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

Re: [Ifeffit] window 10
by manju rao 13 Jul '18

13 Jul '18

Hi Dien I guess this is the problem with new version too. ARTEMIS could run once for any calculation with no time limit, but if I open new data file, it got crashed. So I do one fitting at a time and then restart it for new fitting. Regards Manju Sent from my iPhone

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window 10
by Dien.Li＠srnl.doe.gov 11 Jul '18

11 Jul '18

Hi, Bruce and Matt We just transitioned to Window 10 yesterday. I just found that as I ran Artemis for EXAFS data fitting, it constantly crashed (stopped running) my computer, I am using Demeter 9:24 I believe, is it possible I need a new version, where is the link for latest version? Thanks. Dien Li Savannah River National Laboratory

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Fe Standards
by Naomi Intrator 10 Jul '18

10 Jul '18

Hi all, I'm doing a project on Fe and was wondering if anyone has spectra of Fe(II) and/or Fe(III) standards they wouldn't mind sharing. I'm specifically looking for XANES of Fe2+ and Fe3+ ions in water. Thanks in advance, Naomi ---

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copper fluoride
by Bruce Ravel 10 Jul '18

10 Jul '18

Hi all, I wonder if anyone has a spectrum of copper fluoride, CuF2, that they are willing to share. This would be a big help for my undergraduate student's summer research project. Thanks! B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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imaginary part
by John Hummel 10 Jul '18

10 Jul '18

I have run a feff calculation in artemis and pulled the information from the output file in an attempt to sum the paths in python. However I am having some difficulty in determining the imaginary part of the waves. I was wondering how the artemis program goes about calculating the imaginary values. Any insight would be greatly appreciated. Thank you, John

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using the mail list archive for mac install
by Joel Brugger SAM 10 Jul '18

10 Jul '18

I ran into the problem that some people seem to have with Demeter on mac while upgrading to High Sierra. I found a fix on this mail list, but 1) I can¹t download Template.pm from the archive (bin file that uncompresses to cpgz file that uncompresses back to a bin file) 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). Sorry for the trivial questions :-) All the best, JOEL [Ifeffit] install for mac error Luke Higgins pmljrh at leeds.ac.uk <mailto:ifeffit%40millenia.cars.aps.anl.gov?Subject=Re:%20Re%3A%20%5BIfeffit %5D%20install%20for%20mac%20error&In-Reply-To=%3CD54C3C92-BBDF-484E-83DA-31D EE99F28A6%40leeds.ac.uk%3E> Tue Apr 3 12:47:31 CDT 2018 * Previous message (by thread): [Ifeffit] install for mac error <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009380.html> * Next message (by thread): [Ifeffit] install for mac error <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/009383.html> * Messages sorted by: [ date ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/date.html#938 2> [ thread ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/thread.html#9 382> [ subject ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/subject.html# 9382> [ author ] <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2018-April/author.html#9 382> Hi All, I see this error too. This is a bit of a bodge job, but if you replace: /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With the attached template.pm from p5.24, it seems to work fine. I¹d just rename the old Template.pm in the same directory, rather than deleting it since another program may end up needing the most recent one. Cheers, Luke From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > on behalf of Chris Patridge <patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Reply-To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Date: Tuesday, 3 April 2018 at 19:22 To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > Subject: Re: [Ifeffit] install for mac error Thank you for the input Matt. I am glad to hear that it is not ³user error². I tried it again and I need to correct my earlier statement because Artemis GUI will stay open after the warning however Athena closes/crashes. I will try on a different system. Thanks again, Chris Sent from my iPhone On Apr 3, 2018, at 11:52 AM, Matt Newville <newville at cars.uchicago.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:newville at cars.uchicago.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> wrote: Hi Chris, On Mon, Apr 2, 2018 at 4:15 PM, Christopher Patridge <patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:patridge at buffalo.edu <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >> wrote: Hello everyone, I tried to install demeter on my mac (running high Sierra) and it appeared everything went well. However when I run either Athena or Artemis I get an error shown below about Demeter::Templates: showing a error and I am not sure how I can correct this error. Any help would be appreciated. Thanks in advanced, I can confirm this. I just did a fresh install of Macports on 10.13.3 (high sierra). The MacPorts install was not super easy, but once it got to the demeter install, that part went fine. I see the same problem with athena from demeter 0.9.25. I think the warnings about "Demeter::Templates::F" and so forth are meant to be warnings only -- I think they may not be related to the crash of athena. For me, hephaestus gives the same sort of warnings, but runs fine. I can install and run Demeter 0.9.26 (including using Larch as a backend) using Macports, though there are definitely some Mac-specific weirdness. Anyway, I do not believe that "install from source" is a feasible approach for demeter on OSX. I do not know enough about Macports to update the existing package. I don't know that using some other system would be an improvement. We keep seeing problems with demeter on OSX. I'm not sure what the right answer is. Anyone have any suggestions? --Matt _______________________________________________ Ifeffit mailing list Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> <mailto:Ifeffit at millenia.cars.aps.anl.gov <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Athena for peak fitting or deconvolution
by Dien.Li＠srnl.doe.gov 09 Jul '18

09 Jul '18

Hi, Bruce I am using the Demeter 9.24 version. I saw in the "main" window the peak fitting and deconvoluting data, but as I clicked, it is not available. Any new update now. Thanks. Dien

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Postdoc position
by Anatoly Frenkel 09 Jul '18

09 Jul '18

Please pass this info along to those who may be interested in this opportunity: There is an opening for a postdoctoral research associate in my group. The postdoc will be stationed in Brookhaven National Laboratory and work as a member of a multi-institution team to develop and apply new methods of operando characterization of catalysts. Expert knowledge of XAFS, strong publication record and strong background in condensed matter physics are required. For inquiries please contact me. Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Larch 0.9.38
by Matt Newville 08 Jul '18

08 Jul '18

Hi Folks, Version 0.9.38 of Larch has been released and binary installers are now available for Windows, MacOS, and Linux. There have been many minor improvements made in the past several months, particularly for the XAS Viewer application. XAS Viewer is now very close to having feature parity with Athena and Sixpack, with a few things still missing and a few things slightly improved. This should be of particular interest for Mac users, where Athena has proven difficult to install and buggy, and support for Sixpack has also become harder. At this point, XAS Viewer can read data from plain ASCII files or from recent Athena Project files, but does not yet support quite as many different file types as Athena and Sixpack -- help on this would be greatly appreciated! It can do basic group manipulation such as merging, and groups and plot one or more XAFS spectra in various stages of the XAFS normalization process and can save data to Athena Project file or save multiple data sets to CSV files. XAS Viewer has simple dialogs for doing common data correction steps including recalibration, rebinning of QXAFS data (as per a recent discussion), glitch removal, correcting over-absorption, smoothing, and spectral deconvolution. For analysis, XAS Viewer has a notebook panel for pre-edge subtraction and normalization, and one for basic EXAFS processing (background removal and Fourier transforms to chi(R)). Its main emphasis is on visualization and analysis of XANES spectra and so it includes panels dedicated to fitting pre-edge peaks, Linear Combination analysis, and Principal Component Analysis. Though definitely a Graphical User Interface, with forms to guide the novice user, XAS Viewer goes out its way to do all data processing through basic Larch commands that can be viewed, copied, and turned into batch processing scripts. Documentation for all of Larch is a continual work in progress, and docs with screenshots for XAS Viewer is at https://xraypy.github.io/xraylarch/guis/xas_viewer.html Feedback or suggestions on this or any other aspects of Larch are most welcome. Larch can be installed with simple installers for Windows, Mac OSX, Linux which can be found from https://xraypy.github.io/xraylarch/installation.html At the moment, these installers all assume 64-bit operating systems and now are built using Anaconda Python version 3.6. If anyone needs to use Larch with 32-bit Windows please let me know. Support for this will probably be dropped by the end of the calendar year, but I do not know if this is necessary at all at this point. For people using Larch from Python, it can also be installed as a "conda package" for Anaconda Python, as with conda install -c GSECARS xraylarch Currently, packages are available for Python 3.6, and packages for Python 2.7 should be available within a couple days. Please let me know if you have any questions or problems, --Matt

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data after rebinning look worse in k-space than before?
by Ilya Sinev 04 Jul '18

04 Jul '18

Hi all, I have a question regarding the chi(k) function isolation and rebinning processes. I have some data recorded in quasi channel-cut modus, i.e. with the mono constantly moving and the data points collected with the highest possible rate. With 180 sec measurement in yields to a spectrum of ca. 8600 point, which obviously needs to be rebinned. The rebinned data, however, does not look good in k-space even if multiple data are merged. Moreover, I have an impression that the raw spectrum in k-space does not have those 8000+ points anymore but significantly less. Is there any reduction of the data points number that is not seen (e.g. as a preparation step for FT)? Since the unbinned data has higher quality, does it then make more sense to keep using it for EXAFS analysis? Thank you Ilya Sinev -- Herr Dr. Ilya Sinev Institute for Experimental Physics IV Faculty of Physics and Astronomy Ruhr-Universität Bochum Universitätsstrasse 150 44801 Bochum, Germany Office: NB 4/134 Phone: +49 234 32 23647 Fax: +49 234 32 14173 e-mail: <mailto:Ilya.Sinev@rub.de> Ilya.Sinev(a)rub.de www.ep4.rub.de

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