[Ifeffit] Why different installations of Atoms generate different results?
Tsuei, Ku-Ding
tsuei at nsrrc.org.tw
Sat Sep 22 08:13:50 CDT 2012
Hi Bruce,
Thanks a lot for your reply and comments particularly on how to change
k-weight in (D)Artemis-Atoms. Sorry for not being able to provide clear
results stating exactly where my confusion came from. I was not sure if
an attachment could be readable to this email list but let me try this
time. Certainly I do not know how to retrieve data values from these
plots yet.
The attached pdf file compares the output plots of k^n*chi(k) with n=0,
1, 2 and 3 of the Au L3 EXAFS of the shortest path calculated from
Artemis-Atoms in Demeter and old Artemis. I suppose to read identical
plots of k^n*chi(k) from different programs but they are not. That is
why I feel confused.
Your help on clearing my confusion is appreciated. Then I can move on to
do model fit on real data.
Ku-Ding
Re: [Ifeffit] Why different installations of Atoms generate different
results?
Bruce Ravel
Fri, 21 Sep 2012 11:37:27 -0700
Ku-Ding,
I am not sure how to respond to this. To me, it reads like a rather
rambling rant about the things you don't like in my software. You
haven't really articulated a question. Nor have you provided any kind
of evidence that Demeter is misbehaving in any way that I can
reproduce on my own computer.
Now, don't get me wrong ... I love a good rant and indulge myself all
the time! And I certainly agree that there is ample room for
improvement in my codes. But if you want me to either explain
something or change something, you have to articulate the issue much
more clearly.
That said, I have a few comments that may be helpful....
1. Here is the Artemis Users' Guide:
http://bruceravel.github.com/demeter/artug/index.html
It is not complete and I haven't yet written a description of the
plotting window.
2. The plotting toolbar in Atoms is intended to provide a crude
visualization of the paths just calculated. It is, in no sense,
intended as a complete visualization tool. Rather, it's purpose is
to answer questions like "where in R space is the peak of this
path?" or "which of these paths have substantial spectral weight?"
For such questions it doesn't much matter what k-weight you use.
3. In Artemis, the FT and k-weighting parameters from the Plot window
are used by the plots from the Atoms/Feff window. In stand-alone
atoms, the default values are used. The configuration tab in the
stand-alone Atoms does not, however, offer the plot or gnuplot
configuration groups. I suppose that could consititute a bug if
your expectation of those plots exceeds their intent.
4. I no longer support the 0.8 series. There will be no updates or
bug fixes forthcoming for those older versions.
B
On Friday, September 21, 2012 11:06:00 PM Tsuei, Ku-Ding wrote:
> Hi Bruce,
>
> I am a novice of this community and actually have less than two weeks of
> experience using IFEFFIT (version 1.2.11 with iff_013 update) and its
> front end packages Demeter (version 0.9.11) and its predecessor Horae
> (Athena, Artemis etc. version 0.8.014) running under Windows 7
> Professional SP1. They are excellent software guiding me quickly into
> this EXAFS world. Thanks a lot.
>
> However, I feel confused by viewing different results (chi(k))
> calculated from three installations of Atoms, namely Atoms within
> (D)Artemis, stand alone (D)Atoms, and Atoms within the old Artemis. I
> then used the simplest Au.inp as the input for all. I checked the path
> outputs making sure the generated paths are identical and selected
> individual paths. To my surprise the chi(k) curves have different
> envelopes and magnitudes from 3 Atoms. It seems to me that chi(k) are
> calculated from the same feff6 program and should be identical from any
> installation; no FT range is involved to affect chi(R). Could you help
> clarify my confusion?
>
> Perhaps the new Demeter can be improved further. It seems that only
> k^2*chi(k) is plotted in Atoms within (D)Artemis, and only k*chi(k) is
> plotted in the stand alone (D)Atoms by viewing the vertical labels in
> plots. There seems no obvious place I can change k-weighting like in the
> old Artemis. I have not been able to find where, such as Edit preference
> in the old Artemis, I can change the default parameters, or learn what
> parameters are used in doing FT (kmin, kmax) or window function and so
> on. I learn these preference parameters quickly owing to the extensive
> documents built-in side by side with "action tabs" in the old Artemis
> and the link to html documents in the old Athena. By the way, watching
> your videos is an excellent way to learn Demeter but I had to pause to
> search related projects or files to run side by side with videos; some
> links with video download sites could be very helpful.
>
> Look forward to reading your answers and utilizing the more powerful
> Demeter. Thanks again.
>
> Best regards,
>
> Ku-Ding Tsuei
> ------------------------
> Ku-Ding Tsuei, PhD
> Associate Scientist
> National Synchrotron Radiation Research Center
> 101 Hsin-Ann Road
> Hsinchu Science Park
> Hsinchu, TAIWAN 30076, ROC
> email: ts... at nsrrc.org.tw
--
Bruce Ravel ------------------------------------ bra... at bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
Homepage:http://xafs.org/BruceRavel
Software:https://github.com/bruceravel
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