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

XES calculations in Feff9.
by FonsPaul 08 Mar '19

08 Mar '19

I have been attempting to use Feff9 to calculate x-ray emission spectra. In short, it would appear that one only exchanges the XANES card with the XES card, however, there appears to be nothing in the documentation that clearly states where the output is directed or how it is labeled. The most logical output would be xmu.dat and the spectra is clearly different when the XANES card is swapped out with the XES card. The only column in the xmu.dat card that appears to make sense to be XES spectra would be the mu0 column as it is positive definite while the chi, column, for example, goes negative and appears to be an interference pattern. Can any one shed some light on this? Also while the documentation states that the XES card takes the form “XES emin emax estep”, the example for GeCl4 included with jfeff uses the options “XES 8 0.05 0.0” whereas the jfeff example file for XES of BN uses “XES -20 20 0.2”. While the second example makes sense, I don’t understand the meaning of the card values used for the GeCl4 molecule example. This is especially relevant as I wish to calculate XES for an epoxy polymer and I have no idea what the fields mean. Thanks for help on this in advance!

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Installation of Athena on Linux Ubuntu
by MOHAMED NAJI 07 Mar '19

07 Mar '19

Dear All, I would like to install Athena in my Linux Ubuntu 16.04 OS. Any idea on how to and if there is already a software develloped for Linux OS. I searched but didn't find it and I'm wondering if someone has already developed it. Thank you Mohamed Naji --

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Re: [Ifeffit] cant open Athena project
by fred.mosselmans＠diamond.ac.uk 07 Mar '19

07 Mar '19

Dear Antony, Your data type for these files is xanes, that won't give a chi set for artemis to read it in. You need to change the datatype to mu€ under the group tab in athena Cheers Fred Message: 1 Date: Thu, 7 Mar 2019 07:44:30 +0000 From: Antony Burnham <Antony.Burnham(a)anu.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Can't open Athena project Message-ID: <MEAPR01MB4486896DFADAA39ADB94E966A24C0(a)MEAPR01MB4486.ausprd01.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" I'm having trouble opening my Athena project in Artemis. This contains two transmission spectra of zirconium phases. They plot just fine in Athena but when I try to import them in Artemis it doesn't recognise that there are any files at all in the project (except that one of the two spectra does display in the plot window). There's just a blank space in the left hand pane where the list of files usually appears. I don't have this problem with any of my fluorescence data from the same experiment. And when I have an Athena project with a mix of fluo and transmission spectra, only the former are listed in the import window. I attach the project and the two files that went into it, in the hope that someone can tell me what I (or the software) did wrong. Regards, Antony Burnham

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Error when first opening Athena on Mac
by Laura E Wasylenki 05 Mar '19

05 Mar '19

Hello, I’ve just attempted to install Demeter on a Mac running OS 10.13.6 (High Sierra). When I open Athena, the XAS processing window appears, but then a warning window appears on top of it that says “Demeter::Templates::D” used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm. I think a line number follows, but it is cut off. The warning contains several more lines that are identical to that one, except that D is replaced by other letters. When I dismiss the warning window by clicking “OK,” Athena and Perl just close down. Has anyone seen this, and does anyone know the solution? Thank you! —Laura ____________________________ Dr. Laura Wasylenki Associate Professor School of Earth and Sustainability Department of Chemistry & Biochemistry Northern Arizona University PO Box 5698, 700 S Osborne Drive Flagstaff, AZ 86011 laura.wasylenki(a)nau.edu<mailto:laura.wasylenki@nau.edu>

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Re: [Ifeffit] Ifeffit Digest, Vol 193, Issue 4
by Christopher Chantler 03 Mar '19

03 Mar '19

PS Simon, we are just around the corner [physics] and also link up with the Dementia work, so you might just drop across and have a chat / meeting! -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> chantler(a)me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdA…> ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Monday, 4 March 2019 10:06:37 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 193, Issue 4 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. Re: Cu K edge XANES stds (Simon James) ---------------------------------------------------------------------- Message: 1 Date: Sun, 3 Mar 2019 23:06:19 +0000 From: Simon James <s.james(a)florey.edu.au> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Cu K edge XANES stds Message-ID: <A9A1ED50-AC0D-47F8-9D5D-2208001097E1(a)florey.edu.au> Content-Type: text/plain; charset="utf-8" Hi Drew, Thank you for your swift reply. Apologies for the delay in my response but I was dragged in to other matters. Appreciate the data and ref. Regarding the sanity check I have collected some spatially resolved Cu XANES ?maps? of cultured cells and some of the standards I collected during the run are horribly compromised for unclear reasons and I just wanted some clean data to reference while I work on cleaning up (to the degree possible) my standards. Thanks again. Cheers, Simon Simon James PhD Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Web: www.florey.edu.au<http://www.florey.edu.au> On 28 Feb 2019, at 2:51 am, Latta, Drew E <drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu>> wrote: Hi Simon, Since you are just looking for a sanity check (on what??) here are some Cu-S standards for you. They were published in DOI: 10.1021/es304736y. The Cu-cys sample is not a pure phase, but probably a mixture of cysteine/cystine. But it is likely mostly Cu(I). Further discussion is available in the SI of the paper above. The file is from an old, old version of Athena (0.8x)... hopefully it works for you. Best, Drew Latta ====================================== Drew E. Latta, Ph.D. Asst. Research Scientist The University of Iowa Civil and Environmental Engineering/IIHR 4105 Seamans Center Iowa City, IA 52242 Ph. 319-936-0034 email. drew-latta(a)uiowa.edu<mailto:drew-latta@uiowa.edu> ====================================== -----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Simon James Sent: Tuesday, February 26, 2019 3:18 PM To: Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> Subject: [Ifeffit] Cu K edge XANES stds Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I?m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit <Cu_Samples_athena.prj>_______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Cu K edge XANES stds
by Simon James 03 Mar '19

03 Mar '19

Hi mailing list, I am hoping someone is willing to share their Cu K-edge XANES spectra from biological Cu thiol complexes. I’m particularly interested in Cu(I/II)-GSH, Cu(I/II)-Cys or similar. I need a sanity check on some fluorescence data I am wrangling. Can anyone help? Best regards, Simon This mail was composed on the move via my phone. Apologies for any typos. Florey Institute of Neuroscience and a Mental Health Melbourne Brain Centre 30 Royal Pde Parkville, 3052 VIC

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*****SPAM*****Creating EXAFS coefficient file for reverse monte carlo simulation
by tolga.ulucan＠metu.edu.tr 03 Mar '19

03 Mar '19

Hello everyone, I have synchrotron XRD and XAFS(L3 Tb edge) data on Al90Tb10 metallic glass alloy that i want to use them as constraints in a reverse monte carlo simulation(RMC_POT). RMC_POT manual says i need 2 files for XAFS. 1st chi(k)-k file which i exported from athena as normalized data and 2nd exafs coefficient file which i don't understand what it is or how to create it. I was wondering if anyone can help me on how to create this file or point me on a direction to get more info on this? Best wishes, Tolga Han Ulucan

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Data on Cd5H2(PO4)4·4H2O
by 1510405＠tongji.edu.cn 02 Mar '19

02 Mar '19

Hi all, I have acquired Cd L3-edge XANES spectra of my sample and some Cd standards for LCF analysis. However, I lack the spectra of Cd5H2(PO4)4·4H2O, which was important to my analysis. Therefore, I was wondering if anyone could share the Cd L3-edge XANES data of Cd5H2(PO4)4·4H2O with me? Best regards, Sicong Lei

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Can't load Iffeffit.dll
by Haas, de, W.B. 01 Mar '19

01 Mar '19

Dear mailing list, I recently started using Windows 10 Enterprise. However, now Athena, Artemis and Hephaestus don't launch (I see the the software icon but then it doesn't launch). I tried the suggestions made in an earlier thread but they didn't work for me: 1. Making sure there is permission to read and write in the location where Demeter is installed. 2. Making sure the antivirus software doesn't misidentify it as a threat. The CIT services of my university don't know how to solve this issue either. So I was wondering whether there were any other fixes known for this issue. The earlier thread: [Ifeffit] Problems Running Athena, Artemis and Hephaestus on P.C. with Windows 7 Enterprise Operating System May 2016 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-May/008592.html Kind regards, Winfried de Haas

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Larch 0.9.42
by Matt Newville 26 Feb '19

26 Feb '19

Hi Folks, Larch 0.9.42 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html Version 0.9.42 fixes many problems, especially to the XAS Viewer GUI app which is now pretty close to a replacement for Athena but with better peak-fitting and with none of the limitations that were imposed by the outdated ifeffit library. For MacOSX, Version 0.9.42 can be installed with a standard Mac "pkg" installer file. If you have already installed Larch, you should be able to update to the latest version with conda update -c gsecars xraylarch on Windows, you may have to specify the full path with something like: C:\Users\<YourName>\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can also simply remove the XrayLarch installation and reinstall using one the installers above. For Python programmers, Version 0.9.42 ends support for Python 2. No testing or packaging was done with Python 2 for this release, and going forward the master development branch will not work with Python 2. Please let us know if you having any questions, trouble, or suggestions. --Matt Newville

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Problem with using lincomb_fit function in the Larch
by Tayal, Akhil 26 Feb '19

26 Feb '19

Hello Matt, I could not be able to perform LCA using the lincomb_fit function in the Larch software. I am getting the error message from line number 80 in the lincombo_fitting.py script. I expect the function has some bug with reading the group values. It could not be even able to read the default array 'norm' nither any user-provided 'arrayname' such as 'flat or fpp.' Can you suggest any solution for it? Please find the data files and larch script I am using for this purpose. Thanks, Akhil

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Does anyone have XAS from Cu(I)-GSH and/or Cu(I)-cys
by Simon James 25 Feb '19

25 Feb '19

Hi mailing list, I am hoping someone can help me sanity check some XAS spectra I recorded. I have [Cu(I)cys], [Cu(I)GSH] spectra (recorded in fluorescence) and would be eternally grateful if anyone is prepared to share any of their data on these or similar compounds? I am really only interested in the edge but more data is always more data. Happy to discuss offline if preferred. Happy XAS'ing Best regards, Simon Simon James Senior Research Officer NHMRC-ARC Dementia Research Development Fellow Melbourne Dementia Research Centre University of Melbourne The Florey Institute of Neuroscience and Mental Health Office: +61 (3) 9035 6420 Mob: +61 (4) 3811 0982 Web: www.florey.edu.au<http://www.florey.edu.au> simon.james(a)florey.edu.au<mailto:simon.james@florey.edu.au>

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Hafnia standards
by Mukundan, Vineetha 21 Feb '19

21 Feb '19

Hi All, I am new to EXAFS data analysis and am working on Hafnia based dielectrics. So far, I have not measured reference standards of hafnia. I know my samples have monoclinic and orthorhombic phases. If anyone on this mailing list have these standards and don't mind sharing, please email me. Alternatively if there are ways to generate/simulate it (perhaps using FEFF and the corresponding .cif files), please let me know. Thank you, Vineetha

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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 20 Feb '19

20 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 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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