April 2019 - 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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Demeter Mac issues
by Elizabeth Tomaszewski 29 Apr '19

29 Apr '19

Hello all, Is anyone currently using the Demeter package on a Mac? I have followed the instructions given and have the package installed. However, when I try to open Athena through the terminal window, it gets stuck on the opening Athena image and the question box asking "Athena found an autosave file would you like to import it?" I can open Artemis and Hephaestus, but get the error message as follows: 12:29:30: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563. This message is repeated five times. Only after opening and closing each software several times can I get them to run. Any suggestions as to: 1) how to make the Demeter package run more smoothly and 2) how to get Athena to open at all. Thank you for your assistance, Beth Tomaszewski -- Dr. E J Tomaszewski Postdoctoral Researcher Eberhard Karls Universitaet Tuebingen Center for Applied Geoscience (ZAG) Geomicrobiology Sigwartstrasse 10 72076 Tuebingen Germany

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Question about PCA
by Joselaine Cáceres gonzalez 25 Apr '19

25 Apr '19

Dear all, I performed PCA in a set of 11 XANES spectra and I was trying to use some of the functions and tests developed by Malinowski to extract the number of primary components. I found differences between eigenvalues calculated whit a matrix calculator and those calculated by ATHENA, but they are equivalent in some way since they explain the same amount of variance and when I calculate the IND function or Malinowski F-test I reach the same conclusions. To calculate the eigenvalues with the matrix calculator I first normalized my data matrix (step height normalization) with ATHENA, then I export the data to an Excel spreadsheet where I centered them: z=(value-mean)/standard_dev. Then I used SVD and Eigenvalue decomposition to find the eigenvalues and those obtained with SVD explain exactly the same amount of variance than those found with ATHENA but they are different. In all the calculation I did, I used the same amount of points 161, points in each spectrum in ATHENA and in the matrix calculator, exactly the same energy interval. I´d like to know if I am missing some step in the data pre-treatment that is prevented me to find the same eigenvalues obtained by ATHENA but also I´d like to know if I can straight forward use the values obtained with ATHENA to evaluate the functions proposed by Malinowski since these equations might be different depending if calculations are made using "covariance about the origin" or "correlation about the origin" and I am not sure what is the case. Thanks in advance! Best regards Joselaine

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can't open Athena 0.9.26!
by m.rezaie 23 Apr '19

23 Apr '19

Hi, I upgraded my DEMETER to DEMETER 0.9.26 but I can't open it on my computer which is Win 7, 32 bit. How can I solve this problem? Best Regards Mahsa

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2019 APS/IIT Summer XAFS School
by Carlo Segre 18 Apr '19

18 Apr '19

Greetings: The 2019 APS/IIT Summer XAFS School will be held on the Illinois Tech Campus from July 7, 2019 to July 12, 2019. Please see the attached announcement for details and information on how to apply. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org it helps to get the year right > On Apr 18, 2019, at 10:38 AM, grant bunker <bunker(a)agni.phys.iit.edu> wrote: > > Greetings, All - I would appreciate your help in the disseminating this announcement > > thanks - Grant > > <2019 XAFS summer school announcement.pdf>

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Regarding FEFF9
by Manju 18 Apr '19

18 Apr '19

Hi I am trying to see the effect of crystal defects on XANES. Is there any way that I could create charged vacancy in feff.inp file, before importing it into FEFF9? Regards Manju Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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LANL EXAFS Postdoc position
by Daniel Olive 17 Apr '19

17 Apr '19

Greetings all, Los Alamos National Laboratory has a postdoc position involving EXAFS for use in nuclear forensics/actinide research. The vacancy name is IRC72104, linked below, and contains additional information. https://lanl.jobs/jobs/?q=IRC72104 Please have a look and/or forward to those who may be interested. Best, Dan -- ------------ Daniel Olive Los Alamos National Laboratory MST-16: Nuclear Materials Science P.O. Box 1663 MS E574 Los Alamos, NM 87545 Chemical Sciences Division Lawrence Berkeley National Laboratory ------------

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Re: [Ifeffit] Demeter - Athena Warning, crashing
by Ravel, Bruce 16 Apr '19

16 Apr '19

Hi, The Demeter problem that presents itself with error messages like: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. is one that comes up pretty often here on the mailing list. It is also a problem that is already solved on github, but I haven't made a new release in quite some time. The solution to this particular problem is shown here: https://github.com/bruceravel/demeter/blob/master/lib/Demeter.pm#L994-L996 You could simply edit the copy of Demeter.pm on your computer to have the three lines highlighted at that link. Or you could click the "Raw" button at the top of that page, then save the raw file in place of Demeter.pm on your computer. A bit more effort would be to remove the version of Text::Template that is on your computer and install an older version of Text::Template on your computer. This one should work: https://metacpan.org/release/MJD/Text-Template-1.46 The bottom line is that Demeter uses a perl module for which the documentation of a feature and its implementation used to agree and, at some point, stopped agreeing. The fix that I link to above addresses that problem, but the specific combination of Demeter and Text::Template that makes it onto some people computers expose this problem. Any of the solutions explained above should address this in the short term. Eventually I will make a new release and this problem will go away. Until then, hopefully people will find this email. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Demeter - Athena Warning, crashing
by natalia martin 16 Apr '19

16 Apr '19

Hi, I have just installed Demeter on my Mac and get the following error when trying to Launch ATHENA: 15:36:09: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 15:36:09: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. I saw a previous post from Chris on the 2018-04-02 with a similar error ("Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 563, line 236.) which was solved by replacing the /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With another template from p5.24. https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s… <https://www.mail-archive.com/search?l=ifeffit@millenia.cars.aps.anl.gov&q=s…> This solution does unfortunately now work for my case. Does anyone have an idea of how this error can be fixed? Best, Natalia

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job offers
by Kristina KVASHNINA 12 Apr '19

12 Apr '19

Dear Ifeffit Colleagues, There are two positions available at Rossendorf Beamline of ESRF, Grenoble, France. We are looking for a PhD student and a Postdoc to work on TOP project (Towards the bottom of the periodic table), funded by the European Research Council. Please could you share this with anyone who might be interested in applying? Thank you in advance! Kind regards, Kristina http://www.esrf.eu/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc_4-1.p… http://www.esrf.eu/files/live/sites/www/files/Jobs/giant/ROBL_phd_student_2… -- Kristina Kvashnina Rossendorf Beamline (BM20) The European Synchrotron (ESRF) 71, avenue des Martyrs 38000 Grenoble, France tel +33(0)476882367 TOP group website https://www.hzdr.de/db/Cms?pNid=787

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