May 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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q2xafs2017 in August
by fred.mosselmans＠diamond.ac.uk 08 Jun '17

08 Jun '17

Hi For those of you that are not aware, Q2XAFS2017 (the International Workshop on Improving Data Quality in XAFS Spectroscopy) is taking place at Diamond Light Source near Oxford, which is where the spires dream, on 14/15 August this summer. See http://www.q2xafs2017.com/ for details / registration Although the abstract deadline is currently listed as 5th June, it will be shortly extended to early July. We hope to see you in England Regards 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 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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Hephaestus ion chamber absorption
by George Sterbinsky 30 May '17

30 May '17

Hello, Can anyone explain why the values given by the ion chamber utility in Hephaestus differ from those given for a 10 cm He filled ion chamber in figure 3.14 of Grant Bunker's Intro to XAFS book at high energy? For instance, figure 3.14 indicates an absorption fraction of ~3E-7 at 40 keV, whereas Hephaestus indicates 2E-4 at the same energy. Thank you, George

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Help--save k(q) data in larger k range
by Tao Ma 26 May '17

26 May '17

Hi, I was trying to save my data in k(q). I set the k-range for fourier transform, and r-range for the inverse fourier transform, and was able to see the resultant k(q) figure in whatever k-range I want. But when I hit “save in k(q)”, in the generated file I could only get the data in a k-range of 0-8. Is there a way to get the data in a larger k-rang, e.g., 0-15? Thanks! Regards, Tao ⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘⌘ Tao Ma, Dr, Postdoctoral fellow, Gates Catalysis Group, Dept. Chemical Engineering & Materials Science, University of California, Davis

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Guess Parameters Getting Stuck
by M Solo 25 May '17

25 May '17

Hello. I'm currently in process of fitting some exafs data, and have encountered this issue several times. At some point during fit one or several "guess" parameters get stuck on the initial guess value, even if that value is changed to something that has no resemblance to the data being fitted. Further changing the initial guess value has no effect, and the fit merely takes in the new value as if its been "set". The number of values affected range from 1 to all of the variables in the GDS. Regards Aleks

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Re: [Ifeffit] Self absorption in CeO2 spectrum
by Weizi Yuan 23 May '17

23 May '17

Thank you for your kind suggestion, Fred. It gives me some ideas of how to design my next experiment. And I will also try to do self absorption correction and see if it helps at the current stage. Weizi -- Regards, Weizi Yuan, Graduate Student, Northwestern University, Ph:(+1)312-560-9619

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Self absorption in CeO2 spectrum
by fred.mosselmans＠diamond.ac.uk 22 May '17

22 May '17

Hi Weizi, I know this is rather after the event, but should you do the experiment again, it is probably much easier to get surface sensitivity in this sort of system using conversion electron yield e.g. Schroeder et al Surface Science Volume 324, Issues 2-3, 10 February 1995, Pages L371-L377. That should suffer no over-absortpion issues and bulk fluorescence on a film of this thickness will have only a small amount of over absorption at 45 degrees Regards 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 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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Re: [Ifeffit] Ifeffit Digest, Vol 171, Issue 14
by Weizi Yuan 20 May '17

20 May '17

Got it. Thanks for the response, Anatoly. Weizi On Fri, May 19, 2017 at 4:37 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. Self absorption in CeO2 spectrum (Weizi Yuan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 19 May 2017 16:37:54 -0500 > From: Weizi Yuan <weiziyuan2015(a)u.northwestern.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Self absorption in CeO2 spectrum > Message-ID: > <CAKT5DaVktSW=wr4+jQ7+LFwAo9dgvy6LHdA1CtcAQTd+ > iNzEdg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > I have measured some XANES spectra of CeO2 film(~220nm) in fluorescence > mode at Ce L3 edge with two incident angles of 0.6 degree and 3 degree. My > goal is to get relative surface sensitive (penetration depth~ 20 nm above > edge) information of [Ce3+] from 0.6 o while bulk sensitive information at > 3 o (penetration depth~ 160 nm above edge). In the meantime, I also > collected CeO2 powder reference spectrum under transmission mode. The > comparison is shown in the graph. > The film at 3 degree has a sharper white line than the powder while at 0.6 > degree, it is the opposite. I think this might be because at the surface of > the film,it has more Ce3+ while when we detect the bulk it has more Ce4+. > My question is how can I tell if I need self-absorption correction or not > for the films in this case? Can I say I do not need self absorption > correction because I have a higher normalized u for the film collected in > the fluorescence mode than powder collected in the transmission mode? > Thanks a lot for your comments. > Weizi > [image: Inline image 1] > > > -- > Regards, > Weizi Yuan, > Graduate Student, > Northwestern University, > Ph:(+1)312-560-9619 >

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Self absorption in CeO2 spectrum
by Weizi Yuan 19 May '17

19 May '17

Dear all, I have measured some XANES spectra of CeO2 film(~220nm) in fluorescence mode at Ce L3 edge with two incident angles of 0.6 degree and 3 degree. My goal is to get relative surface sensitive (penetration depth~ 20 nm above edge) information of [Ce3+] from 0.6 o while bulk sensitive information at 3 o (penetration depth~ 160 nm above edge). In the meantime, I also collected CeO2 powder reference spectrum under transmission mode. The comparison is shown in the graph. The film at 3 degree has a sharper white line than the powder while at 0.6 degree, it is the opposite. I think this might be because at the surface of the film,it has more Ce3+ while when we detect the bulk it has more Ce4+. My question is how can I tell if I need self-absorption correction or not for the films in this case? Can I say I do not need self absorption correction because I have a higher normalized u for the film collected in the fluorescence mode than powder collected in the transmission mode? Thanks a lot for your comments. Weizi [image: Inline image 1] -- Regards, Weizi Yuan, Graduate Student, Northwestern University, Ph:(+1)312-560-9619

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jfeff, OS X 10.12, java version "1.8.0_131"
by Jeff Terry 17 May '17

17 May '17

Hi All, Has anyone successfully installed jfeff 9.6.4 on OS X Sierra? The installer crashes after requesting a password when I try to run it. I have tried on OS X El Capitan 10.11 and the same version of java but I get an error message saying it doesn’t recognize java. If I downgrade to java 1.6, the installer runs under OS X 10.11 but then quits with the error message Error changing ownership of /Applications to my user name. I don’t really want the installer changing the ownership of Applications. Is this a common problem? Jeff

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