Re: [Ifeffit] Increase in uncertainty of Eo and fitting mismatch

11 Mar 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.
...
...
...
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)
----------------------------------------------------------------------
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.
...
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
...
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
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.
...
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 
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:
...
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/
------------------------------
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