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

Co K-edge XAS spectra of Co(OH)2 and CoOOH
by Carlos Triana Estupinan 27 Aug '20

27 Aug '20

Dear mailing list, I am looking for the Co K-edge XAS spectra of Co(OH)2 and CoOOH containing both the XANES and EXAFS regions at room temperature. Thank you in advance. Kind regards, -- *Carlos A. Triana* PHD. - LIC.PHIL. Sciences Physics MSC.*-* BSC. Sciences Physics Postdoctoral research fellow University of Zürich Switzerland TEL: +41 076 814 41 60

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web apps for X-ray data and XAS library
by Matt Newville 14 Aug '20

14 Aug '20

Hi Folks, I was fortunate enough to have a summer student this crazy summer and had them work (from home, of course!) on web applications for X-ray data resources, including absorption calculations for materials. The result is a bit like a web version of Hephaestus and is currently at both https://xraydb.xrayabsorption.org/ and https://millenia.cars.aps.anl.gov/xraydb/ While similar to Hephaestus, there are some differences too. There are pages for absorption and fluorescence lines, absorption length calculations, ion chamber flux calculations, mirror reflectivities, scattering factors, and mono Darwin widths. Many of the calculations will show interactive plots, links to data, and/or a link to a python script to reproduce the calculation. Questions, comments, complaints, or suggestions for making this better are most welcome. We may have missed your favorite Hephaestus feature - is so, please let us know. Also: the X-ray Data Library - a collection of XAS spectra - has moved to https://xaslib.xrayabsorption.org/ <https://xraydb.xrayabsorption.org/> This has also expanded some (well, now with about 270 spectra), and added several features, notably interactive plots. Again, any comments or suggestions for making this better would be most welcome. I will be adding more data to this library, but I also ask that if anyone has data they can and would like to share on this site, please let me know. Thanks for any feedback or suggestions you might have. --Matt

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RE-REGISTRATION Request for SSRL Summer School
by Ritimukta Sarangi 05 Aug '20

05 Aug '20

Hello everyone, This message is going out at *11:23 AM PST on Aug 5, 2020*. Our registration website for the summer school has been overwhelmed by requests and we had to stop registration and fix some of the errors. I request that *if you registered before that time, please go ahead and re-register* for the summer school program. I apologize for the issues and request your continued patience with us in determining the best way to support smooth operations for this unprecedented amount of interest in the school. Thank you, Riti Sarangi p.s -please email me at ritis(a)slac.stanford.edu, if you have any questions.

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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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Jupyter/python question for Larch
by Garret Bland 04 Aug '20

04 Aug '20

Hello! I have a Python/Larch related question. I have been developing some python script via jupyter and incorporating Larch as a module. I was able to read an athena prj file with the following code *import larch as lc* *athena_prj = lc.io.read_athena(prjfilename)* Python stores this object as a 'Group' object with each spectrum being an instance. I would like to go through more processing with all spectra. Example: *for spectrum in athena_prj:* * lc.xafs.find_e0(spectrum.energy, spectrum.mu <http://spectrum.mu>, group = spectrum)* This does not work since the 'Group' object is not iterable. I tried to look up some other built-in functionality with python, but couldn't find an efficient way other than manually typing out each spectrum (athena_prj.spectrum1, athena_prj.spectrum2, .... etc). Is there any built-in functionality in larch that can iterate this 'Group' object? Any help would be appreciated. Thank you for your time! Garret -- Garret Bland PhD Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 201 Pittsburgh, PA, 15213

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