- Ifeffit - millenia.cars.aps.anl.gov

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 19 May '17

19 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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Postdoctoral position at SSRL, SLAC National Accelerator Lab
by Bare, Simon R 17 May '17

17 May '17

SUNCAT Postdoctoral Position for Synchrotron X-ray Science A postdoctoral research position is available at SUNCAT at SLAC National Accelerator Laboratory. The position is available immediately to work on a project developing and optimizing data processing techniques, and guiding students and postdocs through the analysis from synchrotron based x-ray techniques, primarily grazing incidence scattering and spectroscopy, to elucidate the composition and structure of catalysts (thin films and nanostructures) under working conditions. The SUNCAT Center for Interface Science and Catalysis is a partnership between SLAC National Accelerator Laboratory and the School of Engineering at Stanford University. SLAC is a multi-program laboratory owned by the U.S. Department of Energy's Office of Science and operated by Stanford University. At SUNCAT, we focus on interface science and the atomic-scale design of catalysts for the sustainable production of fuels, chemicals, and materials. A key strength of the efforts at SUNCAT is the ability to link theory and experiment, which requires a detailed understanding of the electrocatalyst surface under reaction conditions. A focus is placed on probing the electronic, structural and chemical properties of electrocatalyst systems under operando conditions by using the unique X-ray facilities available at SSRL and other National Laboratories. The postdoctoral fellow will play an integral role in all aspects of these X-ray characterization efforts. The position will report to Prof. Thomas F. Jaramillo (Stanford University) and Simon R Bare (SLAC National Accelerator Lab). Specific responsibilities include: Work with SSRL and SUNCAT scientists to conduct data processing and analysis. This will involve developing and optimizing data processing techniques, and guiding students and postdocs through the analysis. Work with a team to plan and design synchrotron based experiments, including the design and modification of in situ electrochemical cell(s) and establishing measurement protocols. Co-ordinate pre-experiment activities with colleagues (students and postdocs) and beamline scientists setup the beamline and conduct data collection for in-situ surface electrocatalysis and related experiments. Interface with theoreticians at SUNCAT and Stanford to interpret the experimental results in terms of changes to the electronic and lattice structures of the surface of the active electrocatalyst under operando conditions. The position is highly collaborative and will involve interacting with students, postdocs and staff scientists from SUNCAT on all aspects of the synchrotron-mediated research. The candidate will also maintain a safe working environment in the laboratory. Qualifications: * Ph.D. in physics, chemistry, materials sciences, chemical engineering, or related fields. * Demonstrated experience in synchrotron X-ray characterization techniques, in particular hard x-ray scattering and spectroscopy. * Proficiency in Python and/or Matlab, with a strong knowledge of data acquisition methodology. * Familiarity with theoretical analysis of x-ray absorption spectroscopy (e.g.FEFF9, MXAN, DFT, etc) and/or knowledge of ab initio DFT methods a plus. * Experience with electrochemical techniques and catalysis is a plus. * Willingness to learn and bridge knowledge/experience gaps. * Ability to work both independently and in a team environment. * Ability to work and communicate effectively with a diverse population; good interpersonal skills are essential. * Leadership, including the ability to coordinate efforts at SSRL, and to guide students and postdocs throughout all stages of the experiments. * Effective written and verbal communication skills. Applicants should include a cover letter, a brief summary of accomplishments/interests, a curriculum vitae, a list of publications, and names of 2-3 references for future letters of recommendation. Please send applications to Olayinka Popoola at opopoola(a)stanford.edu.

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Calculating Ce oxidation state at the L3 edge
by Stephanie Laga 16 May '17

16 May '17

Dear all, I have a (hopefully) quick question about calculating oxidation state of CeO2 at the L3 edge. When calculating ox state by taking the ratio of peak areas, is the pre-edge feature for Ce included in this calculation? This point isn't clear to me from looking at various papers. I've attached an image from Bernardi 2015, which shows that the %Ce III calculation doesn't include the fitted pre-edge feature A. I'm not sure why this would not be included? Is this because we only consider 2p > 5d transitions and the pre-edge is 2p > 4f (forbidden) transition? Thanks! Stephanie

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Calculation of NSS and R-factor
by Marine Albertelli 16 May '17

16 May '17

Good afternoon, Could you please tell me what is the difference between the calculation of the R-factor and the NSS ? I found that R-factor is equal to : sum((data - fit)^2)/sum(data^2) and NSS = sum((data - fit)^2)/sum(data^2)*100 But when I compare the R-factor obtained by Athena and the NSS divided by 100 (calculated by myself) I didn't find the same results. Did I make a mistake somewhere. Thank you for your answer. Kind regards Marine Albertelli PhD student IPREM 2 av du Président Pierre Angot 64000 Pau FRANCE --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Cobalamin XANES: experiments and simulations do not match
by Ganesh Subramanian 15 May '17

15 May '17

Dear all, I have been working on simulating for the K-edge XANES spectra of methylcobalamin (MeCbl) and cyanocobalamin (CNCbl). The only change in the two materials is one bond (the upper axial bond in an octahedral coordination at the Cobalt site) from CH3 to CN. The molecule consists of about 180 atoms in total. We, however, use a truncated (50 atom) structure and more recently, an extended (90 atom) structure. But neither of them seem to predict the relative changes in peak positions and edge chemical shifts accurately. As a quick summary: Experimental XANES spectra show: 1. CNCbl has a 1 eV blue-shifted absorption edge as compared to MeCbl. 2. The shoulder peak in CNCbl (about 6-7 eV lower than the main-peak) is much stronger (than MeCbl) and comparable in intensity to the main (strongest) peak. We use Gaussian to identify the optimized structure and then feed it to FEFF 8.4 to simulate for the XANES. When we do the simulations we note - 1. CNCbl has an approx. 0.1-0.2 eV red-shifted absorption edge as compared to MeCbl. 2. The shoulder peak intensity is comparable to the main peak intensity in CNCbl. However, in comparing with MeCbl, the shoulder peak intensity is still lower. Incidentally, we see the exact same problem repeat with hydroxocobalamin OHCbl as we see with CNCbl as well ! (I do not present that here, since I assume the origin of the problem is same). I thought, maybe truncation is affecting the the optimized geometry when we perform DFT and hence increased the cluster size to about 90 atoms but noticed no significant change. (We did this quite sometime back just with MeCbl to actually justify the use of a truncated structure. But now we are not sure where the error is). Now I wonder if I am performing the FEFF accurately and not missing something here. I attach the input feff files for the truncated and the more elongated structures of both MeCbl and CNCbl. I also attach the (ATHENA deglitched, merged and normalized) experimental XAFS for MeCbl and CNCbl. Any help in identifying the issue is greatly appreciated ! (Sorry for the long email). Thanks, Ganesh Subramanian Post Doctoral Research Scholar, Spence Group, Arizona State University

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