July 2018 - 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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Re: [Ifeffit] using the mail list archive for mac install
by Matt Newville 17 Aug '18

17 Aug '18

Hi Joel, > I ran into the problem that some people seem to have with Demeter on mac while > upgrading to High Sierra. I found a fix on this mail list, but… Yeah, Demeter on MacOS is a continuing challenge. Even when it can be installed, parts of the GUI interaction are pretty buggy (I believe this must be due to wxPerl on Mac). MacPorts seems to need a fair amount of attention and expects the end user to know Unix command line tools well enough to be able to run updates and understand and react to error messages. For sure, it is a useful resource for developers, but it seems like it is not really designed for deploying end-user software. Still , I don't know of a better alternative for getting Demeter working on MacOS. I've tried many of the alternatives, and wxPerl seems to be a real stumbling block for all of them. > 1) I can’t download Template.pm from the archive (bin file that uncompresses to cpgz file > that uncompresses back to a bin file…) I think that the advice from Luke and Bruce back in April was to try to find and install version 1.47 of Text::Template. You might find this at https://metacpan.org/source/MSCHOUT/Text-Template-1.47/lib/Text and try unpacking and installing that. There may be a way to specify particular versions with the "cpan" program, but I do not know how to do it. I don't think we want "install old version of some library" to be a long term solution (this will break other things eventually), but it might work for you. > 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). To clarify, in April I updated MacPorts to the latest versions, installed the packages for Demeter 0.9.25. Then I installed Demeter 0.9.26 from source code on top of that. That might also work , but it's probably more work than most folks would want to do. Cheers, --Matt

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Basic questions about the preliminary data processing in Athena
by Haifeng Li 14 Aug '18

14 Aug '18

Dear ALL, I am a beginner in Athena. Recently I got the spectra and I am confusing about the data calibration and alignment. The manual shows that calibrate the reference data of one scan and align other reference data to that calibrated one. Here I want to show examples. I have two samples A and B, Each sample has three scans with the corresponding reference data. For sample A, 1st scan is calibrated and the other two scans are aligned to 1st scan. Then merge them into merged A. The same procedures for sample B and get merged B. If I want to compare XANES of sample A and B, do I need to align the merged reference data between A and B? If so, why? My understanding is that all scans (original data and merged data) in sample A and B are calibrated to standard edge energy. Why do they need to align? I appreciate your help. Thanks, Haifeng

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Demeter Installation Mac server error
by Laurane Léost 27 Jul '18

27 Jul '18

Dear all, I would like to install Demeter on Mac device. I followed all the instructions with "Installing Demeter on the Mac" in the website. But in the terminal window, when i write : "sudo port install xorg-server demeter", this message appears : "Error: Port xorg-server not found". Did someone had already receive this type of message? Or know a way to install the program. Thanks for your help. -- Laurane Léost

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ZrO2 and HfO2 EXAFS spectra
by Martin McBriarty 23 Jul '18

23 Jul '18

Friends in XAFS, Do you have any EXAFS spectra of single-phase ZrO2 or HfO2 that you'd be willing to share? In particular, I'm looking for the monoclinic (P21/c), tetragonal (P42/nmc), and orthorhombic (Pbca and Pca21) phases of each material. Bulk, interface-stabilized, pure, or lightly doped is fine. I'd prefer mu(E) spectra, but chi(k) would work as well. Thank you for any help or recommendations! Martin Martin E. McBriarty, Ph.D. Scientist III, Intermolecular Inc. San Jose, CA

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Re: [Ifeffit] Fe Standards (Naomi Intrator)
by Denis Testemale 23 Jul '18

23 Jul '18

I'm not sure my previous message went through (I think I screwed up the mailing list adress). So here we go again. Dear Naomi, I attach 2 files with the normalized spectra of Fe2+ (50mmol dissolved FeCl2 in 0.5M HCl) and Fe3+ (??mmol dissolved Fe2(SO4)3 in 2M H2SO4) in solution. In both cases iron is octahedrally coordinated to water molecules. The spectra come from 2 different experimental runs, but the calibration of the beamline was done consistently (Fe metallic foil, 1st maximum of the derivative set at 7112eV). Unfortunately the Fe3+ spectrum is only XANES. If you need EXAFS let me know, I might find something if I dig hard in my hard disk. Cheers denis Date: Tue, 10 Jul 2018 21:23:34 +0000 From: Naomi Intrator<naomii(a)princeton.edu> To:"ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Fe Standards Message-ID: <A986AA38C24BCD4E9BAAC1237600734D0E517089@csgmbx217w> Content-Type: text/plain; charset="iso-8859-1" Hi all, I'm doing a project on Fe and was wondering if anyone has spectra of Fe(II) and/or Fe(III) standards they wouldn't mind sharing. I'm specifically looking for XANES of Fe2+ and Fe3+ ions in water. Thanks in advance, Naomi -- Institut Néel - CNRS http://neel.cnrs.fr/spip.php?rubrique264 +33 476 881 045

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Re: [Ifeffit] XANES from FEFF9
by manju rao 18 Jul '18

18 Jul '18

Hi Matt As I am new to FEFF, I was estimating SO2 to be equal to 1 for XANES. But I don't know if it was good to have such guess or not. By changing Exchange card from 0 0 0 0 to 0 0 0 2, I am getting a noticeable change in absorption edge. The edge showed a little shift to higher energy and also slight fall in amplitude of edge. These changes are not ignorable. So I am confused about what approach to follow. Manju Sent from my iPhone

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set restrain
by Dien.Li＠srnl.doe.gov 17 Jul '18

17 Jul '18

Hi, all I wonder if anyone can suggest me on how to set up restrain of a parameter in GDS, for example, to restrain ss in a certain range or no negative. Thank you so much. Dien Li

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XAFS hands-on course at DESY
by Edmund Welter 17 Jul '18

17 Jul '18

Dear colleagues, we are organising a XAFS hands-on course at DESY this year. The date is 3rd - 7th of September 2018. More information can be found on the attached flyer and on our workshop webpage: https://indico.desy.de/indico/event/21097/overview In case of questions, please do not hesitate to contact us via e-mail. xafs-course(a)desy.de Best regards, Wolfgang Caliebe, Edmund Welter

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micro-XAS Imaging Post-Doc Position
by Ritimukta Sarangi 16 Jul '18

16 Jul '18

Hello, Apologies for the spam email. We have a 3-year position available for micro-XAS imaging for biological applications at SSRL, SLAC, Menlo Park, CA. The details of the position are attached. Please contact me directly if you or anyone you know might be interested. Best Wishes, Riti Sarangi SSRL, SLAC

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