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

Re: [Ifeffit] Ifeffit Digest, Vol 168, Issue 3
by Mikhail Solovyev 13 Feb '17

13 Feb '17

It seems that one of the multiplication signs got cut off during copy/pasting, so the equation was incomplete, and that was the issue with "function_2" message. Found out a day later when looking over the equations. Sorry to have brought it up prematurely. Regards Mikhail Solovyev On Mon, Feb 6, 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. Trigonometric Function in GDS (Mikhail Solovyev) > 2. Re: Trigonometric Function in GDS (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Feb 2017 10:36:07 -0500 > From: Mikhail Solovyev <sarsol89(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Trigonometric Function in GDS > Message-ID: > <CABVdVPyLurVSnT=Yevbfya=_6t+gt2uoJT9QCYVh7zxzT3F_Dw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello to all. > > I am encountering an issue when trying to input a trigonometric function in > my GDS window. When trying to fit the data, i get what appears to be an > error > > GDS: 'FeN0' > function_2 > > And it applies to every GDS that has the trig function in it. > What exactly does the function_2 mean? > > Thank you. >

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Fitting sorption EXAFS data in Artemis
by Gemma Woodward [ee11glw] 08 Feb '17

08 Feb '17

Hi all I have EXAFS data for Co sorbed to kaolinite and want to fit this using artemis. I have a kaolinite cif file but am unsure where to go from here to include the Co so I get Co-Al/Si pathways. In the atoms window do I add a Co into the table at the bottom and make it the core atom? Thanks Gemma Woodward PhD Student Cohen Geochemistry Earth Surface Science Institute School of Earth and Environment University of Leeds Leeds LS2 9JT Telephone: +44 (0)113 34 33647 Twitter: @glw_93 Website: http://www.see.leeds.ac.uk/people/g.woodward

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When opening Artemis "Restore from an autosave file" appears and application is frozen
by Stephanie Moffitt 08 Feb '17

08 Feb '17

Hi All, I recently upgraded my Mac to run 10.12 Sierra. I followed the github instructions for installing the updated version of Demeter (including installing Macports). Athena will open for me but Artemis does not. When I type artemis into the terminal window all the windows for artemis appear but a window which says "Restore from autosave file" appears with the choices "cancel" or "OK". However at this point the application is frozen. I have tried looking for an artemis.autosave file on my computer or even an "anything".autosave file but I can not find anything. The closest thing was AutoSave.pm but when I deleted that artemis refused to open at all so I had to reinstall Demeter. I have also attempted to change the artemis.demeter_conf file so that the autosave portion says "false" instead of "true" however, the file said I did not have permission to change the file. Any help would be much appreciated. Many thanks, Stephanie -- .

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Trigonometric Function in GDS
by Mikhail Solovyev 06 Feb '17

06 Feb '17

Hello to all. I am encountering an issue when trying to input a trigonometric function in my GDS window. When trying to fit the data, i get what appears to be an error GDS: 'FeN0' function_2 And it applies to every GDS that has the trig function in it. What exactly does the function_2 mean? Thank you.

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Some basic questions
by pushkar shejwalkar 02 Feb '17

02 Feb '17

Dear All, I have some basic questions that are more related to the practical handling of the samples rather than the concept. 1) Recently we had to prepare for the Cu and Pd samples and I had carried out the calculations of how much material will be needed for such measurement to get relatively good uT and deltauT values. For such purpose, I used the program developed by SPring-8 (on their website) dedicated for BL-14 beamline. In this program we can put in the cell diameter and what kind of BN thickness is needed. Since my samples are metal immobilized heterogeneous organic materials, it has a lot of background in terms of C,H,Si,N etc. Thus, I use material directly and I do not use BN at all. So my BN thickness is 0. How do I change this mass of material needed into the thickness of cell? What I do, is I use density of material and for the cylinder of pellet I calculate the thickness. My question is, WHAT GETS THE PRIORITY, THICKNESS OR MASS of material that goes in? Becuase thickness of pellet governs the XAFS equation, whereas mass governs the absorption peak (height and high uT). It is difficult to comprehend everything written on website, Since the website is in Japanese and I am not. Also it is kinda difficult to communicate with the authorities directly in free English, I am asking this question here. 2) Secondly, In the mixed metal case of type AB, If I focus the energy for A, how will the B have effect on the scattering of A. A=Cu and B=Pd. I will be measuring Pd in later days. Would it be possible to consider Pd (in this case) as a neighboring atom and purely treat it like I would otherwise e.g. N or O like that? Since this is my first time with mixed metal situation, any reference publications or material to read would be very helpful. 3) In another case of mine, I have Pd and Pd2+ mixture in my sample. Would it be possible to estimate the exact concentration of each of them? Using two analytically pure Pd and Pd2+ salts to make calibration curve would it be possible to get the exact concentration? What will be the independent variable on the graph? . Thank you for your kind help and information, in advance Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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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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