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

Problem with running mback algorithm in the newer version of Larch
by Tayal, Akhil 08 Feb '19

08 Feb '19

Hello Matt, I found that while running the 'mback' algorithm there is an error in accessing f1_chantler database. Weirdly the commands work well for the older (0.9.35) version that happens to be installed on my old computer. But for the latest version (0.9.40), I simply could not able to generate the value of f1 and hence could not use the 'mback' algorithm. Do you have any suggestion to troubleshoot this issue on the latest version of the software? Also is there any inbuilt command to perform 'flattening algorithm' for normalization or one has to do it manually. Thanks, Akhil

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Post doctoral position at Pohang Accelerator Laboratory
by 이국승(에너지환경소재연구팀) 08 Feb '19

08 Feb '19

Dear all, A post-doctoral position is available at Pohang Accelerator Laboratory. Tasks will be development of electrocatalysts for fuel cells and/or water splitting and their XAFS analyses. Candidates should have a PhD degree in materials science, chemistry, chemical engineering, or other appropriate areas and should have experience in XAFS analysis and excellent writing and communication skills. Interested candidates please may contact Dr Kug-Seung Lee (lks3006(a)postech.ac.kr<mailto:lks3006@postech.ac.kr>) with your CV. Additioinal documents may be required, for example, letters of reference, representative publications, etc. Thank you. 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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Larch 0.9.41
by Matt Newville 08 Feb '19

08 Feb '19

Hi Folks, Larch 0.9.41 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html If you have already installed Larch 0.9.39 or later, you should be able to update to the latest version with `conda update -c gsecars xraylarch`, Larch 0.9.41 is about six months in the making. There have been some important improvements in XAFS and XANES analysis, including improved MBACK algorithm (thanks Marco Alsina!) and many bugfixes and in the XAS Viewer GUI for pre-edge peak-fitting and linear combination analysis. Significant improvements have also been made X-ray microprobe analysis, including for XRF analysis as well as XRF and XRD mapping tools, including support for reconstructing X-ray fluorescence and diffraction tomography data. Larch now includes the very useful Dioptas GUI for XRD patterns from Clemens Prescher. At the very least, this can be used to view and calibrate X-ray diffraction data ("replace Fit2D") using pyFAI and related libraries from the folks at ESRF. For Python programmers: Version 0.9.41 makes a small but significant step toward making Larch a "more normal Python library", so that Python scripts using Larch as a library can avoid having to create and keep a running interpreter for many basic analysis steps, including interacting with the database of X-ray properties that includes data from Elam et al, Chantler, and so on. Version 0.9.41 works with Python 3.7, 3.6, and 2.7. The installers linked above are built with Anaconda Python 3.6. Most dependencies are also available as conda or pip packages for Python 3.7, and some are available with Python 2.7. This is the last version of Larch to be tested with Python 2.7. We will not deliberately break Python 2.7 until after 0.9.42 is released, at which point Larch will stop working with Python 2.7. We expect this to happen in two or three months. In the meantime, we will not intentionally break things for Python 2 but will no longer test or support Python 2. Please let us know if you having any questions or trouble. Cheers, --Matt Newville

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Problems Opening a larch saved athena Project in Athena
by Luis Carlos Colocho Hurtarte 05 Feb '19

05 Feb '19

Hi all, I have a some data from CLS, using the plug-in in Athena I could open most of them except a couple. I managed to open the rest using Larch (no Problem there), my interest is solely in saving them as .xmu/csv. Nevertheless when I saved in csv in Larch the axis order is inverted (X1 – Yn and Xn to Y1), also if I save them as an athena Project through larch and open it in Athena, the program crashes. Is this some kind of bug? The data plotted in Larch is fine, but the file is corrupted? Anyone experienced something like that passing from larch to Athena? Kind regards Luis -- Luis Carlos Colocho Hurtarte Lehrstuhl für Bodenkunde (Chair of Soil Science) Technische Universität München Emil-Ramann-Str. 2 85354 Freising Germany Telefon: +49 8161 71 -5266 Fax: +49 8161 71 -4466 http://www.soil-science.com

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Post Doctoral Position at Frei University Berlin/ Uni Bayreuth
by Ditty Dixon 05 Feb '19

05 Feb '19

*Dear All,* *As a part of joint German-Czech Research project "*Operando Fuel Cell" a* post-doctoral position is available for three years starting from 1st of April 2019 at *Universität Bayreuth/Frei University Berlin, Germany. The aim of the joint project with partners from Berlin and Prague is to obtain a more detailed insight into the complex reaction and degradation mechanisms in high temperature polymer electrolyte membrane fuel cells (HT-PEMFC). For this purpose, X-ray absorption spectroscopy (XAS) will be used during fuel cell operation in realistic working conditions. Your tasks will be: • Construction of testbench for HT-PEMFC tests • Design of a suitable in-situ cell for hard X-ray measurements at Pt L2 and L3 edges • Acquisition of beamtimes at BESSY and PETRA • In-operando XAS measurements at different Pt-based catalysts We are looking for a candidate with PhD, having experience in material characterization using spectroscopy techniques. Interested candidate may please contact Prof. Christina Roth (christina.roth(a)fu-berlin.de) or ( kerstin.soellner(a)uni-bayreuth.de) along with your CV. Thank You -- Dr. Ditty Dixon Ramanujan Faculty Electrochemical Power Source Division Central Electrochemical Research Institute (CSIR-CECRI) Karaikudi, India, 630003 Ph:00919400243084

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Plotting flattened feffit simulation results
by FonsPaul 29 Jan '19

29 Jan '19

Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions!

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Job posting: Lead Beamline Scientist at NSLS-II, Brookhaven National Lab
by Matt Newville 27 Jan '19

27 Jan '19

Hi Folks, I was asked to forward this job posting: There is an opening for a Lead Beamline Scientist position at the National Synchrotron Light Source-II, Brookhaven National Laboratory. The candidate will assume leadership of the Inner-Shell Spectroscopy (ISS) Beamline, a high-flux, fast-scanning, damping wiggler spectroscopy beamline, with in-situ and operando instrumentation capabilities. The candidate will also be expected to develop an independent research program that utilizes the beamline capabilities. See https://jobs.bnl.gov/job/upton/lead-beamline-scientist-inner-shell-spectros… for details. --Matt

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Question about parameters of principle components analysis (PCA)
by 雷思聪 26 Jan '19

26 Jan '19

Hello, I see in many publications the indicator values (IND) numbers used to evaluate how many components are included, and SPOIL value used to evaluate quality of target transform in principle components analysis (PCA). However, they are obtained from PCA performed on SIXpack, rather than Athena (version 0.9.26). Hence, I wonder if I can get similar parameters after running of PCA in Athena? If not, how do I evaluate the PCA results? Thanks for your help!

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Larch flattening
by Kirill Lomachenko 26 Jan '19

26 Jan '19

Dear Matt, I have a question and a comment regarding Larch. I would appreciate if you could have a look. 1) The flattening algorithm for XAS in Larch works differently with respect to Athena when linear post-edge function is used for normalization. In Larch the normalized spectrum is always fitted by a parabola for flattening, no matter which function was used for normalization. It works fine when the post-edge function is also a parabola, but when it is a straight line, the resulting flattened spectrum does not stick to Y=1, as it is expected to do (and as it does in Athena). My question is: is it a bug or a feature? Just in case, I made some minor modifications in the pre_edge.py file that allow to get the same results as in Athena when linear post-edge is used. Maybe these corrections are a bit clumsy, but it seems to work. If anyone needs, I can share. 2) There is a typo in the larch web-manual in the description of the nnorm parameter of the pre_edge() function. It is stated that it is the number of terms in the fitting polynomial (i.e., 1+degree) whereas it seems that it is just its degree. So, nnorm=1 corresponds to a linear function and nnorm=2 to quadratic. In the gui help it is partially corrected, but the phrase "Default=3 (quadratic)" stays. It is not critical at all, but may be misleading for beginners... Using the possibility, I would like to thank you for all the great work you are doing on Larch. It really helps for large datasets! All the best, Kirill -- Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu

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Re: [Ifeffit] Dynamic XAFS Simulations?
by Gentle, Cecilia M 24 Jan '19

24 Jan '19

Dear Hunter, I also recommend you to join the mailing list for the ultrafast laser community: dyna(a)listes.epfl.ch [to subscribe: dyna-subscribe(a)listes.epfl.ch] Best, Cecilia Gentle PhD Candidate, Department of Chemistry University of Illinois at Urbana-Champaign https://www.vanderveen-lab.com/ -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, January 23, 2019 4:54 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 191, Issue 13 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. Dynamic XAFS Simulations? (Hunter Allison) 2. Re: Dynamic XAFS Simulations? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 23 Jan 2019 13:26:21 -0800 From: Hunter Allison <hgalliso(a)uci.edu> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Dynamic XAFS Simulations? Message-ID: <CAH6J0e_vk1n4viX8H5A4vX=SRL0e5NQHmSZGEQ43wVxBzpwo5Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, I'm a graduate student at the University of California, Irvine. Firstly, thank you for all the copious resources. It is a treasure trove of information and a beacon of light for someone just starting out. Let's begin with some brief background. In my research group, we intend to perform pump-probe spectroscopy with attosecond x-ray probes. The Professor says that we can use XAFS to study how the electrons move on these very short timescales. While the system is being setup and other experiments are being conducted, my Professor wants me to figure out how to do simulations of XAFS. This is a bit of a daunting order, since I've never simulated anything before and only have basic programming knowledge. The only direction I have is, "Try Google.". So, today, I've been "trying Google" and found my way to here. Since, I don't really know what I'm doing, I thought I try asking and finding out if anyone else does this sort of thing: How/where does one do simulations of dynamic XAFS? Where would I get started? (Please forgive me if this question has been answered somewhere else or if it seems profoundly dumb or too broad. I'm really just looking for some more direction. Perhaps, it could be that nobody does this and, in that case, I need to figure out how to model this myself. Wow! That thought seems daunting.) For example, let's say I want to find out how the x-ray adsorption of a carbon foil like Graphene would change on attosecond time scales as it's heated by a femtosecond laser and electrons move. Is there a program or code out there that people use to model this sort of thing?

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