December 2005 - Ifeffit - millenia.cars.aps.anl.gov

phase shifts
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello, yet another one... sorry today is my day... With Athena it appears that I can simply (maybe too simply) click on a button and plot the phase shifted spectrum in R-space. How can I try to do the same using IFEFFIT from the command line? In practice, using IFEFFIT we can plot the fitted spectrum and the FT'ed experimental spectrum, but the plot does not consider the phase shift. We need to extract the phase shift in oder to translate the plot to show the phase shifted spectrum. How can we do that? What is the parameter in IFEFFIT that allows one - as in Athena - to add a constant number and shift the plot? Stefano PS: needless to say that we are learning... -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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statistical parameters
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello, same old question that emerges again: What formula is used by IFEFFIT to calculate the number of independent points? Does it use the formula 2DkDR/pi? or 2DkDR/pi +1? or 2DkDR/pi +2? And how does it approximate the resulting number to integer? Next: as far as I understand, the conversion from chi^2 to reduced-chi^2 involves dividing the first by the number of degrees of freedom. The latter is obtained by subtracting the number or floating parameters from the number of independent point right?. What if one fixes the value of one parameter, let's say S0^2 to unity? Does the number of parameters includes S0^2 in that case? We consider that it does not. Here is an example. We find with IFEFFIT (we use Dk= 10 (from 2 to 12), DR=5 (from 1 to 6). chi^2 = 87.1 reduced chi^2 = 3.7 parameters: E0, three distances and three sigma^2 we set S0^2 fixed to 1 R-factor: 1.15% The ratio between chi^2 and reduced chi^2 is 23.54, which is not an integer number as we would expect. Plus, this number does not correspond to Ninp -Nvar (31.83 - 5 = 26.83) What are we missing? Sorry if the question sounds silly to most of you. Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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Athena 0.8.046 and the "%" character
by Mauro Rovezzi 14 Dec '05

14 Dec '05

Hi folks, I've just noticed a strange behaviour in Athena. Please, let me know if you can reproduce this "error": - Open a project with two mu(E) - Merge them in chi(k) [noise weighted] - Rename the "merge" group in "something%something_else" - Save the new group as chi(k) - Save the project Well: 1. The generated .chi file contains nothing 2. Artemis fails to open the chi(k) from the Athena project (trapping an error and showing nothing). 3. Re-doing everything *without the "%" character, works!* Cheers, Mauro

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wiggly lines
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello all, I found this funny dialog on the web. I think it is worth a smile :-) Stefano "What is feff," You ask? "Well, I am glad that you asked that," I say. Then I continue, "Feff is a computer program that makes wiggly lines appear on your computer screen." "Not my computer screen," you say. "Yes, I suppose not YOUR computer screen- MY computer screen... Anyways, sometimes the lines are long and really very wiggly, and sometimes the lines are hardly very wiggly at all. But, there are always at least a few wiggles; you can count on that." "And another thing about the wiggly lines," I exclaim. "Sometimes those wiggly lines are pretty good wiggly lines, but then again, sometimes they are pretty bad." "How can you tell the difference," you ask? "Well, that's really very simple. Just go show the wiggly lines to your boss, and if he looks HAPPY then you have just shown him GOOD wiggly lines... If he looks SAD then you have just shown him BAD wiggly lines. And if he says, 'What the hell are all these wiggly lines?' then you probably just went into the wrong office; try down the hall a bit... ...just a little further... ...now on your left... ... next one... that's it! Good luck with those wiggly lines!" -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 14 Dec '05

14 Dec '05

Paul, Is Perl/Tk for 5.8.6 included in the 10.4 installer? Do you have any suggestions for Stefano? Stefano: the Ifeffit apps from the 10.3 installer won't work directly with 10.4. With the 10.3 package installed, several people were able to build horae from source -- see the mailing list archives for directions on how this was done. But I sure hope you don't need to do this. The installer should work. I sort of don't understand what happened to break these apps. It was working for you once, right??? I sort of don't understand what happened. --Matt

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problem with ifeffit 1.2.8 at ESRF
by Carmelo PRESTIPINO 13 Dec '05

13 Dec '05

Hi to all I'm Carmelo (Lello) and I'm working on Bm29 in ESRF. Recently I have updated IFEFFIT to version 1.2.8 a computer in the beamline (OS winXP profesional edition), but I unfortunatly noticed that the applications didn't start. Makinig some test and looking the previus posted newsmail I concluded that this behavior is probably due to the firewall of ESRF. In order to obtain a more susessfull help from the computter service, anyone could explein me wich is exacly the problem Here below there is the runner.exe.log Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out. Best Regards Lello

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 12 Dec '05

12 Dec '05

Stefano, You should NOT need to compile perl/Tk -- it should be included in the installer. You had a working system that somehow got corrupted (though I do not understand how that happened, as a horae_update should have done absolutely nothing). How did you originally get Ifeffit installed on your OSX system? Bruce wrote: > On a similar topic, I see that IfeffitOnMacintosh on the wiki points to a page that hasn't > been written yet. Maybe Stefano or Paul will fill this in. The discussion of how to install Ifeffit+horae on OSX10.4 has been discussed several times on this mailing list in 2005. Several people were able to use the 10.3 installer, fink installed g77, and compile all the perl modules themselves. The installer is supposed to avoid all that. I don't know what's in the 10.4 installer. We should wait to hear from Paul. --Matt

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Ifeffit installer for Mac 10.4 (Tiger)
by Tonio Buonassisi 12 Dec '05

12 Dec '05

Hi Matt, I've just tried installing IFEFFIT (using "install Ifeffit on Tiger") on a new Mac running 10.4. The installer apparently runs to completion, but when I go to the application folder and double-click on the apps themselves (e.g., Artemis), they appear to open up but then immediately close down to the Finder again in less than a second. At the XAFS Summer School I remember this problem on newly-installed machines: we had to download a program from the Apple website (X-server?), although I can't recall what this is... Conscious that this is an old problem, I tried looking in the archives, but without search capabilities I didn't find the right thread... Any assistance would be appreciated, Best, Tonio

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writing beam time proposals
by Bruce Ravel 08 Dec '05

08 Dec '05

Hi folks, Yesterday I received an interesting question about writing beam time proposals. I know that proposal review panel members at least from APS and NSLS are readers of this mailing list (perhaps other synchrotrons as well), so I thought it would be interesting to start a thread on proposal writing strategies. The fellow who sent me mail asked: My question is, since I am a student, should my advisor be the official PI applying for time or should I be the PI? Is there any advantage one way or the other? In principle, I think it should not matter. Beam time should be awarded to a quality proposal. What advice do you all have for this proposal writer? What has your experience in applying for beam time? BTW, this fellow had been a student in a recent XAS summer school. I suggested he mention that in his proposal. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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/exafs/

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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Stefano Ciurli 02 Dec '05

02 Dec '05

Hello Ifeffitters on MAC OSX. Just to finish this thread, I inform you that I have solved my problem. The issue was with the /Library/Perl directory. Once I replaced it with a backup I diligently keep almost weekly, everything works fine with horae-056. Thanks a lot to those who tried to help me out (and also for those who silently sympathyzed about this problem I had created to myself :-)) Stefano

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