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

Larch 0.9.47
by Matt Newville 18 Apr '20

18 Apr '20

Hi Everyone, Larch 0.9.47 is now available, with installers and source code at https://xraypy.github.io/xraylarch/installation.html. For python users, there is a plain python package available on PyPI and conda packages for Anaconda Python. See the installation docs for more details. There have been several improvements and bug fixes, especially for the XAS Viewer application and for XRF modeling in the nearly six months since the last release. In particular, there have been two improvements to basic XAFS and XANES data processing, both based on user reports and comparisons to older versions of Ifeffit/Athena and give a noticeable change in XAFS and XANES processing. First, the ranges used in by the pre_edge() function for finding the edge step for normalization are now better determined from the actual data range rather than simply being hard-wired numbers. These improvements were long over-due and give noticeably better default results for XANES data, especially for relatively low-energy edges such as S and Cl K edges. When reading Athena Project files (say, to import into XAS Viewer), the pre-edge and normalization ranges from the Athena Project file will be preserved. When reading in new raw data, or if you select the "Use Default Setting" button on the Normalization Panel for any group in XAS Viewer, the newer defaults will be used. You can always alter these values, but in playing around with this with a range of datasets, the new defaults seem to give a noticeable improvement in almost all cases and rarely bad. Second, as a few users have pointed out or gently hinted at over many months, there were sometimes significant differences in the background removals between classic Autobk/Ifeffit/Athena and Larch, with Larch sometimes being noticeably and inexplicably worse. I believe this involved two different problems. One was introduced a while back when implementing an estimate of delta_chi - the variance in chi due to the background subtraction. This estimate is important, but I botched some of the configurations of the number of knots, fit range, and Rbkg. The other problem was that "spline clamps" were just done too differently in Larch and Ifeffit/Athena. I believe this is now working much better: the background results are much more consistent, and do not occasionally get "very bad". They also happen to be generally closer to Autobk/Ifeffit/Athena, and perhaps slightly better because the fit range in R-space is now more consistently determined (instead of wandering +/- a few R data points around Rbkg where the misfit will often be the largest). In addition, `delta_chi` (never calculated in Ifeffit/Athena) is now also more consistent. One consequence of this change is that a very small change in Rbkg (of say 0.01 to 0.05 Ang) may actually give no difference at all in mu0(E) or in chi(k). I bring these changes up because I think they will be noticeable. I think they are both improvements, but let me know if you find cases for which you think are now made worse. Possibly related: one thing that I definitely noticed in going through several example data sets was that I tended to favor a k-weight of 2 instead of 1 for background subtraction -- so much so that it seemed like this might be a better default. I did not change this default yet, but if you have a strong opinion on this, that might be a good topic for discussion here. There are some documentation improvements, but this is an ongoing process and never complete. It is also one area where help and feedback would greatly be appreciated. If you or your students have time to work through the larch examples and/or documentation and make improvements or even suggestions for improvements in readability or completeness, it would be greatly appreciated. Thanks, --Matt Newville

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Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8
by Dien.Li＠srnl.doe.gov 14 Apr '20

14 Apr '20

Hi, all I fitted my Cr EXAFS data, but E0 was -2.5. I calibrated the spectrum in energy space by +10 eV, the spectra in K and R space were identical before and after this calibration, in contract to my understanding that the k space oscillations and R magnitude should shift. Could you please provide any direction on how to get E0 to position values or negative E0 is acceptable? Thank you so much. Dien Li Savannah River National Laboratory -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, April 13, 2020 12:04 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 206, Issue 8 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. Artemis crash upon empirical standard import. (George Sterbinsky) ---------------------------------------------------------------------- Message: 1 Date: Mon, 13 Apr 2020 11:02:34 -0500 From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Artemis crash upon empirical standard import. Message-ID: <CALoY8YzT1C+eGx_o2FUmwBbzRYYNeZL8tigM9zTzQMT0QKox5A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

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errors in bond lengths
by George Sterbinsky 13 Apr '20

13 Apr '20

Hello, As is well known, EXAFS is more accurate at determining relative changes in bond lengths than absolute changes in bond lengths due to cancelation of systematic errors in relative comparisons. When comparing the relative changes in bond lengths determined from EXAFS fits, as one might for a temperature series for example, is it appropriate to use the uncertainties returned by Artemis? My question arises in part from Phys Rev Lett vol. 100 pg. 055901 (2008), where the authors state that errors for changes in bond length in a temperature series were determined by empirical means rather than statistical means. This then raises the question as to if the authors believe that statistical means would overestimate the error. My inclination is to think that the uncertainties reported by Artemis would be appropriate because of the scaling by the square root of reduced chi squared. However, I want to see what others think about this before committing to it. Thank you, George

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larch can not deconvolve my data
by Shaofeng Wang 10 Apr '20

10 Apr '20

Dear all, Recently I am trying to deconvolve a As K-edge xafs data using larch. But the xas viewer program always crash. I tried other K edge spetra, it worked well. I attached my data, please give me some help. 祝好运！ Best regards, 王少锋，Shaofeng Wang, Ph.D 中国科学院沈阳应用生态研究所，Institute of Applied Ecology, CAS Email: wangshaofeng(a)iae.ac.cn; sf.wang(a)hotmail.com Address: Wenhua Road 72, Shenyang

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Fe 4+ reference
by George Sterbinsky 05 Apr '20

05 Apr '20

Hello, Does anyone have Fe K-edge XANES from an Fe4+ reference or sample (for example SrFeO3) that they can share? Thank you, George

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Re: [Ifeffit] Ifeffit Digest, Vol 206, Issue 1
by Christopher Chantler 04 Apr '20

04 Apr '20

Dear Anatoly and all Excellent question. The Guest Editors have been working very methodically and professionally through the manuscripts, with several undergoing multiple revisions. Today they have just submitted the last manuscript being the Guest Editorial, so I expect it will reach production within a couple of weeks [even with Covid]. In particular the referees have I believe kept everything to a high standard and perhaps that has taken an extra couple of revisions. Very best wishes to all Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ 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: Friday, 3 April 2020 4:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 206, 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. Chris Chantler, Re: XAFS conference proceedings (Anatoly Frenkel) 2. As(0) XAS spectrum (Richard Collins) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Apr 2020 14:22:06 -0400 From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Chris Chantler, Re: XAFS conference proceedings Message-ID: <CAFsMoZYbgj_YKE38Wv5kUiqeeCmQoiT2AJWJN93ai34PfDQFeA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Chris (if you are reading this), Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference proceedings will be finalized and published online? It currently shows "corrected proofs" but not the articles with pages. Perhaps, it is a bad time to follow up and I am sorry for bothering you. Hope everyone is safe and well. Best regards, Anatoly

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As(0) XAS spectrum
by Richard Collins 02 Apr '20

02 Apr '20

Dear XAFS community, I’m writing to see if anyone has an As(0) K-edge XAS spectrum that they would be willing to share with me. A spectrum obtained at room temperature would be ideal. Many thanks in advance, Richard Dr Richard N Collins Senior Lecturer School of Civil and Environmental Engineering UNSW Sydney Sydney, NSW 2052, Australia Tel: (02) 9385 5214 From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of Anatoly Frenkel Sent: Thursday, April 2, 2020 5:22 AM To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Chris Chantler, Re: XAFS conference proceedings Dear Chris (if you are reading this), Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference proceedings will be finalized and published online? It currently shows "corrected proofs" but not the articles with pages. Perhaps, it is a bad time to follow up and I am sorry for bothering you. Hope everyone is safe and well. Best regards, Anatoly

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Chris Chantler, Re: XAFS conference proceedings
by Anatoly Frenkel 01 Apr '20

01 Apr '20

Dear Chris (if you are reading this), Do you know when the Rad. Phys. Chem. issue with the latest XAFS conference proceedings will be finalized and published online? It currently shows "corrected proofs" but not the articles with pages. Perhaps, it is a bad time to follow up and I am sorry for bothering you. Hope everyone is safe and well. Best regards, Anatoly

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Question on (Combo-) LCF plot output
by t.zahoransky＠mineralogie.uni-hannover.de 30 Mar '20

30 Mar '20

Dear Mailing list, I am a relatively new user in terms of XAS data handling and I encountered a strange problem during LCF in Athena. I am working on LCF-combo fittings for Mn minerals as described in Manceau et al. 2012*. Fitting f.ex. a cryptomelane sample of myself with the open source monovalent manganese mineral standards of Manceau et al. 2012 in a fit range of -20 to +30 k, gives the following result shown below (I´ll attach the Athena project): " LCF fit of Cryptomelane_T_20K_ecd as flattened mu(E) from 6536.79 to 6586.79 Fit included 100 data points and 6 variables, and approximately 41.333 measurements Weights sum to 1: no Weights forced between 0 and 1: no Overall e0 shift used: yes Noise added to data: 0 R-factor = 0.0003537 Chi-square = 0.00815 Reduced chi-square = 0.0000858 . standard weight e0 ======================================================== . Manganosite.dat 0.042 (0.006) 1.631 (0.044) . Groutite.dat 0.030 (0.029) 1.631 (0.044) . Ca2Mn3O8.dat 0.288 (0.026) 1.631 (0.044) . Ramsdellite.dat 0.584 (0.022) 1.631 (0.044) . Mn2O3.dat 0.044 (0.025) 1.631 (0.044) . sum ........... 0.988 " Note that the box “all standards share an E0” is checked before clicking on “Fit this group”. Optically, the fit itself “looks” good compared to the data, yet, it is somewhat shifted on the x-axis compared to the data. I was wondering why, as this was not the first sample where this was the case. When I now uncheck the “All standards share an E0” box, leave everything else just the way it is and just click “Fit this group” again, the fit suddenly is shifted perfectly on my data. The strange thing is: Nothing else in the output-results changes – weights, R-factor, chi-square etc. just stay the same. Only slight changes in the numbers in brackets after the reported weights. The "new" result is: " LCF fit of Cryptomelane_Mikon_T_20K_ecd_reb-a-m as flattened mu(E) from 6536.79 to 6586.79 Fit included 100 data points and 5 variables, and approximately 41.333 measurements Weights sum to 1: no Weights forced between 0 and 1: no Overall e0 shift used: no Noise added to data: 0 R-factor = 0.0003537 Chi-square = 0.00815 Reduced chi-square = 0.0000849 . standard weight e0 ======================================================== . Mn2O3.dat 0.044 (0.024) 1.631 (0.000) . Manganosite.dat 0.042 (0.006) 1.631 (0.000) . Ca2Mn3O8.dat 0.288 (0.024) 1.631 (0.000) . Ramsdellite.dat 0.584 (0.019) 1.631 (0.000) . Groutite.dat 0.030 (0.026) 1.631 (0.000) . sum ........... 0.988 " Can anybody tell me, what is actually happening? I exported both data to excel to replot the fits to exclude a simple plot-bug, but the data behind show that this is real. So, I am changing the data behind the plot, but actually not the output data … what is going on here? You find the project attached – I hope someone can tell me, how to cope with that! Thank you very much, Teresa *Manceau, A., Marcus, M. A., & Grangeon, S. (2012). Determination of Mn valence states in mixed-valent manganates by XANES spectroscopy. American Mineralogist, 97(5-6), 816-827. -- Teresa Zahoransky Soil Mineralogy Gottfried Wilhelm Leibniz Universität Hannover Institute of Mineralogy Callinstr. 3, Room 325 D-30167 Hannover, Germany Phone: +49 (0)511 762-8058 Email: t.zahoransky(a)mineralogie.uni-hannover.de

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Yoshio Waseda database
by Pierre LECANTE 12 Mar '20

12 Mar '20

Dear XAS users, I have a problem and maybe you can help or point me to a suitable source: from time to time I used the database from Professor Yoshio Waseda, especially the structural database on molten metals measured by X-ray scattering, just like Farell-Lytle Database but for PDF studies; address was: http://ies.tagen.tohopku.ac.ip/~waseda/scm/AXS/index.html however it seems to be no more accessible and the change is relatively recent; any information on the problem or actually on a way to access such structural information should be greatly appreciated! sincerely, Pierre -- Groupe SINanO CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/SINanO-Surfaces-Interfaces-et-Nano-Objets Full list of publications: http://www.researcherid.com/rid/A-8745-2011 http://orcid.org/0000-0001-6337-6855

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