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

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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Mac OS X Mountain Lion iXAFS
by Kyler Carroll 19 Sep '12

19 Sep '12

Hello, I havent seen a post yet pertaining to this issue so I thought I would share and perhaps see if there are solutions to my problem. I have recently upgraded my mac to run the new OS X Mountain Lion and in the process noticed that apple no longer supports or includes X11. They instead have moved to XQuartz http://xquartz.macosforge.org. I downloaded the new XQuartz to my computer and obviously still cannot access iXAFS. I was wondering if someone could offer some advice for me so that I can still run iXAFS on my macbook (Macbook pro OS X version 10.8, 2.3 GHz intel core i5). Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Demeter will not start without admin permissions
by Jason Gaudet 17 Sep '12

17 Sep '12

Hi all, I came across another Demeter startup issue that seems different from the mingw and perl conflicts previously discussed, and I'm pretty stumped. System: Demeter 0.9.10 on Windows 7 32bit Issue: All Demeter apps (dathena.bat, dartemis.bat, etc.) will no longer run as a user. Apps will only run when opened as an administrator. Trying to open as a user causes cmd window and splash screen to pop up and instantly disappear. No "compatibility mode" seems to help. The problem seemed to pop up sometime between August 2 and August 8, after upgrading to 0.9.10, but I downgraded to 0.9.0 and the problem persisted, so (likely) something changed in my Windows environment and not Bruce's software. The log: Can't load 'C:/strawberry/perl/site/lib/ auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Demeter.pm line 36 Compilation failed in require at C:/strawberry/perl/site/lib/Demeter.pm line 36. BEGIN failed--compilation aborted at C:/strawberry/perl/site/lib/Demeter.pm line 36. Compilation failed in require at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 5. BEGIN failed--compilation aborted at C:/strawberry/perl/site/lib/Demeter/UI/Athena.pm line 5. Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 25. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 25. I exchanged a few Emails with Bruce before realizing this is a bit more complex than I thought. We've thus figured out (I think) - Explicitly giving myself full permissions to C:/strawberry/perl/site/lib/auto/Ifeffit/ and %APPDATA%/demeter has no effect. - Although I have a cygwin version of perl, demeter is calling up the right one each time. Invoking perl with the full path in e.g. dathena.bat has no effect. I suspect the problem might not be in perl or any of Bruce's code, but in some behavior of ifeffit that was previously condoned by Windows but now requires elevated permissions. I understand ifeffit is written in fortran90 but I don't know if there's any aspect of it that might be affected by recent MS Visual C++ updates I've done on my laptop. (MS Visual C++ 2008 x86 9.0.30729.17 and MS Visual C++ 2010 x86 10.0.30319). I'm pretty sure MSVC2008 coincides with the time Demeter stopped working but it could just be a coincidence. There are also of course various security updates I can't easily sort through. I was hoping Matt might be able to point me in the right direction here; I don't know the inner workings of IFEFFIT and I might be far off track already. Thanks, Jason

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Launching Problem (D)Athena and Co.
by Alfred Hummer 30 Aug '12

30 Aug '12

Ok, I found the problem. There was a version of MinGW installed on the computer. I just placed the MinGW PATH variables after the strawberry ones, and it worked. So it was a special conflict between software packages on my PC. best, Alfred

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Troubles opening saved Artemis (Demeter package) project files.
by Raimundo Lora Serrano 29 Aug '12

29 Aug '12

Hi all, I'm new in the list and I didn't find any problem like this one in the Mail Archive. I have installed Demeter on Windows 7 (Ultimate version, SP1). Upon creating and saving a (new) Artemis project file I tried to open it both by double-clicking or by first launching Artemis and importing it from the "Open project data" option but the Artemis windows stick around a few seconds, and then disappear, along with the black DOS window. No notice of a crash appears; the program just fails to launch. This not only happens with this file but other files cannot be opened also after being saved. Any(s) suggestion(s)? Many thanks in advance. Raimundo

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Washington (Atoms)
by washington gomes 25 Aug '12

25 Aug '12

Dear Colleague, Iwould like you to help me with attached file átomos.inp I am sending to you. Typed parameters atomic position of La0.7Sr0.3CoO3 atoms on the web.Atomsin the program for generating lists of atomic coordinates from crystallographic data and appearedthe following message after running atoms. These sites: "La1" "Sr1" generate one or more common positions and their occupancies sum to more than 1. Yours sincerely: Washington C. M. Gomes

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PCA in D-Athena
by BradleyW Miller 22 Aug '12

22 Aug '12

Hello, I'm new to PCA analyses with my XANES data and started with the D-Athena. Are the TT Coefficients similar to a SPOIL value (SPOIL values are calculated as the quotient of real error in the target divided by the error in the data matrix)? I've seen that one researcher relied on SPOIL values <1 for populating his LCF models. The TT values of some of my standards I know to be unreasonable (e.g. reduced standard used for TT of an oxidized sample) gave me negative values. Should I only accept values >0. Thanks for your time. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW(a)epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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Launching Problem (D)Athena and Co.
by Alfred Hummer 22 Aug '12

22 Aug '12

Hello, I have some problems launching Demter programs on WIN7. The log file says: Can't load 'C:/strawberry/perl/site/lib/auto/Wx/Wx.dll' for module Wx: load_file:Die angegebene Prozedur wurde nicht gefunden at C:/strawberry/perl/lib/DynaLoader.pm line 200. at C:/strawberry/perl/site/lib/Wx/Perl/SplashFast.pm line 60 Compilation failed in require at C:\strawberry\perl\site\bin\dathena.bat line 21. BEGIN failed--compilation aborted at C:\strawberry\perl\site\bin\dathena.bat line 21. First of all Demeter was not able to start at all (no demeter.ini file). The reason was another Perl installation. I had ActivePerl installed on my computer. I removed the PATH variables and uninstalled it from the PC. After that I reinstalled Demeter. Now the demeter.ini is created but the above error occured. Anyone a clue? best wishes Alfred

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XANES-2012 short course at Brookhaven
by Anatoly I Frenkel 20 Aug '12

20 Aug '12

Dear IFEFFIT subscribers: Please find below the information about the short course on X-ray absorption spectroscopy that will be organized at Brookhaven National Laboratory on Nov. 8-10, 2012 Either follow the link in the bottom of the NSLS web page: http://www.nsls.bnl.gov or go directly to the course web site: http://workshops.ps.bnl.gov/default.aspx?w=XANES2012 The short course in X-ray absorption near edge structure (XANES) spectroscopy will be offered on November 8-10 at the NSLS. To qualify for admission, participants should have prior background in XAS theory and/or experiment and data analysis. The course will consist of lectures, in-class demonstrations and hands-on data analysis sessions. The lectures cover the XANES fundamentals, surveys recent developments in theory and data analysis, the commonly used computer codes (FEFF and others), data modeling techniques, and specific applications of XANES to research problems. The course enrollment is limited to 30 participants. Application deadline: September 30, 2012. Best regards, Anatoly Frenkel Yeshiva University

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Re: [Ifeffit] Ifeffit Digest, Vol 114, Issue 15
by Marc Porosoff 15 Aug '12

15 Aug '12

message deleted at request of sender

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