July 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 08 Feb '18

08 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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Artemis Crashing
by Daniel Austin Sheffield Uni 02 Aug '17

02 Aug '17

Hi, I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help, Daniel

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working at the lanthanide K-edges: question about amplitude reduction factors
by Bone, Sharon Elizabeth 28 Jul '17

28 Jul '17

Hello- I recently collected some Nd K-edge EXAFS at APS (~43 KeV). I've started fitting the data and am looking for S02 values in the literature to compare to my own (especially since my fitted S02 values- to two Nd reference materials for which I know coordination numbers- are outside of the typical range of 0.7 - 1), but I haven't found any reported. Has anyone worked at the lanthanide K-edges? Could you point me to a reference for S02? Thanks! Sharon

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Postdoc
by mathieu le meur 24 Jul '17

24 Jul '17

Hello I am very interested with the postdoc doc position with Corwin H. Booth Unfortunately, the link is not working and I cannot apply. Can you help me? Thanks, Mathieu. Get Outlook for Android<https://aka.ms/ghei36>

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LBNL Postdoctoral Fellow Position
by Corwin H. Booth 21 Jul '17

21 Jul '17

Greetings all! I have just posted for a new Postdoctoral Fellow position to work with me at LBNL on projects with the Actinide Chemistry Group here and with Prof. Eric Schelter at U. Penn. Most of the work is to perform and analyze XAFS data. Please take a look at the official posting and apply if you are interested and meet the minimum qualifications. Here is the posting: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=83928 <https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=83928> Very best, Corwin -- Corwin H. Booth Chemical Sciences Division Lawrence Berkeley National Laboratory MS 70A-1150 1 Cyclotron Rd. Berkeley, CA 94720-8175 voice: 510-486-6079 FAX: 510-486-5596 Email: chbooth(a)lbl.gov Web: http://lise.lbl.gov/chbooth/

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Trouble in running Artemis in Mac
by Chang-wook Lee 13 Jul '17

13 Jul '17

I’m using Artemis in Mac. I got a trouble on running the software. Once the Artemis shut down by accident, (during import .inp file), the problem occurred. When I reopen the Artemis, It tries to restore previous file but it never worked. I uninstalled and reinstalled it several times but I can only see same unlimited loading screen… Athena works well. Thanks, Changwook

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Help with running GUI
by Drew Syverson 07 Jul '17

07 Jul '17

Hello everyone, Every time I try to open gse_mapviewer via the terminal on Mac OSX, I keep getting the message: "This program needs access to the screen. Please run with a Framework build of python, and only when you are logged in on the main display of your Mac." I do not know how to get past this issue on my computer. Any help would be appreciated. -Drew ~~~~~~~~~~~~~~~~~~~~~~~~ Drew D. Syverson, PhD Postdoctoral Associate Department of Geology and Geophysics Yale University New Haven, CT, USA ph: +1 (612) 475-0575 email: drew.syverson(a)yale.edu https://sites.google.com/view/drewsyverson/home

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XAFS Tutorial
by Daniel Austin Sheffield Uni 07 Jul '17

07 Jul '17

Hello, I am currently trying to learn how to use the software through the tutorials on the User Manuals. For Athena I tried to download the practice fe.060 data from Github but the data won’t download. I have asked my supervisor and he can’t download it either. Can anyone suggest how i can successfully download it? I realise i may be missing something obvious. Alternatively, if someone has the practice file data already downloaded could they send it to me? Thanks you, Daniel

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Re: [Ifeffit] Ifeffit Digest, Vol 173, Issue 1
by Christopher Thomas Chantler 05 Jul '17

05 Jul '17

Thanks Fred and well suggested. I also encourage all interested. -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Wednesday, 5 July 2017 8:21:22 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 173, Issue 1 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. Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts (fred.mosselmans(a)diamond.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Jul 2017 10:14:17 +0000 From: <fred.mosselmans(a)diamond.ac.uk> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Improving Data Quality in XAFS Spectroscopy Workshop - Q2XAFS 2017 - Reminder to Register & Deadline for Poster Abstracts Message-ID: <CF65047C5B0562499EAFF9FBBC542D640105240B89@exchmbx01> Content-Type: text/plain; charset="iso-8859-1" [cid:image002.jpg@01D2974C.A644EF90]<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> Q2XAFS 2017 will bring together experts in the field of X-ray Absorption Spectroscopy to discuss aspects of the technique that affect data quality in XAFS experiments. The workshop will provide a forum for discussions with the goal of reviewing international standards and protocols, and developing revised recommendations for best practice when performing XAFS experiments. It will also look towards the first agreed data formats and standards for XAFS data and deposition. The workshop is hosted by Diamond Light Source<http://www.diamond.ac.uk/Home.html> and will take place on Monday 14th & Tuesday 15th August at Harwell Science and Innovation Campus, Didcot, UK. The full programme can be viewed on the website here - Q2XAFS 2017 Programme<http://www.q2xafs2017.com/Conference/Q2XAFS2017/Scientific-Programme.html>. Registration is ?220 standard and ?180 for students which includes access to 2 full days of scientific programme, a welcome reception (Sunday 13th August) a workshop dinner (Monday 14th) , optional facility tour and lunches and refreshments each day. The call for poster abstracts will remain open until the 7th July, please see the website for more details on submission<http://www.diamond.ac.uk/Conference/Q2XAFS2017/Participate/Abstract-Submiss…> poster presentation and for the abstract template. Visit the Q2XAFS 2017 website<http://www.q2xafs2017.com/Conference/Q2XAFS2017.html> to register and for details of the programme and further information. http://www.q2xafs2017.com/Conference/Q2XAFS2017.html We hope you can join us in August. Best wishes, Q2XAFS 2017 Local Organising Committee T: +44 (0) 1235 778384 E: q2xafs2017(a)diamond.ac.uk Sorry for this partial spam, but my excuse Is the "godfathers"(?) of this list Matt Newville ,in person, and Bruce Ravel, by videolink, will be presenting, and sometimes it is sunny in Oxfordshire. Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk http://orcid.org/0000-0001-6473-2743 [cid:image002.png@01D27563.28EDA240] -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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