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

Elemental concentrations in XRFMap_Viewer
by Tian, Tony 04 Sep '25

04 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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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 20 Aug '25

20 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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