October 2014 - Ifeffit - millenia.cars.aps.anl.gov

Athena does not React after 2-4 steps
by Michael Kömm 22 Oct '14

22 Oct '14

Dear Bruce and dear mailing list, Athena stops working after doing a maximum of four steps (f.e. removing points, import data,...) when running on my PC with Windows 8. It either says "not responding" or just shuts down. Whenever Athena shuts down the errors in the .txt in the directory of the project differs. But it always looks like this: line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_leqfnhqh" line 0: No data in plot only the file name changes. But there's never a file with that name in that directory. Sometimes there is as well a window opened that says: gnuplot.exe is not working anymore. I've deleted the Roaming\demeter folder but it didn't end the troubles. Hope there is a way to end this problem. Sincerely yours Michael Koemm PS: There is also one of my projects in the attachment.

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multiple absorber atoms
by Jesús Eduardo Vega Castillo 21 Oct '14

21 Oct '14

Hello, This is my first message to the list so I expect to do it right. I need to generate a path list for EXAFS fitting within ifeffit, based on a crystalline structure that has two different crystallographic positions for the absorber atom (edge K of Mo). Is there any way to do this? I would appreciate any information you could give me. Thanks in advance Jesus

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Importing data to Athena
by Samson Vallerie Ann 20 Oct '14

20 Oct '14

Hi Bruce, I have some trouble importing data to Athena even if it's just ordinary column text file. I have attached two sample data. These are processed data from full-field XANES images. Basically I select a region in the image then write/output the total intensity of that region in a text file and I just iterate over several images. I have tried deleting out the headers, putting back the headers, padding some 0's in the energy column, checking some plugins, but to no avail. Your tips, advice is badly needed. Many thanks, Vallerie

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"PCA not enabled" on Mac version of Demeter: Athena
by Ellen Daugherty 16 Oct '14

16 Oct '14

Hello XAFS community, I recently upgraded to the new version of Demeter (0.9.20) for Mac and am trying to run principal components analysis on my spectra. When I click on "Principle components analysis" from the main menu, the window shows the following message: "PCA is not enabled on this computer. The most likely reason is that the perl modules PDL and/or PDL::Stats are not available." Perhaps the solution here is simple, but I am not familiar with perl modules and do not understand the source of the issue. I could not find information about this problem in the Mail Archive, though I may have missed something. Do I need to download the PDL perl modules separately from the Demeter installation? Could there be files that are not located in the proper directory? Or perhaps PCA is simply not available for Macs? Please let me know if further information would help in solving this problem. Thank you! Ellen -- Graduate Student Research Assistant Department of Chemistry Colorado State University

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XAFS Analysis using Ifeffit
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Drew, Thanks for your suggestions. I just checked my original data without normalization. The edge step is about 0.7 (see pic attached). I did the measurement in fluorescence mode at APS, beamline 12-BMB. What do you think about this pic? For the sample preparation, I think I need to mix UO2 with some other materials to dilute it. Do you have any suggestions on the matrix materials? Best, Ke

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(no subject)
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Pushkar, I think the peak value of the first derivative and the zero value of the second derivative does the same thing. My sec deriv is very noisy so it's easy for my to pick the peak value of the 1st deriv instead. I would suggest you to watch the video from Bruce which explained HOW TO PICK Rbkg at: http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html Click the Athena: Data processing II Actually all the other video lectures are very helpful, too! Best, Ke

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iXAFS & xQuartz
by Gaspard Jean-Pierre 16 Oct '14

16 Oct '14

Hi all, On a MacBook under OS X.8.5, I downloaded iXAFS and xQuartz. I start xQuartz. When I try to start iXAFS, it requests X11 that is obviously active, I see it. However iXAFS says : "X11 is not installed". I am missing something but I do not know what. Regards JP

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Ke
by Ke Yuan 16 Oct '14

16 Oct '14

Hello Sin Yuen, Thanks for forwarding me that study materials on E0. I use Athena to find the highest peak on the fist derivative of the spectra and pick that value as E0. I think I did not put E0 above this value. I will try to put it on the high energy side to see what will happen. Tks! Ke

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Ke
by Ke Yuan 15 Oct '14

15 Oct '14

Hi Bruce, Thanks for your comments! I studied Shelly's paper and found my data does looks different, especially the first peak at 1.9 A, seems it splits into two in my case. I prepared this sample by pressing UO2 powder into a hole (2mm deep), which might have significant self-absorption effect, because it's not dilute and thin. Do you think this will change the peak amplitude? Best, Ke

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Possible bug in Athena during alignment
by Leon Clarke 15 Oct '14

15 Oct '14

I'd like to report a possible bug within Athena. Last week I collected Br K-edge data at the APS and have experienced an issue with Athena during data alignment. The beamline energy required calibration and so I did the following data processing steps, in this order: 1. Completed pre- and post-edge corrections, using windows relative to the actual Br K-edge energy, on the raw data exported from the beamline. (In other words these windows were not energy offsets relative to the actual measured edge position). 2. Used the flatten post-edge feature within Athena. 3. 'Calibrated' (Normalised is a better term really) the first derivative of a NaBr measurement to the Br K-edge energy using the calibrate drop-down option. This resulted in the requirement for a -17.39 eV energy offset. 4. Tried to align all of the sample data to the NaBr 'standard' using the align drop-down option. The issue I have had is with step #4. When I aligned, for several samples the XAFS (XANES) plots went wrong. It seems that Athena was not transforming the pre- and post-edge windows correctly for such a large energy shift, i.e. didn't shift these to lower energies by 17.39 eV, and I think this is a bug within Athena. I hope the above makes sense; I can provide an Athena project file, if required. Many thanks, Leon ----- Dr Leon J. Clarke Senior Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.clarke(a)mmu.ac.uk<mailto:l.clarke@mmu.ac.uk> WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 "Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer "

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