December 2012 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 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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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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Larch 0.9.17 available for download and testing
by Matt Newville 08 Jan '13

08 Jan '13

Hi Folks, I'm happy to announce the first full release of Larch, the next generation of Ifeffit. This includes a kit for source installation and a binary installer for Windows. A primitive Larch GUI is included that provides a command-line interface and a browser / help system for data in the Larch session. Essentially all the EXAFS and XANES functionality of Ifeffit 1,2 is reproduced in Larch, with several significant improvements. The current version (0.9.17) should still be considered "beta" software in that bugs should be expected, but Larch is now ready for detailed "field-testing" and use. It you're using Ifeffit for scripting (that is, not using the GUIs Athena, Artemis, SixPack, or Prestopronto that call Ifeffit), you should start using Larch now. Several months ago, I described the goals and status of Larch (see http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-June/010586.html) which is still accurate. Since then, the biggest effort has been in documentation, finishing some of the details of Feffit() fitting, and testing. Larch is available at http://xraypy.github.com/xraylarch/ and http://cars.uchicago.edu/xraylarch/ Any feedback on any part of Larch is welcome. I am especially interested in hearing reports from people trying the Windows installer -- I've tested it only on 3 Windows7 machines. I also reiterate my plea for people to get involved in the development and extension of these tools. A main motivation for Larch's implementation and design was to make it very easy to add new features and experiment with new algorithms and methods for analysis. If you're interested in helping Bruce or I develop these codes, please let us know. Some of you may have noticed that support for the Ifeffit 1.2 series has been very poor recently, including the fact that building for Mac OS X has fallen far behind. With this release of Larch, I'm very happy to formally end support for Ifeffit 1.2. I'm willing to use, and help others use, the older versions of Ifeffit, Athena, etc, but there will be no more releases or bug fixes for the Ifeffit 1.2 series. The code is available if someone else wants to maintain it. Thanks, --Matt Newville

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Demeter installation (under Ubuntu)
by Denis Testemale 01 Jan '13

01 Jan '13

Dear Bruce and mailing list members, I'd like to report about the installation of the Demeter package under Ubuntu where everything went smoothly but a few glitches... ## Background: Ubuntu 12.10 Quantal, 3.5.0-19-generic with everything up to date as of today (December 18th). Demeter 0.9.14 (pulled from git today). I have Horae package installed and running (from Carlo's repos). I followed specific Ubuntu instructions at https://gist.github.com/3959252 (Dave Hughes' installation guide) ##First, one comment. You need to have the package gnuplot-x11 installed. For some reason, it was not installed in my case (although gnuplot was). This lead to many error messages during the './Build test' loop, and obviously the impossibility to plot anything when running (D)athena/artemis/hephaestus. At that time I did not think to try the change of the plotwith variable (gnuplot -> pgplot) as discussed in a previous ifeffit thread. I since reinstalled Ubuntu and this time installed gnuplot-x11 before Demeter. ##Then, a possible bug. It is reproducible everytime: - I launch Dathena from the command line without specifying the name of the project I want to open - I try to open a project (an old style Athena project) from the GUI (for example located at /home/denis/pathtothefolder/athena.prj) - I get an error message (a pop-up window, the terminal is quiet) saying '/home/denis/athena.prj is not readable', i.e. it looks for my file in my home folder and doesn't take into consideration the path to the file I input in the 'import data' dialog. - if I copy athena.prj from /home/denis/pathtothefolder/ to /home/denis/ then it works. - a workaround is: 'dathena /home/denis/pathtothefolder/athena.prj' In the case of Dartemis, it is a bit different: - if I try to open an old-style Artemis project through the dedicated old style import module (say, /home/denis/pathtothefolder/artemis.apj), there is a message at the bottom of the main Dartemis window saying: '/home/denis/artemis.apj is not an old style fitting project file'. Again it misses the complete path to the file. - if I try to open an old-style Artemis project through the 'open project of data' module, Dartemis crashes saying (in the terminal): Can't open($fh, '/home/denis/artemis.apj'): Aucun fichier ou dossier de ce type at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Files.pm line 89 Actually, the crash may not be a bug as I am trying to open an old Artemis project through the bad channel obviously, but notice that the path to the file it refers to is again wrong. ## I must add that my first installation of Demeter (before I reinstalled Ubuntu) was global (not following the non root specific commands of Dave Hughes' installation guide) and I already had this problem. Let me know if you want me to try different things to track the problem down. Many thanks. Cheers Denis -- Denis Testemale Institut Néel FAME beamline at ESRF +33 476 881 045

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The degeneracy and the coordination number
by Zhaomo Tian 26 Dec '12

26 Dec '12

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Re: [Ifeffit] Novice FEFF user question
by Joshua Kas 21 Dec '12

21 Dec '12

Hi Melissa, You will need to set the FMS radius, which is blank at this point as seen in your screenshot. You should also set the SCF radius which is also blank. I would start with FMS 7.0 and SCF 5.0 and you can make them larger to check convergence. Another thing that is a bit strange in your calculation are the options after the XANES card. I would start by leaving these blank, so that the default energy grid is used. Josh Kas Message: 2 > Date: Fri, 21 Dec 2012 16:56:05 -0500 > From: Melissa Menard <mmenard81(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Novice FEFF user question > Message-ID: > <CA+Rj7Q9UmQ0O0FH210GSoAp+FfRSjtvWK9BjmFshrmkq= > 7foBw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I am new to FEFF and I have a small problem. I'm trying to produce a XANES > spectra of Cu (from the examples). I cannot seem to obtain the pre-edge > region in my result. I have attached a screen shot. Could you tell me how > to calculate the area before E0, i.e. from -50 to 50 eV. > > Thanks > Sincerely > > -- > M Menard, Ph.D. >

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Novice FEFF user question
by Melissa Menard 21 Dec '12

21 Dec '12

I am new to FEFF and I have a small problem. I'm trying to produce a XANES spectra of Cu (from the examples). I cannot seem to obtain the pre-edge region in my result. I have attached a screen shot. Could you tell me how to calculate the area before E0, i.e. from -50 to 50 eV. Thanks Sincerely -- M Menard, Ph.D.

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Per-data set R-factor
by Lyle Gordon 21 Dec '12

21 Dec '12

Dear iffefit users, I am using the latest version of Demeter/Artemis to fit some EXAFS data. I'm running Win 7 64. I found in Horae that when I fit multiple datasets it would output the R-factor for each dataset in the fit. I would really like these values in the newest version. I found on the todo list (https://github.com/bruceravel/demeter/blob/master/todo.org) [ ] per-data set R-factor reporting in log file is turned off. Is there a simple way to turn this "on"? If not I guess I can calculate it by hand from the Re/Im terms of the R space data and fit. To that end, if I have a few datasets it is tedious to export the data/fit files for each sample. Is there an automated way to export this data? 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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How to refine the float
by Zhaomo Tian 20 Dec '12

20 Dec '12

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How to refine the float
by Zhaomo Tian 20 Dec '12

20 Dec '12

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