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

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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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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