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

Need an advice
by Steven S. Lim 06 May '05

06 May '05

Dear all, I have a question to ask all of you as follows. We have been investigating the EXAFS of some partially reduced Co materials (by Co EXFAS) and would wish to obtain some qualitative information on the Co metal particles. If, in fact, the Co had some average coordination environment because we have a distribution of Co particle sizes with oxygen adsorption, analyzing the windowed Co-O and Co-Co peaks together as a linear combination and assessing the average oxygen and Co coordination from the Co edge absorption (what we do with Athena) would appear to give a useful answer. However, if what we have is closer to a physical mixture of small Co metal particles and Co oxide particles, it would seem that it would be more appropriate to analyze separately the windowed Co-O and Co-Co peaks in R-space, to somehow normalize the Co-Co to the fraction of metal in the sample and use this as a qualitative measure of metal particle size. Is there a way to do this with Athena or other method? Or do you know of a reference where this has been discussed? Of course, we can (and will) make experimental mixtures as references but wonder if there is a different way of doing the analysis or if there is some literature on this problem (which we have not been able to locate). Thank you. Steven

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new updates for windows
by Matt Newville 05 May '05

05 May '05

Hi Folks, As Gerrit S mentioned earlier, there is now a new updater for Windows that will install the latest versions of Athena, Artemis, Diana, and Hephaestus. In addition, there is an upgrade of the Ifeffit library to 1.2.7... a source release will be available soon -- if you're interested, it's already under http://cars.uchicago.edu/ifeffit/src/ but I haven't updated all the web pages or sourceforge yet. I think Bruce has discussed most of the new features in his programs. One thing that we should warn you about is that these versions of Bruce's programs use a new method to make Windows executables. Really, this is better for many reasons, but it currently means a noticeable lag in startup time, even before a splash screen pops up. We're looking into this, but please be patient! Thanks, --Matt

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How is the path data exported?
by Gerrit Schmithals 03 May '05

03 May '05

Hello, I just started to use Artemis again and at the moment I am a bit confused about the results. In one Artemis experiment I just select two FEFF-paths and choose a "sum of paths" which produces the result shown in the appended picture (SumOfPaths2). Shouldn't the fit be more or less look like the sum of the two paths? I also exported both paths as chi(k)-data and manually added them which produced the same result as the chi(k) of the fit. But when I use more paths I get a different result: the manually summed chi has a greater amplitude (see chi.png). Could that be related to the fact that the fit parameters are applied to the sum of path but not to the exported paths? Cheers Gerrit

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Reporting math expressions in scientific papers
by MauRo 02 May '05

02 May '05

Hi folks, I would like to ask you if it exist one common convention, apart the XAFS society one, to report IFEFFIT results when you have unusual math expressions. In particular, I have used a two-phase model (two FEFF calculations) to fit my sample and for the amplitude variable I have these math expressions: amp_feff1 = amp * x amp_feff2 = amp * y = amp * (1-x) In this way I can estimate the global amplitude variable and introduce a "percentage" of the two chemical compounds (correlation is kept under control). How to explain what I have done to a non-ifeffiter? Mauro --- Mauro Rovezzi <laluvedda(a)gmail.com> Physics student @ GILDA BM08 c/o ESRF (Grenoble, France)

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???
by Elena Ion 02 May '05

02 May '05

Hello, Questions from a beginner in EXAFS...using Athena and Arthemis >From where to get the error bars for number of neighbours, distance and sigsqr (ss)? What are Chi-square,Reduced Chi-square and R-factor and how should be their values in a fit? Sometimes it happen that "R-factor for this data set" does not have the same value as the first R-factor from results. Why? many thanks, Elena

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Fwd: help about Arthemis
by Bruce Ravel 30 Apr '05

30 Apr '05

Mahendra, I am forwarding your question and my answer to the Ifeffit mailing list. I recommend that you make use of that resource for your EXAFS and analysis software questions. Once you make the sum of paths, you should find that, in the File menu, the menu item for "Save fit as" is enabled. I acknowledge that is somewhat confusing -- you made a summation, not a fit. But as far as Artemis is concerned, summations and fits are very similar. In any case, you can use that item in the File menu to save your summation in k, R, or q space. There is a small bug in there. If you have not imported data yet, you can still save the summation in the manner I described, but the information written to the header will be incorrect. That will not preclude using the file, however. Hope that helps, B ---------- Forwarded Message ---------- Subject: help about Arthemis Date: Friday 29 April 2005 15:19 From: koppolu uma mahendra kumar <mahixs(a)gmail.com> To: ravel(a)phys.washington.edu Dear Dr.Bruce Ravel, i am a new user of Arthemis. i calculated an exafs signal using phase and amplitudes calculated from Feff. i used the option "sum of paths(no fit)" in Arthemis. i am not able to save this as an ascii file. Please help me to go ahead. thanking you mahendra kumar ------------------------------------------------------- -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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horae-051 debian packages
by Carlo Segre 28 Apr '05

28 Apr '05

I have built and uploaded the 051 version for Debian. I will convert to rpms as soon as I have time. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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new tarbell, again
by Bruce Ravel 28 Apr '05

28 Apr '05

The 051 release is up on my website and on SourceForge. Carlo, Paul, Stefano, and Matt helped iron out all the problems in Athena and horae_update. Thanks guys! B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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new release of Athena, Artemis, and Hephaestus
by Bruce Ravel 27 Apr '05

27 Apr '05

Hi folks! After a rather long hiatus, I have finally released a new source code tarball for my codes. You can grab it from SourceForge or from my web site. The linux, unix, and Max OSX users can run the horae_update script at any time. If history is any guide, Carlo will have new debian packages on SourceForge lickedysplit ;-) I plan to build new Windows executables on Monday morning. Hopefully there will be a Windows updater package soon after that. The list of new features, improvements, and bug fixes is quite long. Here is a summary of the most important new developments: Athena: ** You can now rebin your data using Ifeffit's rebin() function. Rebinning can be done on the fly in the column selection dialog as the data is imported or you can use the rebinning dialog which is found under the Data menu to rebin data already imported into Athena. ** After editing a parameter in one of the little text entry boxes, you can hit "enter" or "return" and the data will be replotted. This is a keyboard shortcut for the red plot buttons. ** There are several cosmetic changes on the main page intended to convey more information about the state of a data group. The large blue text in each section on the main page changes its shade of blue depending on whether the group is "up to date" with respect to that group of parameters. This will make sense when you see it! Artemis: ** This is almost certainly the last release for which there will be distinct stable and development versions of Artemis. Very soon I will be retiring the 0.7 branch of Artemis and renumbering the development branch as Artemis 0.8. For now the "artemis" program still refers to Artemis 0.7 and the "diana" program still refers to the development version. Soon, there will be no "diana" and "artemis" will refer to version 0.8. Here is a short PDF document with lots of pictures describing the major changes between 0.7 and 0.8: http://leonardo.phys.washington.edu/~ravel/misc/artemis0.8.pdf Hephaestus: ** I added a fluorescence line finder which works almost exactly like the current edge finder. I hope everyone enjoys the latest versions. I encourage everyone to try out the development version of Artemis. Have fun! Bruce -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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this time for sure!
by Bruce Ravel 25 Apr '05

25 Apr '05

Hi! I just uploaded release 050 of the source code tarball for Athena, Artemis, and Hephaestus to SourceForge and my web site. This version fixes some problems related to perl/Tk 804 that surfaced after the previous release two days ago. I think that this version should work well. I'm keeping my fingers crossed! Unfortunately, the horae_updater script that you linux and Mac users have on your computers will not work due to some changes at SourceForge. Grrrr! You can grab an updated version of the updater here: http://leonardo.phys.washington.edu/~ravel/software/packages/horae_update That version should work around the new changes at SF. I built and tested the codes on Windows today. I am using a new system for building Windows executables. Athena and Artemis worked fine, but there was a problem with Hephaestus. Hopefully I'll get that problem solved and a new Windows updater will become available soon. I'm really excited about this release -- Athena has seen lots of improvements and the development version of Artemis is almost ready for widespread use -- so I am eager to get over these hurdles. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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