May 2017 - Ifeffit - millenia.cars.aps.anl.gov

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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E0 on linear combination fitting: fit or not?
by Carrillo Sanchez, Pamela 13 May '17

13 May '17

Hi all, I have gone through the mail archives as well as following the instructions of Athena user's manual as well as Scott Calvin's book but still I find myself with the doubt of how correctly "choose E0". I have aligned the data and standards with the merge of reference foils measurements of the metal (Mn). We did not have a reference foil placed while measuring the data so I used the merge of the references scans when the standards were measured and they showed a consistent energy shift. I have set the same E0 for all the data and standard to the same E0, I chose the first peak of the derivative in the data (6MnRh_RED). When I do the LCF analysis without 'fitting E0' , I get a worse fitting than when I choose the fit E0 on Athena as well as different types of components on the fitting. Which one is the best choice for it ? From what I have read I think that without fitting E0 would be the proper one regardless of the "worse fit". Also, I would like to know which fit range would be appropriate for this, I have chosen -20 to +30 eV due to the features of my data and ranges for XANES. Any recommendation. I have attached the files for the project and screenshots of both fittings. Any help is highly appreciated! Pamela

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(no subject)
by Carrillo Sanchez, Pamela 11 May '17

11 May '17

Hi all, I have gone through the mail archives as well as following the instructions of Athena user's manual as well as Scott Calvin's book but still I find myself with the doubt of how correctly "choose E0". I have aligned the data and standards with the merge of reference foils measurements of the metal (Mn). We did not have a reference foil placed while measuring the data so I used the merge of the references scans when the standards were measured and they showed a consistent energy shift. I have set the same E0 for all the data and standard to the same E0, I chose the first peak of the derivative in the data (6MnRh_RED). When I do the LCF analysis without 'fitting E0' , I get a worse fitting than when I choose the fit E0 on Athena as well as different types of components on the fitting. Which one is the best choice for it ? From what I have read I think that without fitting E0 would be the proper one regardless of the "worse fit". Also, I would like to know which fit range would be appropriate for this, I have chosen -20 to +30 eV due to the features of my data and ranges for XANES. Any recommendation. I have attached the files for the project and screenshots of both fittings. Any help is highly appreciated! Pamela

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Save the date: Nov 1-3, 2017, XAFS short course at BNL
by Anatoly Frenkel 09 May '17

09 May '17

Dear Colleagues: 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 will continue the annual tradition of gathering a group of scientists, active in the field, to share their expertise with those interested in learning about the use of x-ray spectroscopy methods in their research. *The course will be useful for those scientists who are already familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced analysis and modeling 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 techniques. Course instructors will use examples from their research during presentations. Topics covered will include theory of XANES and EXAFS, direct modeling methods using Molecular Dynamics simulations and Reverse Monte Carlo, multiple data set modeling and multiple-scattering analyses. Other topics will include, but not limited to: chemometrics, bonding dynamics and transformation kinetics. During the data analysis practicum on Nov. 3 the course participants will get an opportunity to work with demonstration examples and/or their research projects with the help of the course instructors. The course will be open to 30 participants, selected based on their application materials. The course web page will appear on BNL web site in near future, with instructions how to apply. For any inquiries please contact me. 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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Error importing data into Athena
by Bone, Sharon Elizabeth 03 May '17

03 May '17

Hi, I’m running the current version of Athena on a windows 10 machine. It had been working fine, but now I get an error whenever I try to import new data (.dat file from SSRL). The error tells me the program can’t read the file and asks whether I need a plugin. Do I need a plugin? How do I uninstall and reinstall the program? I’m guessing this might be the best fix? Thanks! Sharon

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Need FEFF9 for Z> 95: how to use in Demeter?
by Bone, Sharon Elizabeth 01 May '17

01 May '17

Hello, I have a problem with demeter that I am hoping to get some help with: My understanding is that the current version of demeter does not support versions of FEFF greater than 6. Usually this isn’t a problem for me, but I recently started working with elements with Z > 95 and FEFF6 can’t handle these elements. I recently tried to download an old version of demeter (ixafs through http://cars9.uchicago.edu/ifeffit/Downloads) but the link was no longer valid. Is there a way to access an old version? I’d far prefer to use the new vesion of demeter. Is there any chance that the capability to run higher versions of FEFF will be incorporated soon? Thanks for your help! Best, Sharon

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