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

spline fitting
by Matthias Filez 29 Aug '14

29 Aug '14

Dear mailing list users, I am trying to fit the spline background function in a proper way to a spectrum (Ga K edge, see attached). However, it doesn't seem to work out, but I don't see why. I already tried the following: * Vary the Rbkg value * Change spline k-weight * Change k-range of spline fitting * Alter the strength of spline clamps ... and the combination of these effects. Since there is a strong white line, I suspect this causes the spline misfit. The data quality is OK. If you have any idea, please post it. Thanks in advance, Matthias _____________________ Matthias Filez Laboratory for Chemical Technology Department of Chemical Engineering Ghent University Technologiepark 914, B-9052 Zwijnaarde, Belgium +32 (0)9 33 11721 www.lct.ugent.be<http://www.lct.ugent.be/> Disclaimer: http://helpdesk.UGent.be/e-maildisclaimer.php<http://helpdesk.ugent.be/e-maildisclaimer.php>

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Demeter OS X plot button colors in Athena
by Schima, Frank 27 Aug '14

27 Aug '14

Hi Bruce, We are seeing an issue in Athena where the plot buttons are not colored correctly. According to section 2.1 of the Athena Users’s Guide, the top row of plot buttons highlighted in the image should be the same color (purple) as the plotting option widgets below them. The 2nd row of plot buttons should be yellowish. However on OS X, all plot buttons appear uncolored. By far the best way to illustrate this is with a screenshot of the Athena UI. I hope the attached image is clear enough to show the issue. I am running Demeter version 0.9.20pre10 via Macports demeter-devel on OS X 10.9.4. BTW, I am happy to work with you on other OS X issues but I am not actually a demeter user and I don’t have much data myself. But if you send me some data, I can follow steps to try to reproduce issues. [cid:F140B9BC-1ABC-4ACE-B222-A833F804F78B] Cheers! Frank

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XAFS short course at Brookhaven
by Anatoly I Frenkel 26 Aug '14

26 Aug '14

Dear subscribers: An annual short course on Methods and Applications of XAFS Spectroscopy will be run at Brookhaven National Laboratory in Nov. 13-15, 2014. The application deadline is Sep. 1. The application form is available at the course web site: http://workshops.ps.bnl.gov/?w=XAFS2014 The application form should filled out first; the 45 participants accepted to the course will be later contacted with registration information. Best regards, Anatoly Anatoly Frenkel, Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

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math functions on GDS page
by huyanyun＠physics.utoronto.ca 21 Aug '14

21 Aug '14

Hi there, When I input math expression in the GDS page, I wonder if Artemis recognizes some general math functions, such as 'sqrt', 'cos', 'sin'. Could anyone help me find a list of all math functions covered in Artemis? Best, Yanyun

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Re: [Ifeffit] Questions for Artemis fit
by 이국승 20 Aug '14

20 Aug '14

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Re: [Ifeffit] Artemis and FEFF interaction in fit process
by Nate Turner 19 Aug '14

19 Aug '14

In an instance of Artemis, the Feff executable is run as needed to make the feffNNNN.dat files. That is, the first time you make a plot or a fit (there are a few other actions that will also trigger this), Artemis will run the Feff executable to make the path that is needed. Thus each path plotted or used in a fit requires a system call. I see, so to be clear if I run FEFF9 and make the feffNNNN.dat paths through it, outside of Artemis, then import the feffNNNN.dat files into Artemis, FEFF6L is still called to when I want to plot or use a path in a fit? Thanks for the quick response. Nate Turner

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Artemis and FEFF interaction in fit process
by Nate Turner 19 Aug '14

19 Aug '14

Hello All, I have a question about Artemis' interaction with FEFF. I know you can either run FEFF6L in Artemis to populate a paths list or externally create the FEFFnnnn.dat files in FEFF and import them into Artemis. We currently do the later using FEFF9, the use of the SCF card gives a better Eo initial guess and our compound has fractional occupancy/disorder that requires us to do some altering of the atoms list after its populated in ATOMS, which we find best to do outside of Artemis. My question is once these external FEFF9 paths are brought in does Artemis use FEFF6L in the fit process or is FEFF in Artemis only to populate the paths list? If Artemis doesn't use FEFF in the fit process then there's no issue but while I've read the mailing list and seen that many do not believe there is any improvement in the EXAFS results from FEFF6L to FEFF9, I'd rather be consistent in which version of FEFF we use throughout the analysis. I would have Artemis calling to FEFF9 instead of FEFF6L if in fact Artemis does use FEFF in the fit. The reason I haven't gone ahead with having Artemis call to FEFF9 making this a non issue is I'm not sure how. I know you can direct Artemis to whatever version of FEFF you want under preferences, but then I'm not sure what file I need to direct to specifically for FEFF9. So to summarize, Does Artemis use FEFF in the fitting process or is its only function in Artemis to create the paths for the fit? If it does use FEFF in the fitting, how do you/is it possible to have Artemis call to FEFF9 instead of FEFF6L? Thanks all for your time, Nate Turner

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importing larch functionality
by Bruce Ravel 18 Aug '14

18 Aug '14

This: use_plugin_path('xafs') from feffdat import feffpath works as expected. It adds the path to larch's xafs plugins into the search path and imports "feffdat" such that it can be used in the namespace of the plugin I am working on. This fails use_plugin_path('wx') from plotter import newplot, plot with this error message: file <stdin>, line 0 ImportError: cannot import name newplot add_plugin('f85ut') What am I not understanding? newplot (and plot) seem to be exported by wx/plotter.py the same way that feffpath is exported by xafs/feffdat.py. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Meaning of linear combination fit reports
by Jens Kruse 18 Aug '14

18 Aug '14

Hi everyone, I doing LCF on my XANES data. I wonder if someone can tell me the meaning of the values in parentheses following the weight value in the Fit results window?. I looked into the respective document section of the Manuel but could not find the answer, yet. I am asking because I did a Fitting with over 20 standards (STD) to find all combination of max 4 standards which describe my unknown sample spectra. This results in a lot of combination with similar chi-square(reduced) and R-values. I know a relative changes between these values are more probably meaningful than absolute values. A lot of the possible combinations provided by after the fit yieled combinations with at lest on STD having a weight of 0.000. (Fit 1). I thought that this would mean, that 3 standards are sufficient to describe the system. However, repeating the fit with only the three standards with weight > 0.0 yielded a complete different proportions (Fit 2). How can this be explain and how should I deal with combinations or standards having a weight of 0.000? Thanks a lot for your thoughts and suggesting, Cheers Paul *Results **Fit 1:* 3: STD3 0.324(0.025) 7: STD7 0.686(0.021) 20: STD2O 0.127(0.016) 27: STD27 0.000(0.036) vs. *Results Fit 2:* 3: STD3 0.473(0.019) 7: STD7 0.620(0.023) 20: STD20 0.000(0.030)

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Questions for Artemis fit
by 이국승 18 Aug '14

18 Aug '14

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