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

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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Hephaestus crash
by Darren Dale 17 Feb '13

17 Feb '13

Hello all, I'm working on getting my ifeffit/demeter environment together, following the instructions at http://bruceravel.github.com/demeter/pods/installation.pod.html . When I run hephaestus, select F'/F'', and then select any element in the table, the program bails and I get some feedback in the terminal: Can't use string ("Demeter") as a HASH ref while "strict refs" in use at accessor Demeter::devflag (defined at /home/darren/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter.pm line 100) line 8. Sometimes, "<F> line 29." is appended to that error message. I'm running the forthcoming kubuntu 13.04. Any ideas how I can improve my install? Thanks, Darren

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demeter windows download
by Darren Dale 17 Feb '13

17 Feb '13

Hello Bruce, All, I wanted to install Demeter on my windows computer this morning. I followed links to instructions at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater , which in turns links to https://github.com/bruceravel/demeter/downloads . Unfortunately, github recently discontinued the downloads service, so that is not a functioning link anymore. Is there a new location available to find the installer? Thanks, Darren

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problem of paths calculation
by wangshaofeng＠iae.ac.cn 17 Feb '13

17 Feb '13

Hello Bruce, I am using demeter-atoms to calculate paths using a cif file (see attachment). When I run feff to calculate paths, there is a dialog box saying "You have defined ipot #1 but not used it in the atoms list". If I change the core atom from Ni to S, the calculation can be done. So how to solve this problem. Shaofeng

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Athena doesn't start - Larch server not running
by Ivan Stijepovic 16 Feb '13

16 Feb '13

Dear Bruce and other people in the list, I have just installed Demeter from the git on Ubuntu 12.04 using instructions given by Dave Hughes ( https://gist.github.com/waveform80/3959252) Everything went fine during installation but then I tried to start Athena using *dathena* command from the terminal and I got this message: Demeter says: Uh oh! You have requested using Larch, but there is no Larch server running! Then I installed Larch (with some problems during installation, but that is different story) and again tried starting Athena with the same result. When I tried starting Larch in a server mode with *larch -r* command it didn't offer a possibility to start Athena in the same terminal window. Then I opened a new tab in the terminal and just typed *dathena* and the GUI appeared. Now, I have two questions: 1. Do I have to start Larch server every time like this before using Athena or is there some other solution for this? 2. I tried Artemis without Larch server running and didn't get the error message. Is Artemis independent from Larch or are there some problems that might occur later? -- Best wishes, Dr Ivan Stijepović Department of Materials Engineering Faculty of Technology University of Novi Sad Bul. cara Lazara 1 21000 Novi Sad Serbia tel: +381 21 485 3750 fax: +381 21 450 413 e-mail: ivan.stijepovic(a)gmail.com

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