March 2020 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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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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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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Unable to access content on millenia.cars.aps.anl.gov website
by Jullieta Lum 09 Mar '20

09 Mar '20

Good Day, I need assistance with accessing content on the iffefit website. I am subscribed to the mail list and receive the digest. However, I am unable to open any of the past questions and answers which I could do before. Hoping you can assist. Kind Regards, Jullieta

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PhD position in XAS for catalysis at ESRF
by Kirill LOMACHENKO 05 Mar '20

05 Mar '20

Dear all, it is my pleasure to inform you that we have opened a PhD position at BM23 and ID24 XAS beamlines of the ESRF (Grenoble, France). The focus of the PhD project is on the operando XAS and XES studies of novel industrial deNOx catalysts. The position is funded by a European program InnovaXN. The student will be hosted in ESRF, but will also have internships at Umicore Denmark (industrial partner) and University of Turin (academic partner). Full description of the project and the application form are here: https://esrf.gestmax.eu/1396/1/phd-position-operando-xas-dor-denox-catalysi… I would be grateful if you could forward this info to your colleagues and students who might be interested. Best regards, Kirill Lomachenko -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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