November 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] Ifeffit Digest, Vol 189, Issue 16
by Enyuan Hu 24 Nov '18

24 Nov '18

Thank you very much for the data, professor Frenkel. You can send your student's name to my email. We will acknowledge him/her for the data. Enyuan On Sat, Nov 24, 2018 at 11:29 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. TiO2 XAS spectrum (Enyuan Hu) > 2. Re: TiO2 XAS spectrum (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Nov 2018 22:06:50 -0500 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] TiO2 XAS spectrum > Message-ID: > < > CAJud35ModfhLUtDpbRFO2NpxRDxeg5yvxfUk+JPOxZ64Cgqqyw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > Can anyone share an XAS spectrum of TiO2? it would be best if a Ti foil > spectrum is also included for calibration. Your help is much appreciated! > > Enyuan >

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TiO2 XAS spectrum
by Enyuan Hu 24 Nov '18

24 Nov '18

Hi all, Can anyone share an XAS spectrum of TiO2? it would be best if a Ti foil spectrum is also included for calibration. Your help is much appreciated! Enyuan

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PhD opportunity at Diamond Light Source: NEXAFS Crystallography
by Sven L. M. Schroeder 22 Nov '18

22 Nov '18

>>> NEXAFS Crystallography: A Novel Approach to Refinement of Proton Positions in Organic Crystal Structures <<<< A PhD studentship for this project is available at Diamond Light Source, for an immediate start. Candidates with an honours degree in Physics, Chemistry, Materials Science, Engineering or related relevant disciplines are eligible to apply. The student will receive a tax-free stipend of 16,760 GBP p.a., for 42 months. The studentship comes with a generous travel budget, to facilitate experiments at other synchrotron sources, e.g. in the US and in other European countries. UK students are eligible to apply. European Union students may be eligible to apply under certain circumstances. Please contact us f you are interested. The student will be registered in the PhD programme at the University of Leeds, with Prof Sven L M Schroeder as lead- and Dr Andrew Scott as co-supervisor. Dr Elizabeth Shotton, Head of Industrial Liaison, at Diamond Light Source will be the Diamond co-supervisor. If you are interested in this position please get in touch as per the contact information provided in the signature below. -- Sven L. M. Schroeder Royal Academy of Engineering Bragg Centenary Chair Diamond Light Soruce Ltd | Harwell Science and innovation Campus | Chilton, Didcot OX11 0DE | UK School of Chemical and Process Engineering | University of Leeds | Leeds LS2 9JT | UK Room 2.41 | Engineering Building T +44 (0)113 343 2401 | F +44 (0)113 343 2384 E s.l.m.schroeder(a)leeds.ac.uk<mailto:s.l.m.schroeder@leeds.ac.uk> | W https://engineering.leeds.ac.uk/staff/690/Professor_Sven_L_M_Schroeder Secretariat: Ms Eve Knaggs E e.knaggs(a)leeds.ac.uk<mailto:e.knaggs@leeds.ac.uk> | T +44 (0)113 343 2498

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data on CdS
by Anatoly Frenkel 17 Nov '18

17 Nov '18

Dear all - if someone could share raw Cd K-edge data of CdS, it would be really helpful! Thank you, Anatoly Frenkel

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Extrating standard deviation value from merged dataset in Athena
by Christian Rein 16 Nov '18

16 Nov '18

Hi, Do anyone know how to obtain the standard deviation value that Athena calculates when merging the data? Best, Christian Christian Rein Postdoc DTU Energy Technical University of Denmark [http://www.dtu.dk/~/media/DTU_Generelt/Andet/DTU_email_logo_01.gif] Department of Energy Conversion and Storage Building 771, room 010 4000 Roskilde Denmark

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LCF and XES
by Samy Ould-Chikh 05 Nov '18

05 Nov '18

Dear, I'm trying to perform LCF using Athena for XES data (Kbeta 13) that has been normalized elsewhere. Combinatorics module is the main motivation. However, LCF module in Athena only use norm mu(E), so that the normalization for XAS data proceed and then it's not possible to perform the fitting. Does anyone know a workaround to perform LCF for XES in Athena, or another alternative software as user friendly ? Many Thanks Best Regards, Samy Ould-Chikh KAUST Catalysis Center Bldg.3,Level 4, #4231 4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom of Saudi Arabia Tel: +966 12 8084486 E-mail: samy.ouldchikh(a)kaust.edu.sa<mailto:eman.ahmedbahjri@kaust.edu.sa> Website: http://kcc.kaust.edu.sa/Pages/Home.aspx

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Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 8
by Raj kumar 02 Nov '18

02 Nov '18

Thanks for the clarification, Anatoly! Regards, Raj On Fri, Nov 2, 2018 at 4:04 PM <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: EXAFS of wine (Anatoly Frenkel) > 2. Re: Ifeffit Digest, Vol 189, Issue 2 (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 2 Nov 2018 06:36:57 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS of wine > Message-ID: <45D3D1E4-6749-463C-9FE3-259B77345304(a)stonybrook.edu> > Content-Type: text/plain; charset="utf-8" > > John, > > Since when theorists started to need real samples? I thought a simulation > is equally enjoyable. > > Anatoly > > > On Nov 2, 2018, at 12:17 AM, John J Rehr <jjr(a)uw.edu> wrote: > > > > Hi everyone > > > > The spectrum is pretty noisy with all the super Tuscano grapes ( > Alicante, Merlot etc) in the mix to give it?s complex berry character and > the 2016 is supposedly better. > > How about we take some samples to the lab ... ? > > > > John > > > > > >> On Thu, Nov 1, 2018 at 16:07 Anatoly Frenkel < > anatoly.frenkel(a)stonybrook.edu> wrote: > >> I thought this mailing list is an appropriate venue to post a picture > of the bottle of wine I bought yesterday in a store on Long Island. > >> > >> > >> > >> Anatoly_______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

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Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 2
by Raj kumar 02 Nov '18

02 Nov '18

Dear Anatoly and Marcus, Thanks for your answers. So in this case, i understood, I shouldn't use the extended XAFS region for the analysis. In the other hand, is it allowed to cut the region till 9150 eV and use the data for the XANES analysis? Regards, Raj On Thu, Nov 1, 2018 at 11:37 PM <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: Bump/oscillating pattern at high energies of EXAFS > (Anatoly Frenkel) > 2. Re: Bump/oscillating pattern at high energies of EXAFS > (Matthew Marcus) > 3. EXAFS of wine (Anatoly Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Nov 2018 17:47:56 -0400 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of > EXAFS > Message-ID: > < > CAFsMoZbm2RMVUeRmuoryw9ehVrZQcvx60zHqufmK39oLRoyZ2w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > It is an effect of inhomogeneity of the sample, that is, the variation in > the metal density throughout the X-ray beam footprint. > Anatoly > > > > On Thu, Nov 1, 2018 at 5:34 PM Raj kumar <rajrk37(a)gmail.com> wrote: > > > Dear All, > > > > I have monitored the growth process of YbVO4 nanoparticles using EXAFS. > > Here, nanoparticles were synthesized in water medium. Both initial and > > final products (EXAFS) of the synthesis were measured using the > continuous > > flow approach whereas the intermediate products were recorded, in the > glass > > capillary, using the stopped flow. In the attached figure, you can find > the > > same (all products). At high energies of EXAFS, both initial and final > > measurements show smooth behavior whereas the oscillating pattern/bump > was > > observed for the intermediate states. > > > > Here, my question is: Is the oscillating pattern appearing in the > > intermediate states due to the sedimentation/in-homogeneity of the > product > > in the capillary or it is the characteristic of the synthesis? > > > > With regards, > > Raj > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > >

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EXAFS of wine
by Anatoly Frenkel 02 Nov '18

02 Nov '18

I thought this mailing list is an appropriate venue to post a picture of the bottle of wine I bought yesterday in a store on Long Island. Anatoly

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