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

EXAFS and XANES Summer School at SSRL
by Ritimukta Sarangi 23 Feb '17

23 Feb '17

Hello folks, I have received several queries over the last 6 months about hosting an EXAFS Summer School in 2017 at SSRL. Typically we host it every other year, so we would have offered the School in 2018. However, if there is very high interest, we would certainly consider hosting a school in 2017. Please reply to me directly at ritis(a)slac.stanford.edu if you or your group will benefit from a school in 2017. Please note that we if go ahead with it, the school will be in the June-July 2017 timeframe. Best wishes, -Riti Sarangi SSRL

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GNU plot crashes
by mfehse 31 Jan '17

31 Jan '17

Hi everyone while working in athena project gnu plot sometimes crashes and gives the following error: Gdk:ERROR:/build/gtk+2.0-KsZKkB/gtk+2.0-2.24.30/gdk/gdkregion-generic.c:337:miSetExtents: assertion failed: (pExtents->y1 < pExtents->y2) Aborted (core dumped) Its a bit strange because I have not observed this error when working with other athena projects before and it also does not happen every time I want to plot something, only sometimes. It seems quite random to me. I have attached the athena project file so you can try yourself many thanks marcus

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XEAFS fitting problems
by Fuxiang Zhang 31 Jan '17

31 Jan '17

Dear all, I am new for XAS analysis and now working on solid solution alloys with EXAFS measurements. Here are some general questions about EXAFS fitting that may need your help. 1. In NiCoCr alloys, I always get obvious smaller ss for the pairs of Ni-Cr or Co-Cr than Ni-Co (0.002 vs 0.008-0.011), when measuring the K-edge of Ni and Co, does it suggest that Cr is favorably bonded with Ni and Co? 2. In order to get the bond length of different pairs in binary AB system, can I use formula alpha1*Reff and alpha2*Reff to refine the length of pairs of A-A, A-B (simple cubic symmetry)? 3. The selection of k range in Fourier transformation Parameters seems to have some effect on the fitting results, how to select the range in order to get reasonable results. Many thanks Fuxiang Zhang

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Re: [Ifeffit] Calculation of SPOIL value for the reconstruction of standard spectra
by LANDROT Gautier 26 Jan '17

26 Jan '17

Hello Emmanuelle, The PCA module featured in the current version of Athena does not calculate SPOIL values. This is actually one of the things that Bruce Ravel has listed in his current "Demeter/Athena/Artemis to do list" of his website, see section 4.5.3. For SPOIL calculations I recommend you to use the PCA/TT module of Sixpack. According to Sam Webb, the latest Sixpack (version 1.4) employs a new/different PCA algorithm from the scikit-learn Python package. Using personal data set, I found that the PCA/target transformation results obtained from the new Sixpack v 1.4 are different from those obtained from an older version (v 1.2.10). It would be interesting to know whether other Sixpack users have come up to the same conclusion. The SPOIL values obtained from a homemade code, following the method detailed in the Malinowski 1978 reference article, are very similar to SPOIL values reported in the Malinowski 1978 paper using mass spec data set from Ritter et al. 1976, and also SPOIL values obtained from an old Sixpack version (v 1.2.10) using personal xafs data set. Therefore, if you have installed on your PC the latest Sixpack version (v 1.4), you may want to select, in the menu bar on top of PCA/TT Sixpack module, "Rotation" then "Use Old PCA" to calculate SPOIL values. The calculated SPOIL values will be then equal to those obtained from the previous Sixpack versions. Good luck, Gautier

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Segmentation fault: 11
by David Sherman 23 Jan '17

23 Jan '17

I often have artemis crash on OS X with segmentation fault 11. It seems to happen simply when I click on one on the windows. David M. Sherman Professor of Geochemistry School of Earth Sciences University of Bristol Bristol BS8 1 RJ UNITED KINGDOM Office: +44(0)117-954-5446 Mob: +44(0)750-348-4312

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Postdoctoral Opportunity at SSRL
by Bare, Simon R 21 Jan '17

21 Jan '17

All: Please see the job posting for an immediate Postdoctoral Position at SSRL for in-situ Catalysis X-ray Absorption Spectroscopy https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Postdoctoral Position at SSRL for in-situ Catalysis X-ray Absorption Spectroscopy The Stanford Synchrotron Radiation Lightsource (SSRL), a Directorate of the SLAC National Accelerator Laboratory, Stanford University, and a national research facility, seeks a Ph.D. Postdoctoral Scholar. This 2-3 year postdoctoral position will involve using in-situ/in-operando synchrotron-based methods, primarily x-ray absorption spectroscopy, to study all aspects of catalysis. The candidate will join a new group at SSRL, under the guidance of Simon Bare, whose mission is to develop a world-class synchrotron catalyst characterization facility. The candidate will work on beamline setup and data collection at SSRL, perform in-situ XAS experiments, and analyze the XAFS data. The candidate will also give instruction on data analysis to graduate students. The candidate will interact with visiting and staff scientists from SUNCAT and other leading research groups, postdoctoral fellows, and students on all aspects of the synchrotron-mediated research; provide guidance to and foster the development of graduate and undergraduate students; publish experimental results in scientific journals and present results at scientific meetings; and maintain a safe working environment in the laboratory. Qualifications: * Ph.D. in physics, chemistry, materials sciences or related fields. * Experience with all aspects of synchrotron X-ray absorption spectroscopy is a must, including demonstrated ability in data analysis and modeling of XAFS data using Athena/Artemis. * Experience with synthesis, testing or characterization of catalysts, desired. * A solid background in materials/catalyst characterization and experience with in-situ cell design and development strongly preferred. * Willingness to learn and bridge knowledge/experience gaps. * Ability to work independently and in a team environment. * Ability to work and communicate effectively with a diverse population; good interpersonal skills are essential. * Effective written and verbal communication skills. Please send a letter with CV and list of publications, and names of two references, to the address below: Simon R Bare, email: simon.bare(a)slac.stanford.edu Simon R Bare Director Chemistry & Catalysis SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629

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Re: [Ifeffit] delR and sigma2 models for multiple Scattering Paths (Bruce Ravel)
by Mikhail Solovyev 19 Jan '17

19 Jan '17

Ok, that makes things much more clear. Thankfully my group has the book, ill be taking a look at that. Thank you for the quick and clear responce. Much Obliged Mikhail Solovyev On Thu, Jan 19, 2017 at 1:00 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. delR and sigma2 models for multiple Scattering Paths > (Mikhail Solovyev) > 2. Re: delR and sigma2 models for multiple Scattering Paths > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Jan 2017 13:27:29 -0500 > From: Mikhail Solovyev <sarsol89(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] delR and sigma2 models for multiple Scattering > Paths > Message-ID: > <CABVdVPzfO9KQ_oSkki4cN3RspBfD9+2Gh7Bf0wdS5soT1-J_jw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello to all. > I'm currently trying to Artemis fit a molecule that is highly symmetric > with multiple scattering paths playing a large role. > delR and sigma2 have been handled rather well for all of the single paths. > I am, however, confused as to how to handle it for multiple scattering > paths. > Reff for them seems to be close to the value of the furthest atom, but is > always ~5-10% off. (which would be my second question, how is Reff > determined for multiple scattering paths) > I've looked at the presentation and examples, such as FeS2. > I am trying to incorporate all of the same variables used in single > scattering paths for multiple scattering paths the best i can. > > Thank you ahead of time. > > Mikhail Solovyev >

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delR and sigma2 models for multiple Scattering Paths
by Mikhail Solovyev 18 Jan '17

18 Jan '17

Hello to all. I'm currently trying to Artemis fit a molecule that is highly symmetric with multiple scattering paths playing a large role. delR and sigma2 have been handled rather well for all of the single paths. I am, however, confused as to how to handle it for multiple scattering paths. Reff for them seems to be close to the value of the furthest atom, but is always ~5-10% off. (which would be my second question, how is Reff determined for multiple scattering paths) I've looked at the presentation and examples, such as FeS2. I am trying to incorporate all of the same variables used in single scattering paths for multiple scattering paths the best i can. Thank you ahead of time. Mikhail Solovyev

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PhD position at SwissFEL
by Czapla-Masztafiak Joanna Agnieszka (PSI) 18 Jan '17

18 Jan '17

Dear All, please find below information about PhD position at Swiss FEL group of Paul Scherrer Institute, Switzerland. Link to an offer: https://www.psi.ch/pa/job-opportunities/1327 PhD position in the field of nonlinear X-Ray spectroscopy With the development of free electron laser (FEL) radiation sources a new area of X-Ray spectroscopy commenced. PSI explores and develops methods for nonlinear coherent optical/X-Ray experiments with the ultimate aim of applying these at the SwissFEL free electron laser facility which is planned to operate by the end of 2017. Within this project the candidate will be involved in experiments that can be performed at the synchrotron, in the Laser-laboratory and at FEL's that contribute to an advanced understanding of nonlinear X-ray processes. A crucial indicator for comprehension of the relation between the optical and X-ray nonlinear spectroscopy is the magnitude of the underlying and competing processes. The candidate is embedded in our team that is responsible for the design and installation of the SwissFEL endstation(ES)-A, which is dedicated for research on time resolved studies on chemical systems in the X-ray regime. The project is in close collaboration with Prof. Thomas Feurer at the University Bern. The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. Our institution is based on an interdisciplinary, innovative and dynamic collaboration. You will profit from a systematic training on the job, in addition to personal development possibilities and our pronounced vocational training culture. If you wish to optimally combine work and family life or other personal interests, we are able to support you with our modern employment conditions and the on-site infrastructure. For further information please contact Dr Gregor Knopp, phone +41 56 310 41 08 / gregor.knopp(a)psi.ch<mailto:gregor.knopp@psi.ch>. Please submit your application online for the position as a PhD Student (index no. 1620-01). Paul Scherrer Institut Human Resources Management, Jacqueline Byland, 5232 Villigen PSI, Switzerland __________________________________________ Paul Scherrer Institut Dr. Joanna Czapla-Masztafiak OVGA/414 CH-5232 Villigen PSI Telefon: +41 56 310 4685 E-Mail: Joanna.Czapla-Masztafiak(a)psi.ch

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boundary issue in artemis
by mfehse 17 Jan '17

17 Jan '17

Dear all, im fitting Ti next neighbour environment and I'm facing the problem that above a k value of 9 the fit deviates completely and does not follow the data any more. I dont really understand what is happening, so im forced to limit my fitting window in order to avoid this effect. i have attached a plot in k space so you can better understand what im talking about. any hints would be appreciated

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