September 2017 - 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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XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 09 Feb '18

09 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). Best regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Metal-Metal Peak Splitting in 5d Transition Metals
by Shoaib Muhammad 19 Sep '17

19 Sep '17

Dear All, I have a question that is not directly related to Athena or Artemis but it is more related with EXAFS theory. I work on lithium metal oxides and sometimes measure their XAS data. XAS data show typical trend, i.e; first prominent peak related with metal-oxygen co-ordination shell and second prominent peak is associated with metal-metal co-ordination shell in my materials. I have noticed that in similar crystal structures Li2MO3-type (where M is transition metal), if metal belongs to 3d transition metal groups I get a single prominent metal-metal peak but for 5d transition metals, the metal-metal peak splits and its intensity also drops. I could not figure out the reason for the splitting of metal-metal peak in case of 5d metals. I have attached a PDF file in which calculated EXAFS spectra for Li2RuO3 (4d transition metal) and Li2PtO3 (5d transition metal) are shown and metal-metal (Pt-Pt) peak in Li2PtO3 shows clear splitting whereas metal-metal peak for Li2RuO3 does not split even though their "ATOMS" input files are very similar. I would appreciate if anybody could briefly explain the reason for metal-metal peak splitting in 5d metals or point me towards any literature. Attachment can be downloaded from the below link as well. https://www.dropbox.com/s/1m3kf764junuukk/Metal-Metal%20Peak%20Splitting%20i n%205d.pdf?dl=0 Thanks, Shoaib Muhammad Department of Energy Science Sungkyunkwan University (South Korea)

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Limit for number of data points in a file to be imported in Athena
by Kaustubh Priolkar 16 Sep '17

16 Sep '17

Hi! I have a QEXAFS data file with 12000 data points but Athena reads it only partially. Is there a limit on maximum number of data points in a file that Athena can import? Is there a way to increase the limit? Thanks in advance, Kaustubh Sent from Mail for Windows 10

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[IFEFIT]Chi(E) in version 0.9.25
by Michael Stockenhuber 15 Sep '17

15 Sep '17

Dear mailing list, Is there any way to save data as Chi( E),i.e., energy one column and chi(E) in the 2nd column? This was possible in the past and it would be great to have that to be able to import into excurv. Thank you for all the help and great programs Cheers Michael Prof. Michael Stockenhuber Chemical Engineering, School of Engineering Faculty of Engineering and Built Environment The University of Newcastle T +61 2 4985 4433 F +61 2 4921 9095 M + 61 (0) 450352239 Michael.stockenhuber(a)newcastle.edu.au<mailto:Michael.stockenhuber@newcastle.edu.au> President Catalysis Society of Australia www.catalysis.org.au<http://www.catalysis.org.au> Co-chair ACEME 2018 https://www.aiche.org/aceme2018 Co-chair ISHHC 2018 http://www.ishhc17.org

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How to use Artemis with feff85L
by José Carlos Conesa 14 Sep '17

14 Sep '17

Hi, I should like to use feff85L within Artemis (from Demeter 0.9.25), just to check in my system whether selfconsistency has a role in unifying E0 values (with feff 6, allowing different E0 for each scatterer leads to E0 differences >10 eV, which seems too much to me). I find that after loading the EXAFS data (from Athena) and a model (a .cif file containing Cu, Ce and O atoms), if I click Run Atoms and then Run Feff with feff6 as executable I get the usual set of paths that allow me doing a fit of the data, but if I try to use the feff85L.exe that comes with the Demeter software (by changing the feff executable in the File/Edit preferences menu), after clicking the Run Feff button (without including the SCF card) a bit of computation happens and after finishing it the path list is empty. ¿Any idea of the possible reason why I get no path list? Thanks in advance -- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Madrid, Spain www.icp.csic.es Tel. (+34)915854766

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1 Phd student and 2 postdocs positions are available at ROBL of ESRF
by Kristina Kvashnina 14 Sep '17

14 Sep '17

Dear Colleagues, We are looking for 2 postdocs and 1 PhD student to investigate the lanthanide/actinide oxides nanomaterials by X-ray absorption/emission spectroscopy and electronic structure calculations. Each contract is for 3 years. I will very much appreciate if you can share that information with anyone who might be interested. Thank you ! Kind regards, Kristina More information is here http://www.esrf.fr/Jobs/CRGJobs http://www.esrf.fr/files/live/sites/www/files/Jobs/giant/ROBL_phd_student_a… http://www.esrf.fr/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc1.pdf http://www.esrf.fr/files/live/sites/www/files/Jobs/giant/ROBL_Postdoc2.pdf

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