Dear matt and Bruce, Thanks for the reply. Bruce i am working in new version (facing some problem) and will write to you soon

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"What does "with and without corrected Copper EXAFS" mean?

For more clarity, in the new file, i have presented single copper EXAFS fit and showed the result. Please see the attachment for that.

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What actual value? You mean the uncertainty in E0 increases when you go from 1 to 3 shells? That increase in uncertainty could easily be due to a worse overall fit.

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The Fourier transform of the data depends only on the k-space data, and the weighting and windowing applied. It doesn't depend on the values of the fitting parameters -- those affect only the Fourier

Here i am mentioning *final fit* value as *actual value* and their *error bar *is uncertainty. If you look at the Eo value from 1 shell (fit 1) to 3 shell (fit 3), it decreases and close to zero whereas the corresponding uncertainty tending to reach more than or equal to 1. This is what i am mentioning here by saying Eo uncertainty increases for the inclusion of shells. transform of the model. I am really sorry, aforementioned sentence has been written in wrong and misleading way. The point i would like to make here is about the fit in R-space. The trouble i am facing is the following: I*f you look at the fit in R-space, similarly, * from 1 shell (fit1) to 3 shell (fit3) fit, the first shell theoretical shape shifts to larger distance (*for three shell fit (fit 3) in R-space*) compared to the only first shell fit (*fit 1*). If you look the third shell theoretical shape, it is shifted towards the shorter distance than the experimental spectrum (in *fit 3*), while the amplitude of second shell fit is always less than the experimental observation. Why it is occurring so? and what i am missing here? I hope i have conveyed the problem in right way. With regards, Raj On Wed, Mar 11, 2015 at 6:00 PM, wrote:

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Today's Topics:

1. Re: Increase in uncertainty of Eo and fitting mismatch (Matt Newville) 2. Re: Data being overwritten in Artemis history window (Bruce Ravel) 3. (D)Artemis shutting down automatically (Raj kumar) 4. Re: (D)Artemis shutting down automatically (Bruce Ravel)

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Message: 1 Date: Tue, 10 Mar 2015 12:08:24 -0500 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Increase in uncertainty of Eo and fitting mismatch Message-ID: < CA+7ESbot-UZAgz3WM9EqaNROc7io+KnBE5NbEoMvxVoixPWGcw@mail.gmail.com> Content-Type: text/plain; charset=UTF-8

Raj,

Some comments and suggestions.

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Dear All,

Recently, I recorded Copper foil EXAFS as a reference in (Dispersive EXAFS) transmission mode at Soleil, Paris. For understanding the data quality (of my sample), i started fitting copper EXAFS through Artemis. After the DATA extraction, i fitted copper in Artemis and found a shift in energy. For

On Tue, Mar 10, 2015 at 11:11 AM, Raj kumar wrote: this

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reason, i have modeled with and without corrected Copper EXAFS in Artemis.

What does "with and without corrected Copper EXAFS" mean?

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Initially, i started with first shell and progressed to three shell fit through step by step. During the course of fitting, some of the following troubles have been faced. Please help me to rectify it.

For first shell fit: Everything goes well and converged to reasonable physical values of copper foil. Whereas for further increment in copper shells leads to increase in Debye-waller factor for all three shells and

By itself would not worry me too mcuh.

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increase in uncertainty value of E0 than the actual value.

What actual value? You mean the uncertainty in E0 increases when you go from 1 to 3 shells? That increase in uncertainty could easily be due to a worse overall fit.

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Moreover, i have noticed that the (increase of shells in the fit) not only changes the physical parameters and also modifies the Fourier transform.

The Fourier transform of the data depends only on the k-space data, and the weighting and windowing applied. It doesn't depend on the values of the fitting parameters -- those affect only the Fourier transform of the model.

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The inference are the following: A shift in first and third shell of Cu-Cu are observed, respectively, to larger and shorter distance than the experimental spectrum with diminished second shell amplitude.

Not sure what you mean.... larger and shorter than what?

I would recommend fitting one spectrum first -- I don't quite understand why you have 2 spectra with an obvious E0 shift between them, and no (unless I missed something) shared parameters.

--Matt

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Message: 2 Date: Tue, 10 Mar 2015 13:50:59 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Data being overwritten in Artemis history window Message-ID: <54FF2F03.8060708@bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed

On 03/09/2015 04:17 AM, Godfrey, Ian wrote:

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In the history window some, but not all, data from previous fits seems to get overwritten when running a new fit. Specifically I've noticed this happening with the information in the "Data set" section. To reproduce run a QFS fit with some R-space fitting windows (say 2-4); at this point the log will be displayed correctly in the history window. Now change the R window (say 1.5-3.5) and run the fit again. When you go to the history window the R window information will be displayed correctly for the most recent fit but, for the previous fit it will have been overwritten by the newer fit. Some of the other info, such as R-factor by k-weight seems to get overwritten too.

I just pushed a fix for this to github and posted new windows installer candidates at

http://bruceravel.github.io/demeter/#windows

If you see any other questionable behavior in the history window let me know. I think I understood the ramifications of the fix I made, but I am not 100% certain.

The windows installers also include the most recent version of gnuplot. Hopefully that will address your problem regarding zooming and scrolling.

If it does not, try changing the gnuplot->terminal configuration parameter to "qt". qt is one of the other terminal options in the new version of gnuplot. It makes a pretty plot, but I like the controls on the wxt terminal more. If you are unsatisfied with that, try setting it to "windows", which is the third (and to my eye, the worst) of the three plot terminal options. Hopefully one of them will work for you.

Cheers, B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Message: 3 Date: Wed, 11 Mar 2015 09:59:54 +0100 From: Raj kumar To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] (D)Artemis shutting down automatically Message-ID: < CAAW7+QMAn0kbe0udnpMzyPpqsb0X_t632Qwk7bWuMhtbzY96WQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

Dear All,

Recently, i have faced automatic shutting down of artemis during the import of chi file. For more clarification, please see the first log file.

Also, i observed emptying of .fpj files. This happens during the saving of old .apj to .fpj or/and during the frequent saving of .fpj files after .apj conversion. Please see the second log file for this problem.

Regards, Raj