# [Ifeffit] Increase in uncertainty of Eo and fitting mismatch

Raj kumar rajrk37 at gmail.com
Wed Mar 11 14:30:10 CDT 2015

```Dear matt and Bruce,

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

>>"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.

>>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.

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.

>>>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.

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, <ifeffit-request at millenia.cars.aps.anl.gov>
wrote:

> Send Ifeffit mailing list submissions to
>         ifeffit at millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> or, via email, send a message with subject or body 'help' to
>         ifeffit-request at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
>         ifeffit-owner at millenia.cars.aps.anl.gov
>
> than "Re: Contents of Ifeffit digest..."
>
>
> 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 10 Mar 2015 12:08:24 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Increase in uncertainty of Eo and fitting
>         mismatch
> Message-ID:
>         <
> CA+7ESbot-UZAgz3WM9EqaNROc7io+KnBE5NbEoMvxVoixPWGcw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Raj,
>
>
> On Tue, Mar 10, 2015 at 11:11 AM, Raj kumar <rajrk37 at gmail.com> wrote:
> > 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
> this
> > reason, i have modeled with and without corrected Copper EXAFS in
> Artemis.
>
> What does "with and without corrected Copper EXAFS" mean?
>
> > 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
> >
> > 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.
>
> > 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.
>
> > 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.
>
> > 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
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 10 Mar 2015 13:50:59 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Data being overwritten in Artemis history
>         window
> Message-ID: <54FF2F03.8060708 at bnl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 03/09/2015 04:17 AM, Godfrey, Ian wrote:
> > 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.
> 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 at 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/
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 11 Mar 2015 09:59:54 +0100
> From: Raj kumar <rajrk37 at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] (D)Artemis shutting down automatically
> Message-ID:
>         <
> CAAW7+QMAn0kbe0udnpMzyPpqsb0X_t632Qwk7bWuMhtbzY96WQ at 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150311/d5ed2f37/attachment.html
> >
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: dartemis.log
> Type: application/octet-stream
> Size: 552 bytes
> Desc: not available
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150311/d5ed2f37/attachment-0002.obj
> >
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: dartemis.log
> Type: application/octet-stream
> Size: 384 bytes
> Desc: not available
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150311/d5ed2f37/attachment-0003.obj
> >
>
> ------------------------------
>
> Message: 4
> Date: Wed, 11 Mar 2015 08:59:59 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] (D)Artemis shutting down automatically
> Message-ID: <55003C4F.5020906 at bnl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 03/11/2015 04:59 AM, Raj kumar wrote:
> > 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.
> >
>
> I need to be able to reproduce these errors on my own computer.  Without
> an example of data that triggers the problems, I can't do much.
>
> http://bruceravel.github.io/demeter/pods/bugs.pod.html
>
> B
>
>
> --
>   Bruce Ravel  ------------------------------------ bravel at 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/
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 145, Issue 17
> ****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150311/98db6a91/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Copperfoilfit.apj
Type: application/octet-stream
Size: 106414 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150311/98db6a91/attachment.obj>
```