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

Re: [Ifeffit] Very large exafs amplitude in collected data - cause unknown
by Bruce Ravel 05 Jun '13

05 Jun '13

On Wednesday, June 05, 2013 02:55:25 PM you wrote: > Hi, > > Sorry about that, I wasn't sure what the best format would be for these > forums. I have converted the data to a different format that should > hopefully be more friendly. > > This has data in the following columns; > > 1 = real time clock > 2 = Mono angle (requested) > 3 = Energy (eV) > 4 = I0 > 5 = I1 > 6 = I2 > 7-9 = blank > 10-44 - fluor channels (SCA) > 45-79 - ICRs for the det elements > > The weights are arbitrarily unity, and the dark currents were not recorded > (assumed zero). > > I have also attached an averaged file generated using average 2.0 if thats > more useful for people. Jason, You replaced one large, unweildy file format with another large, unwieldy file format. You should consider yourself fortunate that I have taken the time to bother with you. The folks on this mailing list, myself included, are volunteers. None of us get anything for offering time to answer these questions other than a sense of community spirit and community service. It is completely unreasonable that you have asked your question in a way that required lots of work simply to understand the question. Had you been a little more thoughtful and a little less unreasonably demanding of the time of volunteer help, you could have converted your data files into simple, 2-column files -- energy and mu(E) -- that would have been trivially easy for your volunteer to examine. Instead, you first sent the data in one basically inscrutable format, then in a second similarly unwieldy format. Awesome. Such a good use of my time. Please read this: http://bruceravel.github.io/demeter/pods/help.pod.html When you are done, please follow the link to the article by Raymond and Moen and read that. Now that I've had my rant, I'll address your question. Attached is your Au nanoparticle data overplotted with a spectrum measured on a gold foil. Clearly your data is awful and probably unsalvageable. Without knowing all the details of your measurement, it is very difficult to know what went wrong. Given that the oscillations in your data are commensurate with those in the gold foil, it is unlikely to be a monochromator problem or a problem with pressure variations in the I0 ionization chamber. I also don't think you had an egregious problem with sample preparation. Problems that fall under the rubric of sample inhomogeneity tend to damp the oscillations rather than enhance them. Also sample inhomogeneity tends to fail to normalize mono glitches away. You data, while problematic, don't seem to have that problem. My guess is that you have a problem of detector linearity, but not saturation of the Ge detector. Saturation (aka pile-up, dead-time) also serves to damp the oscillations. Perhaps there is some sort of coupling in the signal chain between the Ge detector and I0? I'm knd of running out of ideas here.... The bottom line is that this is the sort of problem that needs to be recognized and addressed while still at the synchrotron. I don't see what you can do to correct this after the fact in a way that would leave your data defensible for publication. The slim silver lining is that this teaches an important lesson about evaluating data quality as it is being measured. 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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Very large exafs amplitude in collected data - cause unknown
by Jason F. Alvino 04 Jun '13

04 Jun '13

Hi, We have collected fluorescence data of PPh3 protected Au nanoparticles supported on an anatase surface at the Au L3 edge, which provides some decent looking exafs and seems to fit a bulk gold model rather well (there seems to be agglomeration on the surface, even with our low loadings). We have tried to fit the data using both XFIT and EXAFSPAK, but the strange thing is that the exafs oscillations have a huge amplitude, up to 80 in some cases. Because of this, the only way to fit the data while maintaining sensible Debye-Waller factors is to allow SO2 to become quite large, or to allow the coordination numbers to become very large. We have spoken to a few others in the field and they have yet to be able to rationalize why there is such a large signal. I have attached an example of one of the data sets with very large amplitude, if anyone would be willing to take a look at the data it would be much appreciated. Cheers, Jason -- Jason F. Alvino PhD Candidate (Chemistry) School of Chemistry and Physics University of Adelaide, AUSTRALIA 5005 Ph : +61 8 8313 3707 E-mail: jason.alvino(a)adelaide.edu.au

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Possible bug - dathena does not work on XP mode
by ASAKURA, Hiroyuki 01 Jun '13

01 Jun '13

Dear list, I am trying to use dathena, dartemis and dhephaestus in Demeter 0.9.17 package on Windows XP ("XP mode" on Windows 7), but neither Athena nor Artemis nor Hephaestus works. On Windows 7 (both 32 bit and 64 bit), everything works. The symptoms are similar to the latest post's, the command prompt and the splash screen appears momentarily, disappears, and then nothing happens. In contrast, (stand-alone) Atoms opens. Reinstallation of Demeter does not solve this booting problem. I checked MinGW and demeter.mru problems reported on this ML, but there are no other MinGW installation or corrupted detemer.mru. OS: Windows XP on Virtual PC ("XP mode" on Windows 7 32 bit) (Japanese version) (All updates are applied.) Demeter: 0.9.17 (on standard path C:\strawberry...) (ver. 0.9.13.1 also does not work.) In addition, I've heard that this phenomenon happens at least on Windows XP in many other real machines. (not on virtual machines) Any suggestions would be appreciated. Best regards, ASAKURA, Hiroyuki -- ASAKURA, Hiroyuki Designated Research Associate Synchrotron Radiation Research Center, Nagoya University, Japan h.asakura(a)nusr.nagoya-u.ac.jp

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