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XANES convolution method in FEFF9
by Ying Liu 20 Feb '19

20 Feb '19

Dear all. I am currently running FEFF9 on XANES calculation. However I could not figure out how FEFF transformed LDOS to the final xmu.dat. What function did LDOS data convoluted with to achieve xmu.dat? Looking forward to hearing any answer. Thank you. Ying Queen Mary University of London

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Re: [Ifeffit] questions: EXAFS
by Robert Gordon 19 Feb '19

19 Feb '19

Hi Vineetha, I advised during the course that students should use the ifeffit mailing list for questions post-school. An advantage of doing so is that one could receive assistance from any member of the community and not be at the mercy of the time constraints of any particular researcher. Another advantage is that someone more familiar with the type of problem you are studying might be able to offer more insight. I would like again to encourage you to make use of the mailing list. Other researchers may also see the problem with which you are dealing and it could help them too. Some general advice: Mixed phase samples can be problematic. If you know which two phases are present, you can simulate them separately and examine the local environments. If the near-neighbour environments are very similar, then some fitting can be done with reasonable results. You still need to keep in mind the resolution criteria for being able to resolve closely spaced paths. Looking at your O-scattering paths, not having seen your k-space data and range, I suspect you will not be able to resolve the splitting in the first shell, and so, would treat it as a single path (similar argument for Hf paths in 2nd shell). The starting model serves to give you amplitudes and phases for fitting. In that regard, whether you use monoclinic or orthorhombic starting model should not matter. Once fit, you would examine how well the fit result compares to either model. I would hope you also measured standard(s) of known composition and structure. Fitting such would help guide the fitting of your unknown. Model calculations can be done for your two suspected phases, including temperature effects with the DEBYE card in the FEFF input. A quick google search yielded this paper: https://ceramics.onlinelibrary.wiley.com/doi/abs/10.1111/j.1151-2916.1977.t… which gives a calculated Debye temp of 484K for monoclinic HfO2. You can check the literature further for other research on this material which may give an experimental value. With the model chi(k)'s, you can do linear combinations (manually) and see if you find some ratio that approaches agreement with your data. I don't see how to get the model chi(k) out of Artemis though. I even tried running the feff6 executable manually (with associated dll's) but it did not generate the chi.dat file I was expecting. I would suggest, if you wish to generate models and compare in this fashion, that you invest in a newer version of FEFF that does allow you to generate this output (i.e. get FEFF9). Other thoughts: XANES? Did you measure it for the unknown and standards? If so, are the two phases distinguishable? Background removal? Can you improve it to reduce the amplitude below 1 Angstrom? Always show the original data (merged ok), not simply the transforms when asking for help. That helps one assess the problem better. regards, Robert On 2019-02-19 9:43 a.m., Mukundan, Vineetha wrote: > > Hi Dr. Gordon, > > I am Vineetha and had met you at the EXAFS short course @ BNL in > November’18. I am trying to analyze a couple of my data on Hafnia and > am stuck. So I am seeking help with the following questions. Apology > in advance if it will some of your time. > > 1.I generated the scattering paths. See attached. It is safe to > discard the multiple scattering paths here. So I generated the plots > with Hf-O single scattering paths and Hf-Hf scattering paths. Clearly > it shows the first shell is mostly one or all of O1.1, O2.1 and O2.3 > paths. And the second shell is mostly influenced by Hf1.2, Hf1.3 and > Hf1.5. Am I correct in making this assumptions so far? IS there any > other way to figure out which paths are important or not important, > other than plotting them together with the data. > > 2.While fitting, I am really unsure how to set the parameters for each > path in my example. I am not sure how to set up the parameter when we > have multiple paths contributing to say first shell or second shell. > Also, I know using the Nyquist equation it is possible to figure out > the number of independent variables. I read up the ARTEMIS pages on > FeS2 example described but there the structure is cubic but my sample > is monoclinic. Here I am trying to fit only the monoclinic paths with > my data. > > 3.Also, I know my sample has monoclinic and orthorhombic structure. So > how does one go about generating the simulated EXAFS for a particular > structure on FEFF? say in my case the monoclinic and orthorhombic > ones. I have the .cif files for these 2. For figuring out the % amount > of monoclinic and orthorhombic phases in the sample, I am assuming I > will have to do a linear combination analysis. Am I correct? > > Any help in this regard will be really useful. > > Thank you, > > Vineetha > > *Vineetha Mukundan, PhD* > > Post-doc, Prof. Diebold’s Group > > Colleges of Nanoscale Science and Engineering > > SUNY Polytechnic Institute > > 257, Fuller Road > > Albany, NY 12203 USA > > CONFIDENTIALITY NOTICE > > The pages (including attachments) comprising this internet or > facsimile transmission contain CONFIDENTIAL information. This > information is intended for the sole and exclusive use by the > individual entity named as the recipient hereof and any further > disclosure or dissemination is prohibited. If you are not the > intended recipient, you are hereby notified that any disclosure, > copying, storage, distribution, or use of the contents of this > transmission is strictly prohibited and may be unlawful. If you have > received this transmission in error, please notify us immediately by > telephone or return e-mail, delete it from your mail system, and > destroy all copies in your possession. Thank you. >

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FEFF9 calculations of Tellurium Clusters
by Gentle, Cecilia M 14 Feb '19

14 Feb '19

Dear IFEFFIT Mailing List, I am running FEFF calculations using FEFF9. I am running these calculations on my department's cluster in parallel using a Linux machine Currently, I have run XANES calculations of CdTe and ZnTe at the K-edges of Zn, Cd and Te. I am calculating the XANES of various cluster sizes. I start with a cluster with a single coordination shell and build up to 7 coordination shells, running a XANES calculation with each cluster size. I have run these calculations for the K-edges of Cd, Te, and Zn. Unexpectedly, I receive an error for the Te K-Edge XANES calculation of ZnTe and CdTe for the cluster size of 2 coordination shells. The FEFF calculations run fine for a cluster with a single coordination shell and for clusters with 3 to 7 coordination shells. This is my first experience running FEFF. I have read through the FEFF manual, but I am having trouble interpreting the error message. I have the FEFF input file for Te K-Edge of a CdTe cluster with 2 coordination shells, and the resulting error message attached as a text files. Has anyone else experienced this before? If someone can point me to a section in the manual or another resource to help me understand the error, I would very much appreciate it. Thank you, Cecilia Gentle PhD Candidate University of Illinois

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EXAFS of solid-solution alloy
by Chongchong Mellon 08 Feb '19

08 Feb '19

Hi all, I have some problems in analyzing the EXAFS of solid-solution alloy, let us define as A0.5B0.5. I have searched the mailbox but cannot find similar discussion yet. So I post the question here and hope to get some suggestion from you. 1. A and B are immiscible metals from the phase diagram, which means that I couldn’t get the bulk A0.5B0.5 as a standard reference. In this case, how can I estimate the amp for the K-edge of A or B? 2. A and B are very near (atomic number B-A = 2) in the periodic table. So their lattice parameters are quite close to each other. In this case, when I tried to fit the 1st shell use A-A and A-B paths at the same time, the Happiness parameter becomes worse and the coordination number of A-B is not realistic (large errors!). If I fit with only the A-A path or A-B path, I get a good fit. However, atomic resolution STEM-EDX maps show the homogenous distribution of both A and B atoms. The A-A and A-B bond might have an equal ratio. In this case, how can I do the fitting? Thank you very much in advance! Sincerely, Chong

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Seeking a post-doctoral research in Environmental Chemistry at Carnegie Mellon University
by Gregory Lowry 08 Feb '19

08 Feb '19

Open Position Postdoctoral Researcher Civil and Environmental Engineering Carnegie Mellon University I am seeking a post-doctoral researcher in environmental chemistry. Candidates must have experience using synchrotron X-ray absorption spectroscopy for determining metal speciation in environmental samples (or similar matrices), and/or experience using synchrotron X-ray Fluorescence and XANES mapping (GeoPIXIE) to speciate metals in environmental or biological samples. Experience with mercury and/or arsenic geochemistry, and working knowledge of other characterization methods for metal-based nanoparticles (e.g. XRD, FTIR, XPS, ICP-MS, spICP-TOF-MS) are desirable. A demonstrated ability to publish research in high quality journals, meet deadlines, and write proposals is required. Effective English language oral and written communication are required. The candidate will interact with an interdisciplinary research team of faculty, post-docs, and Ph.D. students and with industry collaborators on a variety of projects including speciating Hg in matrices relevant to oil and gas exploration and metals speciation in plants. The successful candidate will be expected to design and conduct experiments in aqueous and non-aqueous matrices, collect and analyze synchrotron XAS spectra on samples containing mercury, arsenic, and other metals, prepare manuscripts and monthly research reports, assist in proposal writing, and present findings at national and international professional conferences. The position is for a minimum of one year, renewable depending on performance. Interested applicants should contact Prof. Greg Lowry glowry(a)cmu.edu. Please send a brief cover letter, curriculum vitae, a brief statement of research interests and the contact information for at least three references. Applications will be accepted until the position is filled. -- Gregory V. Lowry Walter J. Blenko, Sr. Professor of Civil & Environmental Engineering Deputy Director, Center for Environmental Implications of Nanotechnology Carnegie Mellon University, Pittsburgh, PA 15213

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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 07 Feb '19

07 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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