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

Artemis in Demeter 0.9.17 Crashing Upon Loading Project File
by Anthony Ardizzi 17 Jul '13

17 Jul '13

Dear Bruce and Ifeffit mailing list, I have just started experiencing a program crash in Artemis while trying to load a project I am working on. I am performing a fit on Sr2IrO4 data, and when I try to open the project file, it starts loading all of the usual stuff, and then when it gets to loading the path-lists/data sets screen for one of the two data sets I have, the entire program simply closes. I have attached both my project file, as well as the dartemis log file. I believe the relevant error in the log file is "Illegal division by zero at C:/strawberry/perl/site/lib/Demeter/Data.pm line 922." I am running Windows 7 64-bit. Thanks for any help you can provide, Anthony

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Artemis Autosave Files
by Shoaib Muhammad 16 Jul '13

16 Jul '13

Hi, I am using Demeter 0.9.17, and trying to fit in-situ XAFS data of metal oxides and it is going well other than these minor problems on my Windows 7 PC. A couple of times "Feff" module in Artemis stopped responding and I had to force close the program. Now whenever I click on .fpj files I see a window which asks me to restore from previous autosave files. I click "Cancel" this dialogue box disappears but selected .fpj file is not automatically loaded. Next time when I try to open another .fpj file, I get the same window and behavior again. Is there any way to delete these autosave file? I have searched in mail archieve but there is no querry regarding it for this "Demeter" version. Since I have a bunch of Artemis fits on my PC, to save time I select "File" and then "Close" to close the current fit and then open another Artemis fit instead of "File" and "Exit". In this way when I open another Artemis fit (.fpj) file, I see a couple of "Feff Calculations" in the main Artemis tool bar. How ever I usually don't see these many 'Feff Calculations" if I completely close the Artemis and then reopen the same file. Is there any way to solve this behavior? Screen shots of both the problems are attached. Thanks, -- Shoaib M. Department of Energy Science Sungkyunkwan University South Korea

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Re: [Ifeffit] Ifeffit Digest, Vol 125, Issue 5
by Abhijeet Gaur 14 Jul '13

14 Jul '13

Hi Paul, I think that this research article on Fe K-edge by Westre et al. (1997) will help you in the analysis of your samples. With regards -- Dr. Abhijeet Gaur

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XANES pre-edge peak intensities
by Bingham, Paul A 14 Jul '13

14 Jul '13

Dear Ifeffit forum users I have been working on a batch of Fe K-edge XANES data for dilute glasses some time and I have extracted pre-edge peak positions and intensities, as has been widely used in the literature, to get qualitative analysis of the Fe coordination in my samples. I have also done this for a number of mineral "standards", again as has widely been done in the literature (Grandidierite, Yoderite, Staurolite, etc). However, I have a question: as my samples are considerably more dilute (ca. 0.15 mol% Fe) than all of the mineral standards (these vary in Fe content between a few percent and 10's of percent), how realistic is it to use mineral standards such as these to provide reference points to "calibrate" the integrated pre-peak intensities from the dilute samples? I have found nothing conclusive on this in the literature and would ask this forum for help, or any thoughts you may have on this issue. My own feeling is that concentration will have an effect on integrated pre-edge intensities and I suspect that more dilute samples are likely to give slightly higher integrated intensities than concentrated samples, but it is difficult to unpick and any thoughts or useful references dealing with such issues would be most welcome. Many thanks in advance for taking the time to read this message and thanks for your responses! Kind Regards Paul Bingham

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Basic EXAFS question
by Darren Dale 13 Jul '13

13 Jul '13

Hello All, If I have a Ta(1-x)Ge(x)O(y) thin film, with Germanium concentration of a few percent, is it possible in principle to get useable fluorescence-mode EXAFS spectra around the Ge K edge (11.1 keV)? Or is it likely that the spectra would be complicated by additional Ge fluorescence excited by processes triggered by Tantalum L edge absorption (9.88, 11.13, 11.68 keV)? Thanks, Darren

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User interface question for Demeter
by Scott Calvin 09 Jul '13

09 Jul '13

Hi Bruce, I and my group have finally started using Demeter Artemis, and in general it's wonderful. But there's one aspect of the user interface philosophy that I'm either not getting or finding clunky. In Horae, it was sometimes possible to rearrange the order of lists. For example, the list of groups in Athena could be rearranged by moving groups up and down, while the list of parameters in the GDS screen could be rearranged by using the "move" option. I'm not really finding that functionality in Demeter. The GDS screen does allow copying, but that requires a multiple-step process for a move. And I don't see a way to rearrange the order of groups in Athena at all. In addition, there's a new place where this kind of functionality would be helpful but appears to be lacking: the path list in the Data window. Since that list is now populated by drag-and-drop, it can end up in some pretty oddball orders. Am I just not grokking some UI feature that lets the user rearrange the order of lists? Dragging, for instance, doesn't seem to work. Or are there other features I should be using that make the order of those lists relatively unimportant? Or is ordering lists something that will appear in future versions, but it just hasn't been implemented yet? If the latter, then I also have a further feature suggestion, although it's not high priority. It would be quite useful if the path list in the Data window could be sorted in various ways, perhaps even with primary and secondary criteria. So, for example, sort by feff calculation, and then by importance. Or by number of legs, and then by Reff. While the marks menu lets us quickly select paths in a number of nifty ways, getting them in order of Reff or importance would be quite effective at cleaning up messy lists. --Scott Calvin Sarah Lawrence College

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Unable to import data from HXMA beamline at CLS into Athena
by Anthony Ardizzi 27 Jun '13

27 Jun '13

Hello, I am currently at the HXMA beamline at the CLS facility in Saskatoon, Canada. I have attempted to import some of the data we have taken here into Athena (demeter version 0.9.17), however I continue to receive the following error: "C:\...\xxxxx.dat could not be read as data". I suspect that this might be a problem with the latest demeter release, as an associate of mine seems to have no problem importing these data files into Athena 0.8.056. I have attached a .dat file so that you can verify that the formatting is readable by Athena. Hopefully someone can provide some help. I would prefer not to have to go back to an older version of Athena if possible. Also, I am running Windows 7 64-bit, in case that is relevant Thanks in advance, Anthony

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Disable duplicate data group check
by Jason Gaudet 21 Jun '13

21 Jun '13

Hi all, Not a bug this time, but a feature that occasionally frustrates me. Artemis does a sanity check prior to fitting, and if it detects a project has two instances of the same Athena data group, it will refuse to fit the new data. IME this is not a particularly helpful warning, and a major hassle if I'm trying a couple different treatments of the same data to see how the FEFF fit is affected. (The message is "This data came from the the same source as another data group. You seem to be trying to increase your number of independent points by fitting the same data more than once in a multiple data set fit." But of course I'm not doing this; only one dupe is being fitted at a time.) I don't see any option in the Artemis preferences to disable this warning, which means I have to spend effort deleting and loading data sets, and keeping a "dummy" data set I don't really care about to collect all my paths in. Is the possibility of extremely novice users trying to fit multiple instances of the same data such a serious threat that this function needs to exist? Is there any possibility of disabling this check, or giving an option to disable it in the Preferences? It would save me from the occasional headache ... Thanks, Jason

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bond angle
by washington gomes 21 Jun '13

21 Jun '13

Dear Colleagues, I am structure characterized of La0.8Ba0.2CoO3 by x-ray spectroscopy, used program IFFEFIT 1.2. 10. I wonderif it is possible to determine the bond angle Co-O-CO,used IFFEFIT code in the extended x -ray absorption fine structure EXAFS. If possible, I would like you to indicate the material that shows examples of how to determine the bond angle Co-O-CO. Sincerely yours, Wahington

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Re: [Ifeffit] no so2 term in Artemis
by Bruce Ravel 14 Jun '13

14 Jun '13

On 06/14/2013 02:59 AM, Lei Cheng wrote: > Dear Dr. Bruce Ravel, > > My name is Lei Cheng, I am a graduate student in UC-Berkeley and doing > my research in LBNL. > > I started to learn how to use Demeter for data processing and fitting. I > got this very bizarre problem with Artemis (please see the attached > screen shot). The so2 term is not showing up. (For your information, I > tried with two different computers, Win 7 64-bit, Win 8 64-bit, Demeter > version 0.9.17 and 0.9.13, Demeter is installed in E:\strawberry\ or > C:\strawberry\) > > Thanks for your time and looking forward to your reply > > -Lei Lei, The Ifeffit mailing list exists to handle questions like this one. I am CCing my reply to the mailing list. Please subscribe to and use the mailing list for any follow-up to this issue. Here is information about the list: http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ If I understand your issue, it is a fairly minor one. The label that says "S02" is not being displayed, but otherwise Artemis works as expected. Is that correct? Are you able to perform fits with Artemis? Are you able to access the context menu (normally, one would right click on that label -- see about halfway down this page: http://bruceravel.github.io/demeter/artug/path/mathexp.html)? I have not observed this behavior on any of my windows machines nor on those of any of the folks who visit my beamline. So I am not sure how to proceed. I am suspicious that this is a locale issue, that is, an issue with how fonts and unicode characters are displayed on your machine. Your name suggests that you may be Chinese. Do you have your computers configured to display something other than English? In applications like Word or Explorer, are the menus and buttons labeled in English or some other language? The reason I ask is that it is possible that I have never observed this problem because none of my computers are configured to display an eastern language. 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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