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

Artemis: sum path NAN NAN NAN NAN
by Mauro Rovezzi 06 Oct '06

06 Oct '06

Hi guys, I've found a weird behavior in Artemis: during the fit procedure in the shell normally appears "sum path # # # #" where # = real number, but sometimes the minimization process fall in an infinite loop saying: "sum path NAN NAN NAN NAN". The only solution is to kill Artemis and restart. I've also observed that saving the project and/or removing all files in the .horae directory and/or changing the fit model temporary solve the problem. Well, it's not a problem to manage this "divergence"... Mauro PS: My environment: Artemis 0.8.006 using linux, perl 5.008008, Tk 804.027, and Ifeffit 1.3.0 -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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IFEFFIT with Intel Macs
by Dustin Collier 02 Oct '06

02 Oct '06

Hi everyone, Since there has been a demand for running IFEFFIT on a new Intel-based Macintosh product, I thought I would send this link along. I'm not sure if anyone else has attempted this, but I recently installed Windows XP on my MacBook using Apple's Boot Camp software. All you need is an Intel Mac, a blank CD used to burn drivers for Windows XP (Boot Camp does this for you), and a copy of Windows XP SP2. IFEFFIT runs perfectly on my MacBook running Windows XP, and you can partition your hard drive as low as 5GB if you are only going to use this for this software. It is very easy to switch between OSX and XP, and the user's guide on the website is very helpful. Until someone can develop a working version for the Intel Macs, this might be an useful option for some of you and I thought I would pass it along. The link can be found below: http://www.apple.com/macosx/bootcamp/ If anyone has any questions on running Boot Camp, feel free to let me know. DCC -- Dustin C. Collier Graduate Teaching Assistant Department of Chemistry University of Tennessee Buehler Hall

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Consistency criterion
by Juan Antonio Maciá Agulló 29 Sep '06

29 Sep '06

Hi all, Scott answered my question about consistency but now I have a new doubt. I have two fits (one in k1 and other in k3 weights) with fitted parameters that have uncertainty ranges overlaped, then... in principle, they are consitent, right? But the fit in k1 weight have a R-factor too high (0.06) and therefore is not a good fit. So I do not know if I can say that they are consistent even so. Thank you very much Best regards, JA >I read in Artemis manual that a good fit must be consistent for different >k-weights. When two fits (one with k1 and other with k3) are consistent? I >mean, which is maximum allowed difference, 1%, 5%...between these two fits? Ideally, the fitted parameters should have uncertainty ranges that overlap. For example, one bond length might be 2.03 +/- 0.04 angstroms, and the equivalent bond length using a different k-weight might be 2.09 +/- 0.03 angstroms.

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Incorporating FEFF8 into IFEFFIT
by Richard Mayes 28 Sep '06

28 Sep '06

Bruce, I have just recieved a copy of FEFF8. Is there a way to incorporate it into Artemis on the windows version of IFEFFIT? In theory, we should be able to play a "shell game" with the names of the executable files and get FEFF8 to work while IFEFFIT thinks it's running FEFF6l (by changing the FEFF6l.exe file to something else, and rename the FEFF8 file to FEFF6l.exe) and then replace the DAT files to those for FEFF8. Is this possible or is it just better to run FEFF8 independently and import the .inp files into Artemis? Rich Mayes Barnes Group Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996

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Phase corrected Fourier transforms
by Juan Antonio Maciá Agulló 27 Sep '06

27 Sep '06

Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ¿phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why. I saw many papers dealing with EXAFS fits and they showed a "calculated" bond distance, I think it is: d = Reff + deltaR, right? I also ask for a paper where I can find that deltaE is ok (even for high-Z backscatterers) if deltaE < 10eV. I have high correlations between ss and SO2, and deltaR and deltaE. I tried different fits but I can not eliminate them, then...is the fit wrong? Sorry for these easy questions but I am a novice in XAFS. Thank you very much. Best regards, JA

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Re: [Ifeffit] Artemis error message
by Matt Newville 20 Sep '06

20 Sep '06

Hi Stefano, Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try. Can you verify that you have /Applications/Ifeffit/bin/feff6? --Matt

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Artemis import from the text file
by Victor.Streltsov＠csiro.au 19 Sep '06

19 Sep '06

Hi All, I have the following Artemis problem: when I export variables to text file and then read them back into new Artemis run/project (import variables from the text file), Artemis cuts parts of the expressions starting from multiplication sign '*'. I tried different text editors and character coding as well as different platforms (Windows XP, Linux FC4). It always does the same thing with imported math expressions. It doesn't like '*' character. I am puzzled. I would appreciate your help and any suggestions. Thanks Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov(a)csiro.au

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Short questions
by Juan Antonio Maciá Agulló 15 Sep '06

15 Sep '06

Hi Ifeffit people, I have a couple of short questions for you. I used the "Scott Calvin's rule" (number of variables < 2/3*Nip) to calculate the maximum number of allowed free parameters but I read that some people use the Nyquist theorem, which are the differences between them? and, which one is more correct? And finally, how are errors calculated in Artemis for the parameters N (coordination number), deltaE0, S02, deltaR and sigma^2? Thanks a lot JA

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FW: PhD position@LWV/PSI
by Degueldre Claude A. 12 Sep '06

12 Sep '06

-----Original Message----- From: Bruce Ravel [mailto:bravel@anl.gov] Sent: Montag, 11. September 2006 17:22 To: Degueldre Claude A. Subject: Re: PhD position@LWV/PSI URGENT AND FOR INFORMATION COULD YOU PLEASE VENTILATE THE INFO... We have 1 position free for doctorant with main topic EXAFS. You find the job below: http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was=l iste&kategorie=doktoranden With the KS 4334 If you have any candidate, please let me know... We need to evaluate candidates on Sep. 25. All the best CLAUDE DEGUELDRE ----------------------------------------------------- On Monday 11 September 2006 10:07, you wrote: > Bruce > We have 1 position free for doctorant with main topic EXAFS. You find > the job below: > http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was > =l > iste&kategorie=doktoranden > With the KS 4334 > If you have any candidate, please let me know... > We need to evaluate candidates on Sep. 25. > All the best Hi Claude, I don't know anyone who can fill the spot in the next two weeks, unfortunately. I think you should post this job opening on the Ifeffit mailing list. Matt and I consider that an excellent use of the mailing list. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Installing Tk/Horae on Fedora Core 5
by Bhoopesh Mishra 12 Sep '06

12 Sep '06

Dear All, I am in the process of installing Ifeffit 1.2.9 with latest Horae package (-062) on my a new machine on which I have put Fedora core 5. I followed the instructions for installing the entire package, and had partial success in it. Ifeffit and PGPLOT seem to be working fine. I believe Tk-804.027 is also working fine, I just ran "widget" and it works. However when I tried to ./horae_update, I got error message and it aborted without compilation. To look into the problem, I manually downloaded a previous version of horae (horae-061) from another computer on which everything is working fine (Tk-800.024 with horae-061 on a Fedora Core 2). In the manual installation of horae_061, perl Makefile.PL works fine. But "make" does not complete. It terminates with the same error message as the one with which ./horae_update terminated. (attached as a screenshot) I have attached the screenshots of the error message for horae_update. I have also attached screenshots of "make install" and "make test" for Tk-804-027 just in case you would like to see that. Since Ifeffit and PGPLOT are working, I am inclined to believe that it has something to do with Fedora Core 5 and its compatibility with Tk-804.027 and horae-062. Funny part is that I tried to downgrade the Tk to Tk-800.024, but it failed to install, which indicates some issues of Tk with FC 5. I also tried the combination of Tk-804.027 with horae-060. Has anyone gone through this combination of installing Tk-804.027 with horae-062 on a Fedora Core 5? Any insight would be extremely helpful. Thanks a lot in advance. Please let me know what more information would you need if the given information is insufficient. PS: I have been successfully using all these programs on FC 2 and FC 3 for last few years but some very generous people always helped me with the installation and am now trying to be independent. Thanks again, Bhoopesh

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