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

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 17 Nov '24

17 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 14 Nov '24

14 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 18 Oct '24

18 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 16 Oct '24

16 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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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

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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

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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… >*

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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 08 Aug '24

08 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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