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

k weight in Athena
by koppolu uma mahendra kumar 08 Mar '06

08 Mar '06

Dear All, I have a doubt about k-weights while extracting the signal in ATHENA. In athena Background removal panel conatins one button called k-weight. My question is how significant k weigths at the stage of background removal. Please explain Thanking You Mahendra -- Research Student Material Science Laboratory University of Hyderabad(india) X-ray Synchrotron Radiation Laboratory University of Trento(Italy)

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Re: Tkatoms
by Bruce Ravel 08 Mar '06

08 Mar '06

Linda, I am CCing this question and my (short) answer to the Ifeffit mailing list. > I am installing atoms for the first time on my Windows XP PC. When I > download the file ifeffit.1.2.8.exe I can run the atoms command line > version but I don't find how I can run the TK version on my PC. > Thanks for your answer. http://cars9.uchicago.edu/cgi-bin/ifeffit/faqwiz?req=all#7.3 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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RE: [Ifeffit] Amplitude in Artemis
by Barton, David (DG) 03 Mar '06

03 Mar '06

Balwant, I have done a number of LCF using Athena and have found that this error message is typically associated with the rejection of one of your standards as a possible component in the fit. This error message may be avoided in most cases if you uncheck the options of --weights between 0 &1 and --Force weights to sum to 1 AND you put in an appropriate initial guess for the fit. When you rerun the fit with these options unchecked, it should be obvious what caused the error since one or more of your standard spectra will get a negative weight. When this occurs it is probably a good sign that the standard is not appropriate in the fit and some other standard should be used. Hope this helps, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of bsin1033(a)mail.usyd.edu.au > Sent: Thursday, March 02, 2006 3:41 PM > To: XAFS Analysis using Ifeffit; Kelly, Shelly D. > Cc: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Amplitude in Artemis > > > Hi Ifeffitters, > > I was trying to use the linear combination fitting function > in Athena to quantifying Cr(VI) and Cr(III) species. I used > two endmembers of Cr species as the two standards but the > program fails and gives error message "The fit flagged a > warning--probably that error bars could not be calculated. > That is probably an indication that one or more of your > standards are inappropriate for this fit." It appears I am > either using the wrong settings or even wrong function to do > the job, any suggestions. We have additional 3 spectra with > variable combinations of Cr(VI) and > Cr(III) as well. > > Cheers, > > Balwant Singh > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging > Program. _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 02 Mar '06

02 Mar '06

Hi Paul, Here is an edited version of the Fe project file. I believe that the first shell signal is not isolated from the 2nd and third shells. One way for the fit to look better when not enough paths are present is for the s2 value to be large to spread the signal out with an outrageous coordination number. I added a C and a Zn path to model the region from r=1 to 3.5 Å. The fit is not that great, the background needs to be fixed and I'm not sure that the C and Zn paths are the best choice. If you look at the real or imaginary parts of the fit with kweights of 1 and 2 and 3 you will see that we have done a fair job at reproducing the data. Hopefully this little bit of help will get you going in the right direction. Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Tuesday, February 28, 2006 5:54 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly I've attached the artemis project files. Hopefully you get further with them than I have been able to. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Wednesday, March 01, 2006 1:50 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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Amplitude in Artemis
by Paul 27 Feb '06

27 Feb '06

I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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SPAM score=47.4*** Fonts in document pods
by Dave Baker 22 Feb '06

22 Feb '06

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=47.4,required=5.3) -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0000] 50 STOCKS_APS FULL: Hot Stocks Spam -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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Re: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. 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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error message in help
by Bradley Roberts 21 Feb '06

21 Feb '06

With Ifeffit 1.2.8, Athena 0.8.047, Artemis 0.8.004 running on OS X and plotting correctly, I'm not able to pull up any of the help windows. In either of the GUI programs, when I click on the Help menu and choose Document (or any of the sub-menu items in Athena) X11 beeps in error, and a window opens with the title "pod" and nothing displayed within the window. I mentioned before that I could not get tk::pod to install correctly via CPAN (the response being) Installing tk::pod FAILED windows would pop up during the make test routine that said: Can't find Pod 'perl' with an OK button and that the Text::English and Tk::HistEntry modules were not installed (though they are installed, says CPAN) I recognize that this is probably more of a Perl/CPAN related question but perhaps someone has seen this problem before. -- Bradley Roberts (br2(a)u.washington.edu) Graduate Student, Department of Materials Science & Engineering Roberts Hall 302 Box 352120 University of Washington Seattle, WA 98195 206-616-7485 lab 206-543-3100 fax

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