February 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Calibration for Sb K edge
by Darren Dale 28 Feb '13

28 Feb '13

Hello All, I have the CHESS F3 beamline set up with a dispersive monochromator for XANES at the Sb K edge with ~1 eV resolution. I didn't find a reference spectrum for Sb in Hephaestus, and would like to contribute one. But first I would like to have a little more confidence in the energy calibration. Does anyone know if 30.491 keV corresponds to the inflection point of mu for Sb(0) (or if not, what energy does)? Alternatively, does anyone know the energy of the Sb(0) white line (ideally with a reference)? Thanks, Darren

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Demeter 0.9.15
by Bruce Ravel 28 Feb '13

28 Feb '13

Hi! Today I released an update to Demeter and tagged version 0.9.15 it at GitHub. Windows users can download the updater package from http://bruceravel.github.com/demeter/ Source code installation instructions are near the end of that page. Windows users will notice a new download link for a documentation package. Simply download that package and double-click on it to install the Users' Guides for Athena and Artemis on your computer. If installing from source, the documents will be built and installed as part of the installation. There are a lot of swell new features and important bug fixes in this version. Some of the highlights are: * A fix for last week's report of problems with reference channels * Much improved performance by Athena once data is loaded * Direct links to document pages scattered throughout Athena and Artemis. If you have installed the documentation package, the local version will be displayed in a web browser. If the documentation package is absent, the programs will attempt to fetch the relevant document page from my github site. * Plucking points from the plotting window now works much more reliably For the full list, see https://github.com/bruceravel/demeter/blob/master/Changes.org For those following the development of Matt's Larch project, I have begun work on making Demeter use Larch rather than Ifeffit as its data processing backend. This is going well -- thus far, Athena can import data and do basic data processing using only Larch. Interaction with Larch is normally disabled. If anyone is interested in following along with that development more closely, let me know and I will write a wiki page about how to enable Larch support in Demeter. Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Merging data in Athena
by George Sterbinsky 28 Feb '13

28 Feb '13

I am writing to make you aware of what I believe to be a bug in (D)Athena. To demonstrate the problem, I have attached a project file containing two groups. Both groups have the same energy range but were measured with slightly different point spacings. Attempting to merge the two groups results in Athena excluding one of the groups from the merge "for being too short." Thank you, George

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Peakfit tool - determination of width
by Gudrun Lisa Bovenkamp 22 Feb '13

22 Feb '13

Hey Bruce, I was wondering how the width in the peak fitting tool of Athena is connected to the real data. What I mean is: A gaussian peak with a width of 1 (eV ?) seems to have a FWHM of 2 eV. Is it possible that you mean with "the Gaussians (...) are unit normlized (...)" the width is actually "sigma" and the amplitude is actually "mu" in the pure formula? Thanks, Lisa

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Error in second shell fit
by Devender 22 Feb '13

22 Feb '13

Hi, I am trying to fit Bi2Te3 exafs data using artemis. I am able to fit first shell (screenshot of fit is attached, I have also attached 'atoms' and 'feff' files for reference) but when I am trying to include second shell, I am getting the error (attached file- Fit_error.log). Error reads that- "The R effective for this path is well beyond the rmax value of its Data object." but I am already using Rmax of 6 A and Reff of these path are less than 5 A in my fit. I will appreciate if anyone can guide me or point me where I am making mistake. Regards, -- Devender Graduate Student, Materials Science and Engineering Rensselaer Polytechnic Institute, Troy, NY Website <https://sites.google.com/site/devendermaun/>

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Re: [Ifeffit] Importing Multiple Data Sets into Athena
by John Hayes 21 Feb '13

21 Feb '13

Hello, I am having some issues when importing multiple data sets into Athena. When I try to import more than one file at a time only the reference sample data from the first file are imported and the subsequent files do not import the reference data (only a straight line is imported). There is an error that is reported, and I have saved the error log [log.txt] and attached it in the zip file (as well as the dathena.log file and some sample spectra files). The spectra files are of the Mo K-edge and the reference is an Mo foil. These spectra were collected using the HXMA beamline, and as such, I am using the HXMA plug-in to import the data. The relevant columns for the reference are: col 2: energy col 6: I1 col 7: I2 I searched the archive and found what I think is a similar issue (link: www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03454.html) and hope I'm not over-reporting the error (sorry in advance if I am), but the previous report seemed somewhat different, in that there was an issue with the wrong edge being chosen for the test and ref data (best I can tell). I do have the work around of importing each file individually, so this is no more than an inconvenience, but I thought I'd report it and see if maybe someone had some up with a more elegant solution. I am currently using version 9.14 on a 64-bit windows platform. Thanks in advance for any advice or help the community can provide! -- John Hayes The Grosvenor Group Dept. of Chemistry University of Saskatchewan Two fish are in a tank. One turns to the other and says, "You man the guns, I'll drive."

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Fwd: Re: Use of feff8 with D-artemis?
by Bruce Ravel 20 Feb '13

20 Feb '13

On Thursday, July 12, 2012 05:31:19 PM you wrote: > > I wonder why the new Artemis (from Demeter) is limited to feff6 or feff7 as > the old ifeffit can deals with feff8 and feff9. > > Is it a wish? When you published data using feff7, the reviewers first note > that you should have used more actual version. I would challenge a reviewer to come up with a reliable study demonstrating that Feff8 or Feff9 provides a statistically significant improvement to EXAFS analysis. Obviously, I am not saying that full multiple scattering, self-consistency, and the various potential improvements in Feff9 are not relevant to XANES calculations or to Feff's treatment of other spectroscopies. What I am saying is that it has not been rigorously demonstrated that those things have an impact on the calculation of the extended EXAFS such that the analysis is improved in a statistically meaningful way. In short, I find that such arguments from reviewers boil down to "Feff8 is 33% better than Feff6 because 8 is 33% bigger than 6!" > Is it planned that D-Artemis will work with feff8 too? > > I am using the other programs of Demeter but still have to stick to the old > Artemis as none of my files can be read by D-Artemis (always error due to > feff8 or feff9 files by importing old project) That said, there is no good reason that artemis should not be able to use Feff8 or 9 if you want to do so. I suppose that laziness is the best explanation for why it doesn't yet. The Atoms portion of Demeter writes Feff8 files. The Atoms portion of Artemis simply has the line of code for using that part of Demeter commented out. That's trivial to fix. Getting Demeter to use Feff8 instead of Feff6 is not a lot of work, but it is also not a trivial amount of work. I will put this at the top of my to do list. Given that I will soon be leaving for conferences in distant places on the globe, I probably won't be able to release a version of Demeter that uses Feff8 effectively until Spetember. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ----------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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phase correction
by wangshaofeng＠iae.ac.cn 20 Feb '13

20 Feb '13

Hi Bruce, How can I open the phase correction function in fitting using demeter athena and artemis? cheers, Shaofeng

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Building perl wrapper for ifeffit on OS X Lion for Demeter
by Lyle Gordon 18 Feb '13

18 Feb '13

Dear Ifeffit experts, I am working on building Demeter on OS X. In the process I am trying to build ifeffit, including the perl bindings on OS X. However, upon following the instructions I get a range of errors when I try to build the perl bindings. The main ifeffit libraries appear to build just fine. This might be something trivial as I don't have much OS X experience. Following the (slightly out of date) instructions... cd ./wrappers/perl perl Makefile.PL see output: http://pastebin.com/TGzVjrpi sudo make install see output: http://pastebin.com/qkMYhYsP Any help would be greatly appreciated. Thanks very much, Lyle -- Lyle Gordon Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Cook Hall 2036 Evanston, IL 60208 Tel: (847) 491-3584 Mobile: (847) 400-4071 http://lylegordon.ca

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