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

Correction for self absorption in fluorescence mode XAFS data
by sumitk＠barc.gov.in 08 Jan '13

08 Jan '13

Hi, I am analyzing a Eu-L3 edge XAFS data measured in fluorescence mode. My question is regarding the appropriateness of the self absorption correction of the data. I am aware that by supplying chemical formula along with other requisite informations (angle, etc.) I can execute the self absorption correction in Athena. Also, by comparing data measured in transmission and fluorescence modes the correction can be achieved. I have only six scans of fluorescence mode measurement and by applying the correction to these scans in Athena, I have observed enhanced amplitude in mu(E) data. I am not able to see how to check the appropriate of correction. An Athena file is attached to look into. Expecting the community to help, Sumit Sumit Kumar Scientific Officer Radioanalytical Chemistry Division Bhabha Atomic Research centre, Mumbai India. Ph: +91-22-2559 4093. -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O).

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Deglitching in Athena 0.9.14
by Lyle Gordon 07 Jan '13

07 Jan '13

Dear Bruce and Ifeffit users, I just installed the latest version of Demeter, 0.9.14, on my Windows 7 computer. I tried to deglitch a dataset in x(E). Upon clicking "choose a point" the window pops up telling me to double click in the gnuplot window. I can select a point but there doesn't appear to be any feedback in the UI about which point was selected until after clicking ok. Then after ok I get a large "E". It is difficult to tell sometimes exactly which point was selected as the E is quite large. I guess this is turning into more a "bug" report/feature request, but I felt the previous interface in Athena 0.8.054 gave much more feedback during the deglitching process of removing points. I was wondering if there was a setting that could change back to the old style or if this was a decision based on the limitation of gnuplot/perl. I hope this submission is alright for the mailing list. In the future I could post these "issues" on github. Thanks very much, Lyle

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Using this mailing list effectively
by Zhaomo Tian 07 Jan '13

07 Jan '13

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Using this mailing list effectively
by Zhaomo Tian 06 Jan '13

06 Jan '13

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Using this mailing list effectively
by Ravel, Bruce 06 Jan '13

06 Jan '13

> I think you are really right, I am in too great a hurry that I lost my patience to set a time to learn basics quietly. Thanks for reminding. > And for my second question, could you give me some suggestion too? Mr. Tian, Asking questions is an art. Anyone can barf out sentences that end with a question mark, but asking questions that will prompt a useful and constructive discussion is a subtle and skillful business. Both Chris and I tried to tell you that in our earlier responses, but apparently there is a need to be more explicit. You are doing some things wrongly. I say this not to be mean and not to diminish you, but because I spend a lot of my professional time teaching people how to do XAS. It is important to me that people practice our craft well. This mailing list is a powerful tool to that end. When it is used well, the people who solicit help from this list profit significantly. When it used poorly, the people who volunteer their time answering questions become frustrated and the person asking the questions goes away with nothing. So ... here are three comments: (1) I am frustrated that you are not using the most recent version of my software. You are using a version of Artemis that is about 4 years old. I have no intention of continuing support for the older versions of my software. (2) Your second question refers to 4 sets of data, which you posted to the mailing list not in an Athena project file, but in an Artemis project file. That's odd. It would be much easier to examine the data in the form of an Athena project file. Many of the issues in your recent line of questioning referred to S02. As Scott pointed out, the evaluation of S02 is related to the determination of the normalization and background. If you want people to help you with your actual question, it would be prudent to provide the data in a form that allows examination of all steps of the data processing. My point here is that you simply must think about how you pose your question -- that includes thinking hard about how to present your data to the person whose help you are soliciting. (3) Your first email on the topic of these Cu films was somewhat misleading in that your initial complaint seemed to be about a strange measure of coordination number on a Cu foil. In that email, you gave a hint as to the actual form of the data, but scant information about how the data were measured and none about how the data were processed and analyzed. After prompts from Scott and other, you have provided a bit more information about your actual measurement, but not enough to actually know what's going on. As long as your line of questioning remains vague as to the details of the problem, the best you can expect are vague answers of the sort that you have already received. Since I am suggesting that you be more thoughtful and explicit in how you communicate here on the list, it is important that I do the same. Here is an example of what I consider to be a well-asked question. My example comes from a posting that I myself made to the WxPerl mailing list last year. WxPerl is the programming tool I use to make the GUIs Athena, Artemis, and Hephaestus. At the time, I was having a problem getting menus to post properly when making right-mouse clicks in various places in Athena. While the question is rather technical and I don't expect a non-programmer to follow all the details, it is still instructive: http://www.nntp.perl.org/group/perl.wxperl.users/2011/03/msg7929.html Note first that in five brief lines of text I summarized my problem. I then gave a complete example of how someone else could reproduce my problem on their own computer. I then explained both what I expected to happen and what actually happened. The point here is that I took the time to condense my question into a form that the people at the other end could understand and address with a minimum of effort. Sure enough, I got useful responses from 2 knowledgeable (and, no doubt, very busy) people. Mr. Tian, to the extent that it seems like I am singling you out for special criticism, I sincerely apologize. But you have been posting to this mailing list rather often of late and you are doing so in a way that is probably not getting you the sort of results you would like to see. I understand that this is an English language mailing list and that it is difficult to be as expressive in another tongue as you can be in your own. (I really do understand that -- I have suffered through learning two other languages in my life. It really is hard.) But you have to try if you want to get useful results. B

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Re: [Ifeffit] Problem downloading windows installer for Demeter
by Ravel, Bruce 06 Jan '13

06 Jan '13

Javier, Thanks for reporting this problem. This is related to a recent change in how GitHub handles large binary files. I thought I had fashioned a solution. Turns out that I was mistaken. I have come up with a different solution for distributing the Installer and Updater files and I've updated the links at http://bruceravel.github.com/demeter/ Please go back and try again. Sorry for the inconvenience. Also, please use the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) for this sort of thing rather than emailing me directly. Cheers, B ________________________________________ From: Javier Alonso [jalonsomasa(a)gmail.com] Sent: Sunday, January 06, 2013 7:59 AM To: Ravel, Bruce Subject: Problem downloading windows installer for Demeter Dear Dr. Ravel, Firts, I'd like to personally thank you for Demeter: it really helps me a lot with my XAS data analysis. And now the problem: I'm trying to download the windows installer for Demeter from the webpage: http://bruceravel.github.com/demeter/ but I keep receiving the same error message again and again: Error: blob is too big I think this is something related to Github and the limit of file sizes, but I haven't been able to find an alternative downloading site or similar. Thanks in advance, Javier Alonso -- Javier Alonso Masa Departamento de Electricidad y Electrónica Facultad de Ciencia y Tecnología. Universidad del País Vasco 48940 Leioa(Spain) http://www.gmmmt.net/ Phone: +34 94 601 5400 / +34 695325749

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(no subject)
by Zhaomo Tian 05 Jan '13

05 Jan '13

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(no subject)
by Zhaomo Tian 04 Jan '13

04 Jan '13

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Cu fitting with and without CO adsorption
by Zhaomo Tian 04 Jan '13

04 Jan '13

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Understanding effect of dopant using ARTEMIS
by Devender 03 Jan '13

03 Jan '13

Hi, Happy new year! I am a graduate student in material science at RPI. I am interested in understanding doping of elements in bismuth telluride (Bi2Te3). By understanding I mean, where it is going (interstitial sites or replacing any element in crystal) and what it is doing (changing band structure, electronic states etc.). For that, we carried experiments at beamline X19A at BNL couple of months ago. On primary analysis using ATHENA, we see some indications of interestitial site occupancy (attached is ChiR vs radial distance plots). To confirm this hypothesis, I am thinking of simulating spectra using ARTEMIS. Plan is- 1) First, match spectra of bismuth telluride with standard 2) Add dopant at interstitial sites and other possible sites, and simulate spectra to see if it matches with experimental spectra. I am seeking help/guidance on following, 1) Getting started with ARTEMIS- I have started learning ARTEMIS but still don't understand a lot of parameters. I will appreciate if someone can send me tutorials on recent version of ARTEMIS, feff tutorials on some websites are for command line version. I don't understand many of the parameters in ARTEMIS and any detailed tutorial will really help. I don't want to tweak parameters without understanding them completely. 2) Input atom file for ARTEMIS- I have cif file for Bi2Te3, how can I import that in "ATOMS" for making input file for ARTEMIS? Once I can create Bi2Te3 crystal using ATOMS, I think I can add Cl (dopant) to simulate other spectra easily. I would love to hear any feedback on approach too. Thanks and regards, Devender www.rpi.edu/~devend/

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