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

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

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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,

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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,

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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

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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

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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

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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

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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…

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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

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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

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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 ***************************************

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

12 Dec '24

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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

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

09 Dec '24

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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!… >

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

22 Nov '24

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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

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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!… >

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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

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

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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

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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

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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

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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

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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)_/¯

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