also provide the project files and larch script I used for the dataset, but I am mainly interested in understanding the differences seen in the theoretical parts first. I tested this using Larch v 0.9.72 and Demeter 0.9.26 Thank you ver much for the help, and If I need to provide any additional info please let me know. kind regards, Ava -- Ava Rajh

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Re: [Ifeffit] Ifeffit Digest, Vol 248, Issue 2
by bikov＠phys.uni-sofia.bg 13 Oct '23

13 Oct '23

Dear Edmund Welter, Dear Matt Newville, Thank you for the answers and very informative explanations. With best regards, Konstantin > 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. Fitting mechanism of Artemis (bikov(a)phys.uni-sofia.bg) > 2. Re: Fitting mechanism of Artemis (Edmund Welter) > 3. Re: Fitting mechanism of Artemis (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Oct 2023 11:09:55 +0300 > From: bikov(a)phys.uni-sofia.bg > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fitting mechanism of Artemis > Message-ID: > <1936f567bb85f017cc9aa404a2a49fda.squirrel(a)mail.phys.uni-sofia.bg> > Content-Type: text/plain;charset=utf-8 > > Dear all, > I have a general question regarding the mechanism employed in the fitting > procedures implemented in Artemis. > How exactly is performed a fit? Do we have a fixed > central atom (absorbing/emitting atom) and only the distances to the > neighbors included in the probed pathways are varied, i.e. by varying the > coordinates of the corresponding neighbor atoms, or during > the fitting process Artemis can vary the position of the absorption center > too? Could the procedure be constrained in such a way that the scattering > pathways are adjusted by only varying the coordinates of the central atom? > > With kind regards, > Konstantin Bikov > PhD Student at the Physics Department > of the University of Sofia, Bulgaria > > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Oct 2023 11:05:26 +0200 > From: Edmund Welter <edmund.welter(a)desy.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Fitting mechanism of Artemis > Message-ID: <1ac7d9c6-e37f-2b17-82c5-bb382af973ba(a)desy.de> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear Konstantin, > > why would you want to do that? If you change the distance between A-B > you the distance between B-A changes by the same amount. If you move the > absorber away from let's say the centre of an octaeder you would split > the (next) nearest neighbours shell into different shells with different > distances. If the differences are large enough and the resolution of > your EXAFS spectrum sufficient you would see more than one (first > neighbours) peak in the FT of your EXAFS spectrum. But that would be > another model that you would feed into FEFF before you start your second > fit. Technically you would fneed to define the position of all atoms in > your model in world-coordinates. So the absorber would no longer be at > 0,0,0. I would guess that this would make the computation and the model > more complex or at least less intuitive. > > Best regards, > > Edmund > > > On 06.10.23 10:09, bikov(a)phys.uni-sofia.bg wrote: >> Dear all, >> I have a general question regarding the mechanism employed in the >> fitting >> procedures implemented in Artemis. >> How exactly is performed a fit? Do we have a fixed >> central atom (absorbing/emitting atom) and only the distances to the >> neighbors included in the probed pathways are varied, i.e. by varying >> the >> coordinates of the corresponding neighbor atoms, or during >> the fitting process Artemis can vary the position of the absorption >> center >> too? Could the procedure be constrained in such a way that the >> scattering >> pathways are adjusted by only varying the coordinates of the central >> atom? >> >> With kind regards, >> Konstantin Bikov >> PhD Student at the Physics Department >> of the University of Sofia, Bulgaria >> >> _______________________________________________ >> 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 > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Oct 2023 11:41:17 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Fitting mechanism of Artemis > Message-ID: > <CA+7ESbpV-FtSVhjEpoTdV72ntx4wAibjZHqZdeAq7ShpSZZiiw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Konstantin, > > > > On Fri, Oct 6, 2023 at 3:11?AM <bikov(a)phys.uni-sofia.bg> wrote: > >> Dear all, >> I have a general question regarding the mechanism employed in the >> fitting >> procedures implemented in Artemis. >> How exactly is performed a fit? > > > > That is a pretty open-ended question to be able to answer with precision. > Is the question more about how fitting works in general, or about what is > modeled and allowed to change in the mode for EXAFS? > > There are plenty of writeups and resources on both topics, including > program documentation. > > Do we have a fixed central atom (absorbing/emitting atom) and only the >> distances to the >> neighbors included in the probed pathways are varied, i.e. by varying >> the >> coordinates of the corresponding neighbor atoms, or during >> the fitting process Artemis can vary the position of the absorption >> center >> too? > > > > Within the context of the software here, the answer is sort of that the > central atom is fixed. > > The way we model EXAFS is effectively (more below, as some might object > to > this) as a 1-dimensional problem. Single scattering EXAFS depends only on > the scalar distance between the atoms (or path length for the > photo-electron). Now, some aspects of EXAFS scattering definitely depend > on more than just distance. The Z of the scattering atom definitely has a > large effect. The angle of the X-ray polarization vector with the > three-dimensional bond direction can also have an effect. These are > folded into the scattering amplitude and phase shift. But even the > disorder terms, sigma^2, and so on, are really capturing the disorder in > R, > not the 3-D disorder. > > For sure, multiple-scattering paths will have 3D information baked into > them. With Feff and the way we use it, this 3D info *is* folded into the > scattering amplitudes and phase shifts calculated for a path and all we > really vary is the distribution of path lengths for those paths. > > In 1-D, it does not matter whether the absorber or scatterer moves, the > only thing that matters is the distance. In fact, to the extent that > neighboring atoms move together in the same direction, there is no effect > on the EXAFS -- an atom in a solution or melt will have EXAFS (it might be > weak, but it does not fall to 0 at a phase transition). EXAFS is much > more > sensitive to "optical phonons" (neighboring atoms moving in opposite > direction) than to "acoustic phonons" (neighboring atoms moving in the > same > direction). > > Now, one can take a reverse-monte-carlo approach: calculate a lot of > different local structures, sum the EXAFS for each calculation, and see > which is best. One can also do something sort of in-between: calculate > a > set of "undistorted paths" and one or more sets of "distorted paths" and > then do a linear (or for some multiple-scattering case, quadratic) model > to > combine these. > > > Could the procedure be constrained in such a way that the scattering >> pathways are adjusted by only varying the coordinates of the central >> atom? >> > > Yes. In fact, this has been done several times. If you imagine a metal > ion > (let's say Ti) surrounded by six neighbors (let's say O) in an octahedron, > a common thing to try to model is if that Ti atom moves away from the > center of the octahedron, say in a perovskite-like structure. > > For the simplest case (ie, what I would start with ;)), you could > calculate > the EXAFS with Ti at the center of a perfect octahedron and get 6 > equivalent paths, and add those to give the EXAFS. If the octahedron is > distorted, you might have 2, 3, 4, or 6 paths. Let's go all the way to > "general" 6 paths. Each path would use a different Feff calculation (or > a > copy). You would not be limited to varying the change in each of the six > path lengths (our 'delr' parameter) to have the same delr for all paths. > Instead, you could define 3 new fitting variables, let's say "dx", "dy", > and "dz" for the displacement of the absorbing Ti from the position used > in > the Feff calculation (let's just call that "origin"). > > If you only have "dz", then one path gets shorter by dz, one gets longer > by > dz, and the other four get longer by sqrt(reff*2 + dz**2), where "reff" is > the magic "R used for each path Feff calculation. I'll leave the more > general case for you ;). > > Hope that gets you started, > > --Matt >

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Re: [Ifeffit] Contents of Ifeffit digest...
by charvi singhvi 07 Oct '23

07 Oct '23

Dear Team, I want to subscribe to the Ifeffit mailing list. I am very new to XAS analysis and I aim to gain expertise in it. I have visited ESRF beamline recently and have promising data. I need to do a proper analysis in order to extract useful information. Your help through this mailing list is much appreciated. Kind Regards Charvi Charvi Singhvi c/o Prof. Vivek Polshettiwar Graduate Student Department of Chemical Sciences (DCS), Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Colaba, Mumbai 400005 India Phone: +91-22-2278 2986/2051 Email: charvi.singhvi(a)tifr.res.in Home page: https://www.nanocat.co.in/ https://www.tifr.res.in/~dcs

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Fitting mechanism of Artemis
by bikov＠phys.uni-sofia.bg 06 Oct '23

06 Oct '23

Dear all, I have a general question regarding the mechanism employed in the fitting procedures implemented in Artemis. How exactly is performed a fit? Do we have a fixed central atom (absorbing/emitting atom) and only the distances to the neighbors included in the probed pathways are varied, i.e. by varying the coordinates of the corresponding neighbor atoms, or during the fitting process Artemis can vary the position of the absorption center too? Could the procedure be constrained in such a way that the scattering pathways are adjusted by only varying the coordinates of the central atom? With kind regards, Konstantin Bikov PhD Student at the Physics Department of the University of Sofia, Bulgaria

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Larch 0.9.72
by Matt Newville 03 Oct '23

03 Oct '23

Hi Folks, It's been a few months since the last release, but Larch 0.9.72 is now available. There have been several fixes and a few new features. The XAS analysis GUI application has been renamed from the rather dull name of "XAS Viewer" to "Larix" (the genus of trees for the Larch family). We (well, mostly Mauro Rovezzi and others at ESRF) put in a lot of effort over the summer to generate FDMNES inputs from structural information (CIF files, structural information from the Materials Project). This effort to convert structure information to input files for Feff, FDMNES, etc. has been evolving over the past several months, and there will probably be more done on this in the coming months. If you are interested in getting involved, let us know. There are new binary installer scripts for Windows, MacOS, and even Linux, and the "GetLarch" scripts have been updated too. These all will now install a Python 3.11 environment. Although installation is not fast, it is somewhat faster than it has been in the past due to using the Mamba variation of the Anaconda Python tools. More release notes are at https://github.com/xraypy/xraylarch/releases/tag/0.9.72 If you have a fairly recent version of Larch installed, you should be informed that a new version is available, and be prompted to install or run the Larch Updater script. Let us know if you have any troubles with this version or questions, comments, or suggestions for improvements! --Matt

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TiOx K-edge spectra
by Rebecca Katharina Pittkowski 20 Sep '23

20 Sep '23

Dear community, I am preparing a teaching exercise for a course on nano-structure characterization, and I was hoping that someone has some K-edge spectra of titanium oxide nanoparticles lying around that I could reuse for the course. I have been through the NIMS Material Data Repository and found some useful references but it would be great to have a nano-sized example as well. That could very well be from a published article, which I could include in the teaching. Thanks for any input. Greetings from Copenhagen, Rebecca Rebecca K. Pittkowski Tenure-track Assistant Professor University of Copenhagen Center for High Entropy Alloy Catalysis Department of Chemistry Universitetsparken 5 2100 Copenhagen Ø DENMARK Rebecca.pittkowski(a)chem.ku.dk [/var/folders/gc/lhyz4xy96q77x4sbrrh4l46r0000gn/T/com.microsoft.Outlook/WebArchiveCopyPasteTempFiles/cidimage009.png(a)01D5C49F.F68E4220]

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P K-edge EXAFS
by Marcelo Eduardo Alves 15 Sep '23

15 Sep '23

Hi there, I begin by examining phosphorus adsorption by goethite, hematite, and gibbsite. Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K edge that can be properly used, i.e., spectra with a high signal-to-noise ratio, especially for dilute samples? Would it be possible to use arsenic as a phosphorus proxy to get conclusions from As K-edge EXAFS data that could be extended to P? Thank you.

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EXAFS-50 symposium and short course, Oct. 30-Nov. 3 at BNL
by Anatoly Frenkel 08 Sep '23

08 Sep '23

Dear subscribers: Sharing here my Linkedin post: I am excited to share that Brookhaven National Laboratory will be hosting the Symposium ("EXAFS-50") that will mark the 50th anniversary of Stern-Sayers-Lytle team's introduction of the Extended X-ray Absorption Fine Structure (EXAFS) technique in early 1970s. The Symposium will open the week of events, hosted by Brookhaven National Laboratory, that will include the talks of the experts in the field on the past, present and future of the EXAFS technique on Oct. 30 and 31, and culminate by the three-day long short course on advanced data analysis methods of EXAFS, from Nov. 1 to 3. Both events will be in-person. The web sites below have all the information for registration for the symposium (registration begins on Aug. 21) and for application/registration for the short course (application deadline is Aug. 31). Although the Symposium and the Short course are organized and run as separate events, attending both of them will be ideal for graduate students and postdocs. No registration fee is charged for attending these events but registration is required. EXAFS-50: https://www.bnl.gov/exafs-50/ XAFS short course: https://www.bnl.gov/xafscourse/ ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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CatMASS - XAS "Catalyst" Sample Mass Calculator
by Hoffman, Adam S 07 Sep '23

07 Sep '23

Hi All, We would like to announce the release of CatMASS - a XAS (and X-ray scattering) sample mass calculator for complex sample compositions most commonly found in catalysis science. This software builds off of codes found in Hephaestus and XAFSMass allowing for more complex sample descriptors (multiple metals/supported organometallics) and allows for the inclusion of diluents. The absorption can be visualized in E- or k-space highlighting potentially competing edges in the sample that may limit the range of your EXAFS data collection. The documentation can be found in the recent publication: https://onlinelibrary.wiley.com/iucr/doi/10.1107/S160057752300615X To download the executable file (windows only) please see the link here: https://web.slac.stanford.edu/coaccess/resources/software To download the python-based version or collaborate on the GitHub project please go to: https://github.com/ahoffm02/catMass If you have any questions please reach out to Jorge Perez-Aguilar (jperezag(a)slac.stanford.edu<mailto:jperezag@slac.stanford.edu>) or myself, Adam Hoffman (ashoff(a)slac.stanford.edu<mailto:ashoff@slac.stanford.edu>). Cheers, Adam Hoffman, Jorge Perez-Aguilar, and the Co-ACCESS team

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Shift in Eo when fitting PtO2 and similar samples
by Zi Qi Chen 07 Sep '23

07 Sep '23

Dear all, I am looking at EXAFS of PtO2 powders and Pt particles supported on TiO2. I used a beta-PtO2 crystal structure data for the PtO2 EXAFS and after the first shell fit, I observed a large shift in Eo (delta Eo of ~14 eV) in my fit parameters. When I tried to fit the Pt foil to obtain the So2, the energy shift also seemed high (delta Eo of ~7 eV). I am wondering if there could be a problem in the selection of Eo prior to EXAFS analysis? I left the Eo as the energy at the first peak of first derivative (ifeffit default). All of the data were also aligned using the reference foil in Athena before looking at EXAFS. I am wondering what would have caused this shift? Any help is appreciated, thank you. Best regards, Yanny

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Shift in Eo when fitting PtO2 and similar samples
by Clément Laskar 23 Aug '23

23 Aug '23

Dear Yanny Chen, You can find recorded and fitted EXAFS and HR-EXAFS spectra of PtO2 in our following paper: Laskar, C., Bazarkina, E. F., Kokh, M. A., Hazemann, J. L., Foulon, S., Leynaud, O., ... & Pokrovski, G. S. (2022). Exploring Platinum Speciation with X-ray Absorption Spectroscopy under High-Energy Resolution Fluorescence Detection Mode. *Minerals*, *12*(12), 1602. The spectra can be directly downloaded at the following link on the sshade database: https://www.sshade.eu/data/experiment/EXPERIMENT_GP_20181107_001 https://www.sshade.eu/data/experiment/EXPERIMENT_CL_20210211_001 Maybe it could help you to deal with your fitting problem to compare your spectra and your fit with ours, Regards, Clément LASKAR -------------------------------------------------------- Dear all, I am looking at EXAFS of PtO2 powders and Pt particles supported on TiO2. I used a beta-PtO2 crystal structure data for the PtO2 EXAFS and after the first shell fit, I observed a large shift in Eo (delta Eo of ~14 eV) in my fit parameters. When I tried to fit the Pt foil to obtain the So2, the energy shift also seemed high (delta Eo of ~7 eV). I am wondering if there could be a problem in the selection of Eo prior to EXAFS analysis? I left the Eo as the energy at the first peak of first derivative (ifeffit default). All of the data were also aligned using the reference foil in Athena before looking at EXAFS. I am wondering what would have caused this shift? Any help is appreciated, thank you. Best regards, Yanny

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Postdoc position in XAS and catalysis is open at BNL
by Stavitski, Eli 21 Aug '23

21 Aug '23

Postdoctoral Research Associate Catalysis and X-ray Spectroscopy https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-catalysis-an… Postdoctoral Research Associate Catalysis and X-ray Spectroscopy Description at Brookhaven National Laboratory<https://jobs.bnl.gov/job/upton/postdoctoral-research-associate-catalysis-an…> Learn more about applying for Postdoctoral Research Associate Catalysis and X-ray Spectroscopy at Brookhaven National Laboratory jobs.bnl.gov Job ID 3913Date posted 08/11/2023 Brookhaven National Laboratory (www.bnl.gov) delivers discovery science and transformative technology to power and secure the nation’s future. Brookhaven Lab is a multidisciplinary laboratory with seven Nobel Prize-winning discoveries, 37 R&D 100 Awards, and more than 70 years of pioneering research. The Lab is primarily supported by the U.S. Department of Energy’s (DOE) Office of Science. Brookhaven Science Associates (BSA) operates and manages the Laboratory for DOE. BSA is a partnership between Battelle and The Research Foundation for the State University of New York on behalf of Stony Brook University. Organizational Overview The Hard X-ray Scattering & Spectroscopy (HXSS) program at BNL’s National Synchrotron Light Source II (NSLS-II) offers world-class capabilities for studying complex and heterogeneous materials under in situ and operando conditions. The program provides advanced spectroscopy, diffraction, and imaging x-ray tools, supported by computational resources for high-throughput analysis and modeling. One of the leading research directions in the HXSS science program is heterogeneous catalysis with emphasis on in situ and operando characterization. The Inner Shell Spectroscopy (ISS) beamline is a frontier X-ray spectroscopy instrument allowing high throughput and high energy resolution studies of a variety of catalysts. ISS is aimed at establishing structure-function relationships under relevant reaction conditions. Position Description NSLS-II is seeking exceptional candidates for a research associate position in the Hard X-ray Scattering and Spectroscopy program. The successful candidate will work collaboratively with the ISS team and supporting technical, engineering and controls staff. They will be involved in developing, commissioning, and testing custom sample environments for catalysis experiments, including high pressure gas and integration of the high energy resolution spectrometers in the ISS operando catalysis research infrastructure. They will also be involved in the support of the users at the beamline, including industrial partners. Leveraging the technical developments, the successful candidate will conduct mechanistic studies of catalytic carbon dioxide hydrogenation at high pressures in collaboration with ISS scientists. Essential Duties and Responsibilities: * Develop, commission, and test new catalysis infrastructure at the ISS beamline. * Take part in the logistic work required for successful beamline user operation * Participate in experiment planning, execution, translation of results into new scientific knowledge. * Disseminate scientific results as manuscripts, conference presentations, progress reports etc. * Develop and maintain safe practices and working conditions. Position Requirements * A PhD in chemistry, chemical engineering, or materials science * Understanding of heterogeneous catalytic reaction mechanisms, demonstrated by a publication record * Knowledge of in-situ/operando characterization applied to heterogeneous catalysis, relevant instrumentation and data analysis methods * Experience with synchrotron X-ray characterization techniques * Excellent written and oral communication and presentation skills * Demonstrated organizational and planning skills and methodical record-keeping * Ability to work in a collaborative team environment Preferred Knowledge, Skills, and Abilities: * Demonstrated record of applying X-ray absorption spectroscopy to solve problems in heterogenous catalysis * Knowledge of X-ray absorption spectroscopy data modelling including advanced quantum methods * Expertise with sample environment development and applications * Proficiency in programming using Python or equivalent languages OTHER INFORMATION: * BNL policy requires that after obtaining their PhD, eligible candidates for research associate appointments may not exceed a combined total of 5 years of relevant work experience as a post-doc and/or in an R&D position, excluding time associated with family planning, military service, illness or other life-changing events. At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes, but is not limited to: * Medical, Dental, and Vision Care Plans * Flexible Spending Accounts * Paid Time-off and Leave Programs (vacation, holidays, sick leave, paid parental leave) * 401(k) Plan * Flexible Work Arrangements * Tuition Assistance, Training and Professional Development Programs * Employee Fitness/Wellness & Recreation: Gym/Basketball Courts, Weight Room, Fitness Classes, Indoor Pool, Tennis Courts, Sports Clubs/Activities (Basketball, Table Tennis Pong, Softball, Tennis) Brookhaven National Laboratory and the Energy and Photon Sciences Directorate are committed to your success. We offer a supportive work environment and the resources necessary for you to succeed. Brookhaven National Laboratory (BNL) is an equal opportunity employer that values inclusion and diversity at our Lab. We are committed to ensuring that all qualified applicants receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, status as a veteran, disability or any other federal, state or local protected class. BNL takes affirmative action in support of its policy and to advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities. We ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation. *VEVRAA Federal Contractor Brookhaven employees are subject to restrictions related to participation in Foreign Government Talent Recruitment Programs, as defined and detailed in United States Department of Energy Order 486.1A. You will be asked to disclose any such participation at the time of hire for review by Brookhaven. The full text of the Order may be found at: https://www.directives.doe.gov/directives-documents/400-series/0486.1-BOrde…<https://www.directives.doe.gov/directives-documents/400-series/0486.1-BOrde…> [cid:7661b08b-12f2-48e3-8920-20aae481d8b3] Eli Stavitski Sr. Scientist Inner Shell Spectroscopy (ISS) Lead Beamline Scientist. Phone: 631-344-8641 Email: istavitski(a)bnl.gov<mailto:istavitski@bnl.gov> National Synchrotron Light Source-II Bldg. 743, Brookhaven National Laboratory Upton, NY 11973-5000 [NSLS-II ISS]<https://www.bnl.gov/nsls2/beamlines/beamline.php?r=8-ID>[Title: LinkedIn - Description: image of LinkedIn icon]<https://www.linkedin.com/in/eli-stavitski-a033a713/>[Google, scholar Icon in SuperTiny]<https://scholar.google.com/citations?user=cVxErOsAAAAJ&hl=en>

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sulfur XAS for Li2SO3
by Enyuan Hu 21 Aug '23

21 Aug '23

Hi all, I am wondering if anyone has sulfur XAS for Li2SO3. Data/help is much appreciated and relevant reference will be cited. Thank you. Enyuan

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Larch and calculation of theoretical EXAFS via cif -files part 2
by Mangold, Stefan (IPS) 14 Aug '23

14 Aug '23

Dear all, i have another set of cif files, which also don't work on larch. They work with Artemis, except that they hit the 500 atoms limit per cluster. This won't be a problem in larch, because of the option to exclude the H-atoms. One problem seems to occur on the line _chemical_formula_moiety ; 2(C18 H36 K1 N2 O6 1+),Bi2 2- ; which I rewrote to _chemical_formula_moiety '2(C18 H36 K1 N2 O6 1+),Bi2 2-' but still I got the message Error reading CIF File: /Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif Traceback (most recent calls last): File "/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/wxlib/cif_browser.py", line 618, in onImportCIF cif_data = parse_cif_file(path) File "/Users/stefanmangold/xraylarch/lib/python3.10/site-packages/larch/xrd/amcsd.py", line 142, in parse_cif_file raise ValueError(f'Cannot read symmetries from file {filename:s}') ValueError: Cannot read symmetries from file /Users/stefanmangold/Documents/eigene_Daten/Messdaten/PrepMessungen/XPS-Proben/Bi2-crypt-222_e.cif Anybody an idea, I attached the unchanged file (Bi2-crypt-222.cif) and the edited file (Bi2-crypt-222_e.cif). Any idea what’s wrong? best regards Stefan

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Larch and calculation of theoretical EXAFS via cif -files
by Mangold, Stefan (IPS) 10 Aug '23

10 Aug '23

Dear all, i have some cif files, which doesn’t work on larch. One example is KBi2, which works well on Artmenis with feff6. The same file (and also the cifs found in the database) won't work on larch (not with feff 6 nor feff8). There is no error message displayed -> just, that feff is started. ######## ### # Run Feff in folder: /Users/Name/.larch/feff/Bi1_L3_Bismuth_potassium__2_1__cif200012_13 ### ####### no result even after hours. Any ideas? Best regards Stefan

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request for comments on XDI and NeXuS data formatting
by Matt Newville 08 Aug '23

08 Aug '23

Hi Folks, As some of you are aware, there is a Q2XAFS meeting in a few weeks. I will be presenting some work on using NeXuS and HDF5 to store and distribute XAS data. This builds on and closely follows the XDI format from Bruce Ravel. While XDI is a great way to represent a single XAS spectrum, it is not able to contain multiple spectra. It also is not very specific about how to deal with data files with a large number (say, > 20) columns as might be found coming from many beamlines with multi-element detectors. I think that many of us are starting to see the need to regularly provide "raw" or "nearly raw" data as supplementary data for published articles or as part of datasets made available under FAIR data principles. While XDI could be one way to do that, I think it is also reasonable to reconsider formats other than plaintext files holding one spectrum. As I am preparing to present this, I've put together something like a blog post on a proof-of-concept for a NeXuS file format based on XDI at https://millenia.cars.aps.anl.gov/nxxas/. There are a few example data files using the proposed layout at https://millenia.cars.aps.anl.gov/nxxas/nexus_xas.html. There is also a Pull Request in with the NeXuS developers for this. If you are interested and have time over the next week or two, please read the pages above and let me know your thoughts on this. I know that not everyone is interested in this, but I also know that some who might be interested are not able to attend Q2XAFS. I think the discussion on this topic should be as wide as possible, which is why I am posting this here and before the meeting. Thanks, --Matt Newville <newville at cars.uchicago.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 3
by laavakyan 05 Aug '23

05 Aug '23

Dear Daria, thank you very much for your reply, supplied reference and hint about data processing Best regards, Leon On 8/4/23 09:32, 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: Ifeffit Digest, Vol 246, Issue 1 (Daria Boglaienko) > 2. Re: EasyXAFS - any experience with? (laavakyan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Aug 2023 17:18:35 +0000 > From: Daria Boglaienko<dbogl003(a)fiu.edu> > To:"ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1 > Message-ID: > <DM6PR05MB60587A50DD443C31FFD2EAF08B08A(a)DM6PR05MB6058.namprd05.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hello Leon, > > I frequently use the easyXAFS instruments in Pacific Northwest National Laboratory. If samples are well made, then even the troublesome fluorescence lines can be managed and cancelled out during the data processing once you collect both It and I0 at the same power making the dead time and count rate to match. > This is a paper I published where we collected XAS data both in the lab and APS: Boglaienko D, Andersen A et al X-ray absorption spectroscopy of trivalent Eu, Gd, Tb, and Dy chlorides and oxychlorides. J. Allows Compounds. 2022. > > Also, easyXAFS company has an excellent customer support. > > Daria -- Авакян Леон Александрович профессор каф. теор. и выч. физики физический факультет Южный федеральный университет +79185630854 laavakyan(a)sfedu.ru

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Re: [Ifeffit] EasyXAFS - any experience with?
by laavakyan 04 Aug '23

04 Aug '23

Dear Michele, thank you very much for your reply! It is very valuable, Best regards, Leon On 8/3/23 20:00, 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: Ifeffit Digest, Vol 246, Issue 1 (Michele Piana) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Aug 2023 20:13:13 +0000 > From: Michele Piana<michele.piana(a)tum.de> > To:"ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1 > Message-ID:<0c838f5f84a14ae5a5b130a8dbeea2cc(a)tum.de> > Content-Type: text/plain; charset="us-ascii" > > Dear Leon, > you can request the publications relative to easyXAFS here (it takes a few minutes to receive them): > https://www.easyxafs.com/copy-of-links > I am currently analyzing XAFS data from that instrument and I can tell that the data in the XANES region look good in terms of signal-to-noise ratio, also collecting them for just 1 hour. > To get sufficiently good data in the EXAFS region would need much longer data collections. > One annoying disadvantage is coming from spurious fluorescence peaks from the standard X-Ray tubes used. > The measurable elements and edges are limited, of course. > > Best regards > Michele Piana > > > -----Original Message----- > From: Ifeffit<ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Ofifeffit-request(a)millenia.cars.aps.anl.gov > Sent: Wednesday, 2 August 2023 19:00 > To:ifeffit@millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 246, Issue 1 > > 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. EasyXAFS - any experience with? (laavakyan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Aug 2023 17:23:48 +0300 > From: laavakyan<laavakyan(a)sfedu.ru> > To:Ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] EasyXAFS - any experience with? > Message-ID:<50478bcd-56fa-536a-3a62-bb8de37e844e(a)sfedu.ru> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear Ifeffit and XAFS society, > > I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). > > Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? > > The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. > > Regards, > Leon Avakyan > > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > > ------------------------------ > > End of Ifeffit Digest, Vol 246, Issue 1 > *************************************** > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > > ------------------------------ > > End of Ifeffit Digest, Vol 246, Issue 2 > *************************************** -- Авакян Леон Александрович профессор каф. теор. и выч. физики физический факультет Южный федеральный университет +79185630854 laavakyan(a)sfedu.ru

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Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1
by Daria Boglaienko 03 Aug '23

03 Aug '23

Hello Leon, I frequently use the easyXAFS instruments in Pacific Northwest National Laboratory. If samples are well made, then even the troublesome fluorescence lines can be managed and cancelled out during the data processing once you collect both It and I0 at the same power making the dead time and count rate to match. This is a paper I published where we collected XAS data both in the lab and APS: Boglaienko D, Andersen A et al X-ray absorption spectroscopy of trivalent Eu, Gd, Tb, and Dy chlorides and oxychlorides. J. Allows Compounds. 2022. Also, easyXAFS company has an excellent customer support. Daria ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, August 2, 2023 10:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 246, Issue 1 Note: This message originated from outside the FIU Faculty/Staff email system. 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. EasyXAFS - any experience with? (laavakyan) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Aug 2023 17:23:48 +0300 From: laavakyan <laavakyan(a)sfedu.ru> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] EasyXAFS - any experience with? Message-ID: <50478bcd-56fa-536a-3a62-bb8de37e844e(a)sfedu.ru> Content-Type: text/plain; charset=UTF-8; format=flowed Dear Ifeffit and XAFS society, I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. Regards, Leon Avakyan ------------------------------ Subject: Digest Footer _______________________________________________ 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 ------------------------------ End of Ifeffit Digest, Vol 246, Issue 1 ***************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 246, Issue 1
by Michele Piana 02 Aug '23

02 Aug '23

Dear Leon, you can request the publications relative to easyXAFS here (it takes a few minutes to receive them): https://www.easyxafs.com/copy-of-links I am currently analyzing XAFS data from that instrument and I can tell that the data in the XANES region look good in terms of signal-to-noise ratio, also collecting them for just 1 hour. To get sufficiently good data in the EXAFS region would need much longer data collections. One annoying disadvantage is coming from spurious fluorescence peaks from the standard X-Ray tubes used. The measurable elements and edges are limited, of course. Best regards Michele Piana -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, 2 August 2023 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 246, Issue 1 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. EasyXAFS - any experience with? (laavakyan) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Aug 2023 17:23:48 +0300 From: laavakyan <laavakyan(a)sfedu.ru> To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] EasyXAFS - any experience with? Message-ID: <50478bcd-56fa-536a-3a62-bb8de37e844e(a)sfedu.ru> Content-Type: text/plain; charset=UTF-8; format=flowed Dear Ifeffit and XAFS society, I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. Regards, Leon Avakyan ------------------------------ Subject: Digest Footer _______________________________________________ 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 ------------------------------ End of Ifeffit Digest, Vol 246, Issue 1 ***************************************

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EasyXAFS - any experience with?
by laavakyan 02 Aug '23

02 Aug '23

Dear Ifeffit and XAFS society, I am regularly receiving the advertisements from EasyXAFS with their in-laboratory XAFS setups, but can not find any publication track record about the usage of their setups (except for XES ones, which are a few). Is there any information or user feedbacks about EasyXAFS? May be there are results in synchrotron proposals, etc? The question rises since I have recommended them to colleagues in Republic of Armenia and they are going to purchase one of the setups. Regards, Leon Avakyan

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Advanced EXAFS analysis course Nov. 1-3
by Anatoly Frenkel 21 Jul '23

21 Jul '23

Dear colleagues: Please share this info with your students and postdocs. The application deadline is Aug. 31. https://www.bnl.gov/xafscourse/ Remember to state your expertise with EXAFS data analysis and modeling in the application. Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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Deglitch the data
by Shailendra 17 Jul '23

17 Jul '23

Hi, IFEFFIT community, I am Rachna, a Ph.D. student working on IrO2 based OER catalyst. I am a new XAS user. Recently, we recorded some XAS on amorphous IrO2 electrode samples however some of the samples show a dip in adsorption at high energy. The glitches are similar to the one in the attached photo. I am attaching the Athena file for the measurements too. I was wondering if there is a way to remove such glitches. I would greatly appreciate any tips or tricks you may have for dealing with this situation. Thanks, Kavya Rachna

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Re: [Ifeffit] Help installing Demeter on a Mac
by Fowler, Joseph W. (Assoc) 01 Jul '23

01 Jul '23

Hello Kyle, I agree that putting /opt/local/bin in your PATH should be adequate, so this isn’t totally obvious. The executables athena, hephaestus, and artemis should all be in /opt/local/bin/. Are they? What is the result if you execute the following? $ port contents demeter I’m the official maintainer of the Macports version of Demeter. Unfortunately, I’m not a regular user. In fact, it’s not installed on the everyday computer that I’ve had for four years (to give you an idea of what “not regular” means to me). Worse, there’s a chronic problem that I have never worked out how to solve. The Demeter ports depends on many things. One is ifeffit, which is not really still supported, but Demeter can’t just magically start using Matt Newville’s replacement for ifeffit, known as Larch. It feels to me like Mac-Demeter is doomed to break permanently pretty soon, if it has not already. [Bruce, Matt, have I stated that accurately? Please correct me if I’m wrong.] Still, there exists a port for ifeffit and for demeter, and one should be able to install them. I’m trying it right now on a Mac that lacks them. It will take me a while, because I’m not a Perl user either, and there are dozens of dependencies to install first. Let’s see how it goes for me… This install is taking a very long time. I’m going to send this note as-is and report later about whether I can make athena run, and where the executable is located. (But I’m sure it will be /opt/local/bin/ ) Could I suggest that, if you get it to work, and you use it regularly, and you’re an open-source supporter, would you think about helping as a second official maintainer of the Demeter port? Other users could benefit from me teaming up with an actual demeter user, to be sure! Best wishes, Joe Fowler NIST Boulder Labs On Jun 30, 2023, at 11:00 AM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.c…<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<mailto:ifeffit-request@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov<mailto:ifeffit-owner@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. Help installing Demeter on a Mac (Kluherz, Tk) From: "Kluherz, Tk" <Tk.Kluherz(a)nrel.gov<mailto:Tk.Kluherz@nrel.gov>> Subject: [Ifeffit] Help installing Demeter on a Mac Date: June 30, 2023 at 10:02:03 AM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>" <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Hello All, I’m a new postdoc at NREL, trying to install Demeter on my NREL Mac. I have previously only installed it on a Linux system. I followed the instructions<https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…> for installing on a Mac, including the logout/login, and the installation appeared to be successful, with no errors. However, when I then try to run athena/artemis/hephaestus from the command line, I get a ‘command not found’ error. Has anyone encountered this problem before? I thought I found a thread in the archives from 2014, but there was not response to the issue. I suspect it may be that the command location was not added to the $PATH, but am not sure where it is in order to add it. Here’s the output from echo $PATH: /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin Any help would be appreciated! Thanks, Kyle _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@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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Help installing Demeter on a Mac
by Kluherz, Tk 30 Jun '23

30 Jun '23

Hello All, I’m a new postdoc at NREL, trying to install Demeter on my NREL Mac. I have previously only installed it on a Linux system. I followed the instructions<https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h…> for installing on a Mac, including the logout/login, and the installation appeared to be successful, with no errors. However, when I then try to run athena/artemis/hephaestus from the command line, I get a ‘command not found’ error. Has anyone encountered this problem before? I thought I found a thread in the archives from 2014, but there was not response to the issue. I suspect it may be that the command location was not added to the $PATH, but am not sure where it is in order to add it. Here’s the output from echo $PATH: /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin Any help would be appreciated! Thanks, Kyle

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EXAFS course at BNL: Nov. 1-3, 2023
by Anatoly Frenkel 29 Jun '23

29 Jun '23

Dear subscribers: The information about the upcoming XAFS short course is here: https://www.bnl.gov/xafscourse/ The course will be taught in-person. The place in the course is limited, and, due to the emphasis on advanced methods, the preference will be given to those participants who have prior experience with EXAFS data modeling and analysis. The info about the past course topics (2005-2022) is at the SCC website: https://you.stonybrook.edu/scc2/xafs-workshops/ Regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering (primary appointment) Department of Chemistry (affiliate appointment) * Stony Brook University * Stony Brook, NY 11794 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 Joint Appointment: Senior Chemist Chemistry Division, *Brookhaven National Laboratory* Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/staff/frenkel -------------------------------------------------------------------

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Postdoc position at BM23 ID24 XAS beamlines
by Kirill LOMACHENKO 28 Jun '23

28 Jun '23

Dear all, we are looking for an excellent postdoc to work with us at BM23 and ID24 XAS beamlines of the ESRF (Grenoble, France) in the field of chemistry (catalysis, electrochemistry, energy materials, etc). Cutting-edge research, state-of-the-art equipment, friendly team, competent users, great location, competitive salary and all other things to make a scientist happy. If you are good at applying XAS for chemistry (or know someone who is), please find the link to the position below (in case the link is not visible, just google "ESRF jobs"). Do not hesitate to contact me for more details. Best regards, 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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Brain teaser
by Anatoly Frenkel 15 Jun '23

15 Jun '23

Hello, all. It is a low- to medium- level brain teaser. Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? Anatoly [image: image.png]

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Re: [Ifeffit] [Ext] Brain teaser
by Anatoly Frenkel 15 Jun '23

15 Jun '23

Thank you, Robert, Matthew, Jeff, Kirill, Terry and Sirine for great suggestions. I initially thought that the explanation for the linearity or the transmission signal is a superposition of two opposite trends: 1) increase of flux with energy due to the mirror effect and 2) similar decrease with energy due to the photon removal by first effect in the I0 detector. But I did not look into the main reason for the curving up of the I0 signal and I agree it is not a result of the reflectivity. I fill follow up on all suggestions, and, if something more definitive transpires, will report back. Thanks again for your time and advice! Anatoly > On Jun 15, 2023, at 2:10 AM, matthew marcus <mamarcus(a)lbl.gov> wrote: > The mirror was set up for a run at the Pd K-edge, according to the problem statement. Therefore, its nominal angle must be such as to put the critical energy >25keV. An angle of 3mrad would do it. At that angle, the reflectivity (assuming no roughness) goes up with energy in the relevant range, but only by a few percent. > > We're not told what the ratio of gains of the current amps is, or whether the ion chambers have the same path length, so we can't tell whether the signals are comparable, as shown on the graph, or orders of magnitude different. > mam > > On 6/14/2023 10:17 PM, Jeffrey Terry wrote: >> Well, I’ll take a shot. Looks like the mirror angle is totally fubared, you are getting Bragg peaks from the coating or substrate that are giving you the peaks in Io. Since you have no idea what angle those are going through Io, they are unlikely to make it into either the sample or It. Since those photons are removed from the beam hitting the sample, they would show up as intensity dips in It. I’d bet that most (all?) of the reflected beam is not going into the sample. I’m kind of surprised It signal is as clean as it is, but then I don’t know the gains on either measurement amplifiers. I couldn’t find a flat mirror angle that would cause the cutoff at 12870? eV but since it is a collimating mirror who knows what range of angles were actually being hit. >> Jeff Terry >> Interim Chair, Department of Biology >> Interim Chair, Department of Social Sciences >> Professor of Physics >> Professor of Mechanical, Materials, and Aerospace Engineering >> Editor, Applied Surface Science >> Illinois Institute of Technology >> 3101 S. Dearborn St. >> Chicago IL 60616 >> 630-252-9708 >>> On Jun 14, 2023, at 7:27 PM, Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu <mailto:anatoly.frenkel@stonybrook.edu>> wrote: >>> Hello, all. It is a low- to medium- level brain teaser. >>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >>> Anatoly >>> <image.png> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >> _______________________________________________ >> 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 > _______________________________________________ > 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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Re: [Ifeffit] Brain teaser
by Kirill LOMACHENKO 15 Jun '23

15 Jun '23

Hi Anatoly, maybe the high voltage of the I0 chamber is off? All the best, Kirill 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 On 15/06/2023 08:09, 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: Brain teaser (Anatoly Frenkel) > 2. Re: [Ext] Brain teaser (Jeffrey Terry) > 3. Re: [Ext] Brain teaser (matthew marcus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 15 Jun 2023 00:30:41 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Brain teaser > Message-ID: <866EACCF-DAD2-4486-AAE0-AC3F6B28023E(a)stonybrook.edu> > Content-Type: text/plain; charset=utf-8 > > Amazing idea. I thunk you were the only one who succeeded to use third harmonic of Si for taking EXAFS at high atomic number elements. But that does not explain the peaks and dips. > > Anatoly > >> On Jun 15, 2023, at 12:22 AM, matthew marcus <mamarcus(a)lbl.gov> wrote: >> >> ?Suppose the mono is being used at the 333 reflection (for Si), intentionally working at the 3rd harmonic. In that case, if the fundamental isn't filtered out, you could get just what we see, with the sample doing the filtering before the beam gets to the transmission chamber. >> mam >> >>> On 6/14/2023 9:16 PM, Anatoly Frenkel wrote: >>> Thank you, Matthew and Robert, but I think the explanation is more simplle. The fact that there are peaks in I0 and dips in transmission is a clue that explains why transmission is almost linear while I0 curves up. >>> Anatoly >>>>> On Jun 14, 2023, at 11:34 PM, matthew marcus <mamarcus(a)lbl.gov> wrote: >>>> ?One thing that's pretty odd is that the glitches are peaks in I0, and dips in It. It would be much easier to explain if It was the one that increased steeply and I0 was more linear, but the presence of the edge in It shows that you didn't switch them. Red = It. What's that sudden drop at the end? >>>> >>>> Could it be that the I0 chamber is misaligned so that beam is scraping one of the plates? That could cause all sorts of odd things to happen. >>>> mam >>>> >>>>> On 6/14/2023 5:27 PM, Anatoly Frenkel wrote: >>>>> Hello, all. It is a low- to medium- level brain teaser. >>>>> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >>>>> Anatoly >>>>> image.png >>>>> _______________________________________________ >>>>> 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 >>>> _______________________________________________ >>>> 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 >>> _______________________________________________ >>> 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 >> _______________________________________________ >> 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 > > > ------------------------------ > > Message: 2 > Date: Thu, 15 Jun 2023 00:17:35 -0500 > From: Jeffrey Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] [Ext] Brain teaser > Message-ID: <C024E52C-2EDF-49C0-9B5A-168A2B14F8D3(a)iit.edu> > Content-Type: text/plain; charset="utf-8" > > Well, I?ll take a shot. Looks like the mirror angle is totally fubared, you are getting Bragg peaks from the coating or substrate that are giving you the peaks in Io. Since you have no idea what angle those are going through Io, they are unlikely to make it into either the sample or It. Since those photons are removed from the beam hitting the sample, they would show up as intensity dips in It. I?d bet that most (all?) of the reflected beam is not going into the sample. I?m kind of surprised It signal is as clean as it is, but then I don?t know the gains on either measurement amplifiers. I couldn?t find a flat mirror angle that would cause the cutoff at 12870? eV but since it is a collimating mirror who knows what range of angles were actually being hit. > > Jeff Terry > Interim Chair, Department of Biology > Interim Chair, Department of Social Sciences > Professor of Physics > Professor of Mechanical, Materials, and Aerospace Engineering > Editor, Applied Surface Science > Illinois Institute of Technology > 3101 S. Dearborn St. > Chicago IL 60616 > 630-252-9708 > > > > > >> On Jun 14, 2023, at 7:27 PM, Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> wrote: >> >> Hello, all. It is a low- to medium- level brain teaser. >> >> Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? >> >> Anatoly >> >> <image.png> >> _______________________________________________ >> 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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Larch 0.9.70 released
by Matt Newville 09 Jun '23

09 Jun '23

Hi Folks, We have been releasing a version of X-ray Larch every few months, steadily adding features and improving bugs in XAS Viewer and in the general library. We have not felt the need to announce every release, but I would like to address a problem that many people have seen with automated updates, especially on Windows. Basically, automated updates from XAS Viewer do not work on Windows, and running the automated updates can (and I think even "usually will") lead to a broken installation. This can be (and needs to be) fixed by running C:\Users\YourName\xraylarch\Scripts\pip install --upgrade xraylarch from a Command Prompt terminal. With the latest version, XAS Viewer will only inform you (in the status bars at the bottom of the main window) when an update is available, and not continually prompt you to update now. A new desktop application called "Larch Updater" will also be installed that will run the above command. Unfortunately, the current version you have installed will still prompt you for an automated update. I recommend that you do not do this, but run the above command yourself, and then going forward, we'll all be able to use the updater at our own pace. --Matt PS: Some of the other changes in the latest version can be seen at https://github.com/xraypy/xraylarch/releases/tag/0.9.70

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Post-doc position at SSRL
by Ritimukta Sarangi 06 Jun '23

06 Jun '23

Hello Folks, We have an open post-doc position in XAS/EXAFS/advanced spectroscopy at SSRL. We are looking for someone with expertise in or interest in biological/molecular applications of XAS. Please see the job listing here: https://careers.slac.stanford.edu/sites/default/files/SSRL_X-ray_Spectrosco… If you have any questions, please do not hesitate to reach out. We are hoping to fill this position asap but can wait for for a few months for the right candidate! Kind regards, Riti Sarangi SSRL Sent from my iPhone

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python accesses outlook PST files during X-ray larch binary installation on Windows 10 computer
by Voegelin, Andreas 06 Jun '23

06 Jun '23

Dear All I apologize for this question related to IT safety rather than science and the use of Larch. Today, I installed Larch for Windows on an institute computer using the latest Windows 64-bit binary installer (0.9.68). Now I got the following alert from our IT security: “The process c:\users\%USER%\appdata\local\xraylarch\python.exe accessed Outlook files. The user who ran the process was XXXX. The accessed files were: XXXX.pst, YYYY.pst”. It seems that during the installation of Larch, python.exe accessed some outlook archive files in another folder on the C drive, and I do not know if this should be a matter of concern. Has anyone experienced a similar behavior before, or does anyone with Larch/python skills have an explanation for this? Cheers, Andreas

2 2

calibrated Fe(CP)2 and beam effect
by Esmael Balaghi 26 May '23

26 May '23

Dear All, Does anyone happen to have a spectrum of bulk ferrocene (Fe K edge), by any chance? It would be even more helpful if it includes the spectrum of Fe foil or calibrated ferrocene. I'm trying to determine the extent of the beam effect, whether it caused reduction/oxidation or decomposition, during data acquisition. I would greatly appreciate any tips or tricks you may have for dealing with this situation. Thank you in advance. Esmael

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Re: [Ifeffit] Problems with FEFF calculation using CIF file (Matt Newville)
by Volker, Anouk 26 May '23

26 May '23

Dear Matt, Thank you for the quick response. The first error gets indeed resolved by removing the atoms labeled with a B. I was not very clear in my first post that I had to do this to have the ATOMS window run properly in Artemis. The problem I am stuck on is that when I have them removed and then run the FEFF window, it seems to all work fine, until I try and drag the paths into the Path window in Artemis. At that point the paths seem to no longer exist. I hope this clears up my question a bit more. Kind regards, Anouk On Thu, May 25, 2023 at 7:02 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: Problems with FEFF calculation using CIF file (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 May 2023 12:29:01 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file > Message-ID: > <CA+7ESbpH97zi+-xbK2R62m8ND-MG+6OgMB= > R16zSqXE2za7yCA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Anouk, > > I am not sure what is happening with that CIF file. When I try to read > that with pymatgen, I get > > >>> from pymatgen.io.cif import CifParser > >>> structs = CifParser('VOXZAJ.cif') > >>> structs.get_structures() > .../site-packages/pymatgen/io/cif.py:1145: UserWarning: Error is Species > occupancies sum to more than 1!. > warnings.warn(f"Error is {str(exc)}.") > .../site-packages/pymatgen/io/cif.py:1148: UserWarning: Issues encountered > while parsing CIF: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, > 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If they are within the > occupancy_tolerance, they will be rescaled. The current occupancy_tolerance > is set to: 1.0 > Species occupancies sum to more than 1! > warnings.warn("Issues encountered while parsing CIF: " + > "\n".join(self.warnings)) > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > .../site-packages/pymatgen/io/cif.py", line 1150, in get_structures > raise ValueError("Invalid cif file with no structures!") > ValueError: Invalid cif file with no structures! > > If you remove all the atomic sites that have a "B" in their name, that gets > resolved, but I do not know if that is still the correct structure - or > what the "B" means. > > CIF is complicated, but just from a practical point of view, I think we are > going to take `pymatgen` as the arbitrator of "valid CIF". > > > On Wed, May 24, 2023 at 11:30?AM Volker, Anouk <a.volker(a)student.rug.nl> > wrote: > > > Dear all, > > > > I hope this email finds you well. I have encountered a problem that I > have > > not been able to fix on my own. I have a specific CIF file (from the > CCDC > > database) that is attached to the e-mail. After removing the duplicate > > atoms in the file, the ATOMS window seems fine. The FEFF calculation will > > run without any errors and within the FEFF window the paths are displayed > > and can be plotted. The problem arises when I try to take some of the > paths > > from the FEFF window and drag them into the Path window. Now the paths > can > > no longer be plotted and when trying to use them to fit, it seems like > the > > paths are non-existent as well. > > > > Is there something wrong with the CIF file that causes this to happen and > > if so, what can be done to fix it? I have already tried to make a > feff.inp > > file from the xyz data (after opening the CIF file in any viewer), but > this > > gives the same problem. > > > > Thank you in advance, > > > > Kind regards, > > Anouk Volker > > > > Master student, Browne Group > > Stratingh Institute, University of Groningen > > _______________________________________________ > > 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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Problems with FEFF calculation using CIF file
by Volker, Anouk 24 May '23

24 May '23

Dear all, I hope this email finds you well. I have encountered a problem that I have not been able to fix on my own. I have a specific CIF file (from the CCDC database) that is attached to the e-mail. After removing the duplicate atoms in the file, the ATOMS window seems fine. The FEFF calculation will run without any errors and within the FEFF window the paths are displayed and can be plotted. The problem arises when I try to take some of the paths from the FEFF window and drag them into the Path window. Now the paths can no longer be plotted and when trying to use them to fit, it seems like the paths are non-existent as well. Is there something wrong with the CIF file that causes this to happen and if so, what can be done to fix it? I have already tried to make a feff.inp file from the xyz data (after opening the CIF file in any viewer), but this gives the same problem. Thank you in advance, Kind regards, Anouk Volker Master student, Browne Group Stratingh Institute, University of Groningen

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Re: [Ifeffit] [Attachment Removed] Re: Low amplitude chi signal of first shell calculated by FEFF
by Matt Newville 24 May '23

24 May '23

Hi Fan, If you included an attachment, I did not see it. If so, can you send it some other way? I would not expect that the Sr K-edge of SrTiO3 needs much playing around with parameters in the feff.inp file prior to running Feff. I would advise against doing that unless you know what you are doing. Don't set Vi to be below 0. I would be more inclined to believe that the data treatment had problems or that the use of the feff paths had problems. Without knowing what you did, it is very hard to speculate what might be going wrong. On Tue, May 23, 2023 at 9:38 PM Dongxiao <dongxiaofan01(a)gmail.com> wrote: > An attachment on this email message was removed because it contained > potentially dangerous content. If you are expecting a file from the sender, > request that they provide access to it via a file sharing service. > ------------------------------ > > Hello, Matt, cc: who is interested, > > > > Thank you very much for your reply. > > The low amplitude chi signal is common when I calculated the A site EXAFS > signal of perovskite structure. > > Especially the chi signal of first single scattering path (A-O) is > unreasonable low. > > In my case (Sr K-edge EXAFS of SrTiO3), the intensity of calculated chi is > smaller than the low-temperature experimental chi. > > I have been struggling with this problem for some time. I am looking > forward to somebody who can give me some advice.. > > I attached the related files for your check. > > > > I try to vary Vr and Vi value and want to see how the amplitude change. > > If set the Vi to negative, it indeed can increase the amplitude, but I > don’t know if it is proper. > > Maybe the problem is caused by the bad muffin-tin potential, but I don’t > know how to improve it. > > > > Can you give me some advice? > > > > Best regards, > > Fan > > > > -----Original Message----- > > Matt Newville > <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=f…> > Fri, 12 May 2023 14:25:36 -0700 > <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=d…> > > > > Hi Fan, > > > > On Fri, May 12, 2023 at 9:56 AM <dx...(a)post.kek.jp> wrote: > > > > > Hi, All > > > > > > > > > > > > The problem I meet is the low amplitude chi signal of first shell > > > calculated by FEFF. > > > > > > The consequence of the fitting is large value of SO2 (1.5-2.0), which is > > > quite unacceptable. > > > > > > I tried to fit the dataset measured by different people at different > > > beamline, the consequence is same. > > > > > > > > > > > > My data is T-dependent Sr K-edge EXAFS of SrTiO3, path file generated by > > > FEFF10, fitting process by Larch+python. > > > > > > By check the email list, it seems the long shell distance (2.7 A) is the > > > origin of the problem. I am not sure for that. > > > > > > I also try to vary the Vi value to improve the amplitude, the change is > > > small. > > > > > > Can any body give me some advice? > > > > > > > I would not expect that a Sr-O distance of 2.7 to 2.8Ang would cause an > > amplitude problem. I would tend to expect that being off by a factor of 2 > > would > > imply normalization issues. You could try to vary Vi, but I would not > > guess that you need to do that. Why do you set Vi to 2 (eV)? > > > > Do you have data and/or analysis steps (script or Larch session file) you > > can share? > > > > > > > > > > > Best regards, > > > > > > Fan > > > > > > > > > > > > My feff.inp file is like: > > > > > > -------------------------------------------- > > > > > > * This feff8 file was generated by Demeter 0.9.26 > > > > > > * Demeter written by and copyright (c) Bruce Ravel, 2006-2019 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * space = 221 > > > > > > * a = 3.90500 b = 3.90500 c = 3.90500 > > > > > > * alpha = 90.00000 beta = 90.00000 gamma = 90.00000 > > > > > > * rmax = 9.00000 core = Sr > > > > > > * polarization = 0 0 0 > > > > > > * shift = 0 0 0 > > > > > > * atoms > > > > > > * # el. x y z tag > > > > > > * Sr 0.00000 0.00000 0.00000 Sr > > > > > > * Ti 0.50000 0.50000 0.50000 Ti > > > > > > * O 0.00000 0.50000 0.50000 O > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * total mu*x=1: 32.298 microns, unit edge step: 44.289 microns > > > > > > * specific gravity: 5.118 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * normalization correction: 0.00029 ang^2 > > > > > > * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- > > > > > > * Sr K edge energy = 16105 eV > > > > > > EDGE K > > > > > > S02 1.0 > > > > > > > > > > > > * pot xsph fms paths genfmt ff2chi > > > > > > CONTROL 1 1 1 1 1 1 > > > > > > > > > > > > PRINT 1 0 0 0 0 3 > > > > > > > > > > > > * ixc [ Vr Vi ] *** ixc=0 means to use Hedin-Lundqvist > > > > > > EXCHANGE 0 2 1 -1 > > > > > > *** Radius for self-consistent pots (2 shells is a good choice) > > > > > > * r_scf [ l_scf n_scf ca ] *** l_scf = 0 for a solid, 1 for > > > a molecule > > > > > > SCF 7 0 100 0.1 1 > > > > > > * kmax [ delta_k delta_e ] *** Upper limit of XANES > > > calculation. > > > > > > * XANES 4.0 > > > > > > * r_fms l_fms *** Radius for Full Mult. Scatt. l_fms = 0 > > > for a solid, 1 for a molecule > > > > > > * FMS 16.77392 0 > > > > > > * emin emax eimag *** Energy grid over which to calculate DOS > > > functions > > > > > > * LDOS -30 20 0.1 > > > > > > *** for EXAFS: RPATH 5.0 and uncomment the EXAFS card > > > > > > CRITERIA 0 0 > > > > > > * POLARIZATION 0 0 0 > > > > > > COREHOLE FSR > > > > > > RPATH 7.0 > > > > > > LDOS -30 20 0.1 > > > > > > EXAFS 20.0 > > > > > > > > > > --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 243, Issue 10
by Shuting Xiang 17 May '23

17 May '23

Thank you very much! We really appreciate it! Shuting On Wed, May 17, 2023 at 12:02 AM <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. In2O3 and In foil XAFS spectra in need (Shuting Xiang) > 2. Re: In2O3 and In foil XAFS spectra in need (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 16 May 2023 22:29:22 -0400 > From: Shuting Xiang <shuting.xiang(a)stonybrook.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov, "Li, Zhengyuan (li3zn)" > <li3zn(a)mail.uc.edu>, "Jimenez, Juan" <jjimenez1(a)bnl.gov> > Subject: [Ifeffit] In2O3 and In foil XAFS spectra in need > Message-ID: > < > CAPi4yra21_O6RT+KoZCJRUL8rk2ST-USoB_wMpRB7XFPyF5GZA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I hope this email finds you well. I am writing to inquire if any of you > might have the XAFS spectra of In oxide (In2O3) and In foil. We are in need > of these spectra as references for our ongoing research. If anyone would be > kind enough to share these spectra with us, we would greatly appreciate it. > > Please feel free to reach out to me if you are able to assist. Your support > would be greatly appreciated. > > Thank you very much for your attention and consideration. > > Best, > > Shuting Xiang > Department of Material Science and Engineering > Stony Brook University > Shuting.xiang(a)stonybrook.edu >

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Question about EXAFS fitting of mixtures
by Soyoung Kim 17 May '23

17 May '23

Dear all, While fitting EXAFS for tiny Pt nanoparticles, a simple question occurred to me. For these two scenarios: 1. All Pt atoms are coordinated to 3 O atoms and 3 Pt atoms each. 2. Half of the Pt atoms are coordinated to 6 O atoms and half to 6 Pt atoms. If we fit only single-scattering paths, would it be possible to tell apart these two scenarios with EXAFS fitting? What about linear combination analysis of the XANES? Thank you, Soyoung

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Not possible to install larch on actual system and Mac M1 system
by Mangold, Stefan (IPS) 17 May '23

17 May '23

Dear all, from binary package: can’t write to system partition by script and by anaconda I got the following message back: Collecting fabio Using cached fabio-2023.4.1.tar.gz (724 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error System ist 13.3.1, tried to install the newest version completely from scratch, because the update killed my larch version …. best regards Stefan

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In2O3 and In foil XAFS spectra in need
by Shuting Xiang 17 May '23

17 May '23

Dear all, I hope this email finds you well. I am writing to inquire if any of you might have the XAFS spectra of In oxide (In2O3) and In foil. We are in need of these spectra as references for our ongoing research. If anyone would be kind enough to share these spectra with us, we would greatly appreciate it. Please feel free to reach out to me if you are able to assist. Your support would be greatly appreciated. Thank you very much for your attention and consideration. Best, Shuting Xiang Department of Material Science and Engineering Stony Brook University Shuting.xiang(a)stonybrook.edu

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customized dead-time correction in Larch
by Esmael Balaghi 16 May '23

16 May '23

Dear Matt, Dear All, Is there a way to use our customized dead-time correction function in XAS viewer/Larch? Bests, Esmael

2 3

Question about Artemis
by María Elena Montero Cabrera 13 May '23

13 May '23

Dear IFEFFIT-friends, I am working with Demeter version 0.9.26. In older versions of Artemis, I remember being able to load FEFF9 to produce the model for fitting, but I can't figure out how to do it in this version. I have only found how to write the Atoms results to be read by FEFF8. Is there a way to use the version of FEFF9 for this version of Artemis? Can anyone tell me how it's done or instead recommend where to get documentation on it? Thank you very much in advance Regards María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Complejo Industrial Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123

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Low amplitude chi signal of first shell calculated by FEFF
by dxfan＠post.kek.jp 12 May '23

12 May '23

Hi, All The problem I meet is the low amplitude chi signal of first shell calculated by FEFF. The consequence of the fitting is large value of SO2 (1.5-2.0), which is quite unacceptable. I tried to fit the dataset measured by different people at different beamline, the consequence is same. My data is T-dependent Sr K-edge EXAFS of SrTiO3, path file generated by FEFF10, fitting process by Larch+python. By check the email list, it seems the long shell distance (2.7 A) is the origin of the problem. I am not sure for that. I also try to vary the Vi value to improve the amplitude, the change is small. Can any body give me some advice? Best regards, Fan My feff.inp file is like: -------------------------------------------- * This feff8 file was generated by Demeter 0.9.26 * Demeter written by and copyright (c) Bruce Ravel, 2006-2019 * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * space = 221 * a = 3.90500 b = 3.90500 c = 3.90500 * alpha = 90.00000 beta = 90.00000 gamma = 90.00000 * rmax = 9.00000 core = Sr * polarization = 0 0 0 * shift = 0 0 0 * atoms * # el. x y z tag * Sr 0.00000 0.00000 0.00000 Sr * Ti 0.50000 0.50000 0.50000 Ti * O 0.00000 0.50000 0.50000 O * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * total mu*x=1: 32.298 microns, unit edge step: 44.289 microns * specific gravity: 5.118 * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * normalization correction: 0.00029 ang^2 * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- * Sr K edge energy = 16105 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 * ixc [ Vr Vi ] *** ixc=0 means to use Hedin-Lundqvist EXCHANGE 0 2 1 -1 *** Radius for self-consistent pots (2 shells is a good choice) * r_scf [ l_scf n_scf ca ] *** l_scf = 0 for a solid, 1 for a molecule SCF 7 0 100 0.1 1 * kmax [ delta_k delta_e ] *** Upper limit of XANES calculation. * XANES 4.0 * r_fms l_fms *** Radius for Full Mult. Scatt. l_fms = 0 for a solid, 1 for a molecule * FMS 16.77392 0 * emin emax eimag *** Energy grid over which to calculate DOS functions * LDOS -30 20 0.1 *** for EXAFS: RPATH 5.0 and uncomment the EXAFS card CRITERIA 0 0 * POLARIZATION 0 0 0 COREHOLE FSR RPATH 7.0 LDOS -30 20 0.1 EXAFS 20.0

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Beamline Scientist at APS
by Kelly, Shelly Diane 09 May '23

09 May '23

Hello Fellow XAS scientists: We have a position open for beamline scientist in the Spectroscopy Group at the APS. Please reach out to all those that might be interested in joining our team here in Chicago-land area. https://argonne.wd1.myworkdayjobs.com/en-US/Argonne_Careers/job/Lemont-IL-U… Kind regards, Shelly Kelly

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Co(OH)2 spectrum
by Christian Wittee Lopes 09 May '23

09 May '23

Hi folks, Does anyone have a spectrum of bulk cobalt hydroxide Co(OH)2 by chance? Thank you in advance. Christian Wittee Lopes -- 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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Re: [Ifeffit] Ifeffit Digest, Vol 242, Issue 18
by Jyoti Pandey 26 Apr '23

26 Apr '23

Thank you! With Best Regards Dr. Jyoti Pandey, Ph.D. Postdoctoral Researcher Department of Physics Central Michigan University, MI, USA Mobile No. +1-928-265-0599 ..................................... On Tue, Apr 25, 2023 at 9:52 AM <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: (no subject) (Anatoly Frenkel) > 2. Re: (no subject) (Kelly, Shelly Diane) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Apr 2023 13:04:16 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] (no subject) > Message-ID: > < > CAFsMoZZZy_-1G5hnw1UNEbGMA+zB6pRMBZR2OPCpXqd8bBUjCg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Joyti, > > The coordination number of Rh-C bonds is defined as the total number of > Rh-C bonds in the sample divided by the total number of Rh atoms in the > sample. > Anatoly > ------------------------------------------------------------------- > Anatoly I. Frenkel > Professor > Department of Materials Science and Chemical Engineering (primary > appointment) > Department of Chemistry (affiliate appointment) > Stony Brook University > Stony Brook, NY 11794 > Email: anatoly.frenkel(a)stonybrook.edu > < > https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb… > > > http://you.stonybrook.edu/frenkel > Co-Director and Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL > http://you.stonybrook.edu/scc2 > > Joint Appointment: > Senior Chemist > Chemistry Division, Brookhaven National Laboratory > Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 > Email: frenkel(a)bnl.gov > https://www.bnl.gov/staff/frenkel > ------------------------------------------------------------------- > > > On Mon, Apr 24, 2023 at 12:25?PM Jyoti Pandey <jyotipandey51092(a)gmail.com> > wrote: > > > Hello everyone, > > > > I have a cluster of 13 Rh atoms above the graphene sheet. The first > > coordination number that I am getting is around 1.65 (which is obtained > by > > choosing a Rh-C) path. I am curious to know whether this value is the > > "exact" or the "average" coordination number w.r.t all the Rh atoms. > > > > Thanks > > > > With Best Regards > > > > Dr. Jyoti Pandey, Ph.D. > > Postdoctoral Researcher > > Department of Physics > > Central Michigan University, MI, USA > > Mobile No. +1-928-265-0599 > > ..................................... > > > > _______________________________________________ > > 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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