June 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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Exporting Curves (as Data rather than Images)
by Felix E. Feiten 26 Jun '17

26 Jun '17

Dear all, I think the title is almost enough explanation. I would like to export the data corresponding to fits, chi(k), fourier-transform and back-transform to plot them with a different software. I couldn't figure out how, can someone please help me? With kind regards Felix

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Nearest neighbor statistics in a random alloy
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear all, I am fitting a Pt9Co1 foil sample. I assume the sample to be basically fcc platinum with every 10th atom randomly replaced by cobalt. Here are the assumptions I make: 1. every atom has 12 nearest neighbors 2. every Pt atom has (on average) 10.7 Pt nearest neighbors and 1.3 Co nearest neighbors 3. every Co atom has (on average) 11.7 Pt nearest neighbors and 0.3 Co nearest neighbors I have been told that assumptions 2 and 3 are not precise. Here is what I'm confused about: In order to determine the number of Pt or Co nearest neighbors I looked at an ensemble of 13 atoms: 1 absorber and 12 scatterers/nearest neighbors. I assume that the Pt/Co ratio in this ensemble is 9/1 and therefor, statistically, 1.3 out of those 13 atoms should be Co. That means that if Co is the central atom only 0.3 Co atoms are remaining for the 12 nearest neighbors. On the other hand, if Pt is the central atom, (all) 1.3 Co atoms are remaining for the 12 nearest neighbors. I have been told that the ratio of Pt/Co should be 9/1 in the 12 nearest neighbors, not in the 12 atoms including the central atom (quote: "because we have a bulk sample"). But I do not understand why. Can someone please explain the correct answer to me? With kind regards, Felix

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Automatically doing many fits / Scripting
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear Ifeffit mailing-list, first of all sorry for writing another mail to the list in such a short time span, I hope people will not get sick of me too quickly. I want to do many fits for the same data with varying start-parameters. More specifically, I am doing fits to EXAFS data of the Pt L3 edge of PtCo(X) nanoparticles and want to vary sigma^2 for each of the two paths (Pt-Pt and Pt-Co) that I fit. I want to 1. start a fit with certain parameters, 2. save the log file, 3. change one parameter many (120 for now) times. If there is no functionality to do this in Artemis I'll have to resort to using some external script that abuses Artemis. In that case I will report on how it went. But obviously, it would be much more comfortable if Artemis had something like this implemented. Any way to start a fit from the windows command line (I'm using Windows 10) would also be very helpful as that would probably allow me to do the scripting in PowerShell relatively easily. With kind regards, Felix

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nonsensical negative values / restrictions
by Felix E. Feiten 23 Jun '17

23 Jun '17

Dear all, I have the following problem: In some fits using Artemis (Demeter 0.9.25) I will get negative values for parameters where it makes no sense at all. For example, when trying to fit two first shell paths, Pt-Pt and Pt-O, for a Pt nanoparticle, sigma^2 for the Pt-O path becomes negative. Obviously, sigma^2 has to be a positive number. My questions: 1. Why does the fit algorithm do this? 2. What can I do to avoid this? I know that there are most likely significant problems with my fit if this behaviour occurs. As far as I know it's possible to impose restrictions in Artemis and if anyone could point me towards a tutorial explaining how to implement restrictions that might be a first step in the right direction. Currently, the chapter "Constraints and restraints" in the Artemis documentation is "Coming soon......". With kind regards, Felix

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Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 15
by Weizi Yuan 22 Jun '17

22 Jun '17

Hi Anatoly, Thanks for your quick response. Yes, I actually asked the self absorption question about CeO2 a few weeks ago. And your answer that it is due to self absorption leads me to study more about it and I appreciate it. In that last question, the strong attenuation of signal occurs in the incident angle = 0.6 o . However, when the incident angle is 3 o under room temperature ,air, the peak intensity is stronger than the CeO2 measured in transmission mode, which leads me to think that no over absorption correction needed here. And I try to conduct the correction which gives me crazily high (~9 after normalization) peak intensity. This makes me further confirm that no strong self absorption effect here. And if no strong self absorption in RT, air ,then why strong attenuation in RT, vacuum condition(case ii in my question)? For your answer,I am a little confused. Are you saying self absorption occurred in only case ii or in both cases, even though the result of case i spectrum has a higher signal than the transmission mode data? Thank you, Weizi On Thu, Jun 22, 2017 at 10:16 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. Self absorption or Ce4+ reduction in the CeO2 film? (Weizi Yuan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 Jun 2017 10:11:05 -0500 > From: Weizi Yuan <weiziyuan2015(a)u.northwestern.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Self absorption or Ce4+ reduction in the CeO2 film? > Message-ID: > <CAKT5DaU1U2UX7bVUx9ffhvTfE7txqnZDgGu3cNujM6ceQyp6Hg@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > I have measured some spectra of a CeO2 film(~200nm) grown on Yittria > stablized Zirconia(YSZ) substrate under 2 conditions. > (i) room temperature, ambient atmosphere > (ii) room temperature, vacuum (pO2~1E-6 atm) inside a graphite dome of the > DHS 1100 anton paar, > The spectra are collected in fluorescence mode. The incident angle is 3 o > and the fluorescence collection angle is 90 o. > > My questions are: > (i) From the theory behind the FLUO program developed Dr. Daniel Haskel, > CeO2 spectra collected with a 3 o incident angle *would have a strong self > absorption effect and need* > > correction , however, *the signal *is not attenuated compared with the > CeO2 powder taken in a transmission mode, shown in attached plot. > I've gone through many literature and people sometimes tell that whether > they have a successful self absorption correction by comparing the > spectrum with a spectrum taken under a transmission mode. > So I'm wondering if I can say that I don't need a self absorption > correction in this case? > (ii) > The Ce4+ peak in the spectrum collected under condition (ii) has a much > lower intensity. I think it is due to the reduction of Ce 4+ under vacuum, > however, the Ce3+ peak does not show an increased signal here. Which makes > ma doubt whether this is simply reduction of Ce *or might be from over > absorption? * > > Thanks for any response. > > [image: Inline image 1] > -- > Regards, > Weizi Yuan, > Graduate Student, > Northwestern University, > Ph:(+1)312-560-9619 >

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Self absorption or Ce4+ reduction in the CeO2 film?
by Weizi Yuan 22 Jun '17

22 Jun '17

Dear all, I have measured some spectra of a CeO2 film(~200nm) grown on Yittria stablized Zirconia(YSZ) substrate under 2 conditions. (i) room temperature, ambient atmosphere (ii) room temperature, vacuum (pO2~1E-6 atm) inside a graphite dome of the DHS 1100 anton paar, The spectra are collected in fluorescence mode. The incident angle is 3 o and the fluorescence collection angle is 90 o. My questions are: (i) From the theory behind the FLUO program developed Dr. Daniel Haskel, CeO2 spectra collected with a 3 o incident angle *would have a strong self absorption effect and need* correction , however, *the signal *is not attenuated compared with the CeO2 powder taken in a transmission mode, shown in attached plot. I've gone through many literature and people sometimes tell that whether they have a successful self absorption correction by comparing the spectrum with a spectrum taken under a transmission mode. So I'm wondering if I can say that I don't need a self absorption correction in this case? (ii) The Ce4+ peak in the spectrum collected under condition (ii) has a much lower intensity. I think it is due to the reduction of Ce 4+ under vacuum, however, the Ce3+ peak does not show an increased signal here. Which makes ma doubt whether this is simply reduction of Ce *or might be from over absorption? * Thanks for any response. [image: Inline image 1] -- Regards, Weizi Yuan, Graduate Student, Northwestern University, Ph:(+1)312-560-9619

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GRC on clusters
by Anatoly Frenkel 21 Jun '17

21 Jun '17

Hello, There is an opportunity for those interested in applications of XAFS methods to nanomaterials, in particular to nanoclusters, to participate in the Gordon Conference on Clusters and Nanostructures in Mt. Holyoke College from July 8-14. For more information please see attached flyer. Best regards, Anatoly Frenkel Stony Brook University/BNL

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Athena Bug Report
by Nicholas Marcella 20 Jun '17

20 Jun '17

Hello, *Bug:* Although the [Natural log] box was checked, the natural log was not being applied to the data (figure 1). This was very easy to miss. Data imported under the conditions of figure 1 (Purple) resulted in a deviation from Bruce Ravel’s Au foil (Blue), the original March import (Green), and the June import after ensuring the μ(E) box contained the natural log of (mkxpq.i0)/(mkxpq.i1) (Red) – Figure 2. *Replication of the bug:* The bug only appears if the following steps are followed: 1) In a new file X, fluorescence data is imported, i.e. natural log box is unchecked. 2) File X is saved and Athena is closed. 3) Athena is started and File X is opened. 4) When importing a new dataset, the natural log box will be checked but the natural log will not be applied to μ(E). *Solution:* 1) Uncheck and then check the natural log box. Ta-da… [image: Inline image 2] [image: Inline image 3] Regards, -- *Nicholas J. Marcella* | Masters Student *Materials Science and Chemical Engineering* *Stony Brook University* *Tel: (914)-703-9843* *Structure and Dynamics of Applied Nanomaterials | Brookhaven National Lab <https://www.bnl.gov/chemistry/SDAN/>* *Senator - MSCE | Graduate Student Organization <http://sbgso.org/index.php/about-us/senators>* *Senior Coordinator | Campus Recreation <http://studentaffairs.stonybrook.edu/rec/>*

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FEFF8/FEFF9 in Demeter
by 이국승(에너지환경소재연구팀) 16 Jun '17

16 Jun '17

Dear Ifeffit users, I remember that one of you have posted the method how we can use FEFF8/FEFF9 in Demeter program. But I cannot find the posting in the archives. Could you please kindly let me know how can I find it or directly write again? Best, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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