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...@nsrrc.org.tw

-- Bruce Ravel ------------------------------------ bra...@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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit