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

[OT] Ifeffit mailing-list available also on Gmane
by Mauro Rovezzi 20 Feb '10

20 Feb '10

Dear all, A short off-topic message to inform you that I have subscribed (in accord with Matt) the Ifeffit mailing-list to the http://gmane.org archive. This will permit to follow this (traffic-growing) discussion forum also via a newsreader or RSS feeds. Below a copy of the subscription. MR Begin forwarded message: Newsgroups: gmane.discuss.subscribe Subject: Re: subscribe ifeffit(a)millenia.cars.aps.anl.gov The following message is a courtesy copy of an article that has been posted to gmane.discuss.subscribe as well. * mauro.rovezzi (at) esrf.eu [2010-02-06 16:21]: > #gmane.science.physics.ifeffit ifeffit(a)millenia.cars.aps.anl.gov > Discussion of Ifeffit, Athena, Artemis, and SixPack, as well as > related X-ray Absorption Fine Structure (XAFS) analysis programs. > mailman dummy encode=encrypt > spam=ignore > lang=eng > url=http://cars9.uchicago.edu/ifeffit/ Subscription messages for the requested mailing lists have been sent. The resulting groups will be created when the first message arrives from the mailing lists. Wolfgang -- Gmane -- Mail To News And Back Again: http://gmane.org

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How to evaluate the fitted result by LCF?
by 康明亮 18 Feb '10

18 Feb '10

Dear, I want to consult how to evaluate the fitted result by LCF. R-factor within what range is reasonable and allowable? Attached are the fitted results, athena-SSRF.prj extention and .gif picture.Why there is still a large deviation for sample K (excluded FeSeO3 from this sample)? Thanks a lot! Best wishes Mingliang

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Athena Freezing Desktop
by David Ehle 16 Feb '10

16 Feb '10

Bruce, Sorry for the accusatory subject line - I can't prove Athena is the culprit but I figured that others with the same problem would be searching for similar terms. Running Athena from the current debian package for Lenny (2:1.2.11d-1) we have been seeing desktop freezes after some hard to characterize period of use. The time period seems to usually be a few hours, and there is a belief that it is connected to having more than a few raw data files open in Athena. Users have previously seen Athena crash/freeze when they have "too many" files open, or Athena open for "too long" but I haven't been able to get any firm numbers. The concern is that while previously when Athena crashed or froze, only Athena was effected. Now it seems that the whole desktop becomes non-responsive. The reason I'm suggesting there is a link between Athena and the Desktop (XFCE4) problem is that if you connect to the system via SSH and kill Athena, the Desktop becomes unfrozen and the user can continue with what they are doing. We have seen this occur on both beamlines, with different users and different data sets so I doubt it is data specific, but can send your some sample files if that will be useful. In one case I was able to collect an error message from the .xsession-errors file of a user who was experiencing the problem: ** (xfwm4:21854): WARNING **: Unmanaged net_wm_state (window 0x3800008) X Error: BadWindow (invalid Window parameter) 3 Major opcode: 7 Minor opcode: 0 Resource id: 0x329 kbuildsycoca running... Reusing existing ksycoca kbuildsycoca running... Reusing existing ksycoca kbuildsycoca running... Reusing existing ksycoca Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. I'm afraid I don't know if the lines before the lines that explicitly mention athena are related, or if these messages have anything to do with the desktop freezing problem - I think I have the seen the freeze without the errors. Please advise if we can provide you with other information to make figuring out easier. When this problem occurs at 3AM it really upsets our users (which tends to upset the staff when they get called about it...) so we have started running a second system just for Athena. Can you make any suggestions on the minimum vs optimal hardware for Athena? For tracking many (30+) raw data files to see how a run is progressing, can you suggest minimum RAM, CPU power, # of Cores? Thanks!! Please CC ehle(a)iit.edu with any responses as I'm not an active subscriber to this list. David Ehle MRCAT -IIT

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Is possible to shift the spectra in athena?
by 康明亮 16 Feb '10

16 Feb '10

Dear, I want to consult if is possible to shift a spectra in athena? As shown in the attached file athena.prj, I want to include red-(Se) to do LCF. But I forgot to measure the red-Se(0) spectra, only grey-Se(0) was measured. However, according to the literature, these two references have the same energy position only with different amplitude at the white line peak. Since the white line peak would shift if the same sample was measured at different facility, thus I need to do horizontal translate the spectra of red-Se(0) which measured at another facility. is it possible to do this in athena? Thanks! Best regards Mingliang

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Bruce ayuda, problemas con athena
by Jaziel Soto 14 Feb '10

14 Feb '10

Me encuentro usando el athena 0.8.061 y el ifeffit 1.2.11c instalado en windows vista de 32 bits. Tengo puesta la compatibilidad de windows xp service pack 2, ejecutándolo con privilegios de administrador y después de haber trabajado algo, cuando quiero grabar los .prj no pasa nada. Entonces lo que trabajo no tiene sentido por que no lo puedo guardar.

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Lanthanides convergence
by Eugenio Otal 09 Feb '10

09 Feb '10

Hi, I am performing some simulations for Er2O3 and found that the best agreement with experimental data are found when I use UNFREEZEF card. With this card I find some coditions I cannot acchieve convergence, I atach the inp and output files. At the end of the output fila I find: Electronic configuration iph il N_el 0 0 1.601 0 1 1.494 0 2 10.380 Found bad counts. Occupation number in getorb is 1.000 Will repeat this iteration 0 3 0.656 1 0 0.371 1 1 6.451 1 2 1.822 1 3 9.026 2 0 1.985 2 1 5.571 2 2 0.000 2 3 0.000 Core-valence separation WARNING: fatal error in subroutine corval. Try to reduce ca1 in SCF card. If does not help, SEND bug report to AUTHORS CORVAL-1 I tried to change the ca en SCF card and no good results. Thanks in advance, euG

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Iffeit oin snow leopard
by Jose Mustre 05 Feb '10

05 Feb '10

Hi Jeff, I would like to try the beta version of iXAFS for Snow Leopard. We have here in Cinvestav-Merida sevral MAC Pros's with Snow Leoprad, and we have been relying on iFeffit for our ddata analaysis. So I would appreciate very much to have this version. Thanks very much, Jose Jose Mustre Departamento de Fisica Aplicada Cinvesatv-Merida 999 942-9435 mustre(a)mda.cinvestav.mx

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consultation
by 康明亮 04 Feb '10

04 Feb '10

Dear, I want to to ask a question about using Linear Combination Fitting in Athena. I normalized all the references(measured in transmission mode) and samples (fuorescence mode) with Athena, and then wish to use LCF to quantify each unique component in the samples. But I noted that the normalized samples spectra had lower height at the white line peak than any references(shown pic-1.emf in annex), thus the fitted spectra were also higher than the original sample spectra (shown pic-2 and -3.emf in annex). I do not know why? I also attached all the original data(before normalization). Wish to obtain guidance from you. Thanks! Best wishes Mingliang

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about energy error in XANES
by mzhu＠udel.edu 29 Jan '10

29 Jan '10

Dear All, My XANES data were collected with Si(111) monochromator with a step size of 0.5 ev. I want to determine the energy position of the white line (the maximum absorbance) after internal energy calibration. I am wondering how to determine its error. Is it -0.5 ~ +0.5 ev, due to the step size(0.5ev) for data collection? Does it depend on the monochromator? Thanks. Best wishes, Mengqiang ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html

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ATHENA on Ubuntu
by Andi Idhil 27 Jan '10

27 Jan '10

Dear All, I ve installed ifeffit on my ubuntu desktop. I try to load it and apparently faster than in my windows desktop. The problem is, when i have selected the EXAFS data file in athena data column, i could not find the OK button in the lower left part of the window so i could not continue to work. Does anybody have solution for this ? Thank you very much Andi Villigen

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