[Ifeffit] Why different installations of Atoms generate different results?

Mon Sep 24 16:45:24 CDT 2012

The APJ files can be opened by changing their extensions to .zip and using an unzip utility.
----- Original Message ----- 
From: "Tsuei, Ku-Ding" <tsuei at nsrrc.org.tw>
To: <ifeffit at millenia.cars.aps.anl.gov>; <newville at cars.uchicago.edu>
Cc: <bravel at bnl.gov>
Sent: Monday, September 24, 2012 2:21 PM
Subject: Re: [Ifeffit] Why different installations of Atoms generate different results?


> Dear Matt,
> 
> Thanks for your positive reply. You are opening a door to solving my 
> problem. Attached are the fpj file generated by (D)Artemis and the apj 
> file by the old Artemis, respectively. They cannot be opened by Note Pad 
> nor by Word Pad, so I do not know their contents.
> 
> I actually generated these projects from scratch solely by File -> open 
> project or data (Au.inp) in (D)Artemis (or alternatively from Feff 
> calculations -> Add) or by File -> Open file in the old Artemis without 
> inputting any data. I just wish to look at what kind of EXAFS spectra 
> generated purely by calculation before using them for model fitting.
> 
> For (D)Artemis I went through Run Atoms -> Run Feff  and could select 
> any path from the path list, click chi(k) and then Plot selection. Of 
> course now I know how to change k-weighting in the Plot window. I know 
> which path is plotted because each path corresponds to a single curve 
> with its own color and the path names are included in the legend.
> 
> For the old Artemis I went through Run Atoms -> Run Feff and clicked 
> import All paths. Again I could select any path in the list and Plot k, 
> R and q with a choice of k-wieghting. Similarly each path corresponds to 
> a single curve with its own color and the path names are included in the 
> legend.
> 
> These steps illustrate how I copied these plots into the pdf file I sent 
> to the mail list.
> 
> The path page in the old Artemis contains some more information as Path 
> parameter math expression side by side to the Data & Paths list. They 
> are N:6, S02:amp, delE0:enot, delR:delr and sigma^2:ss. Indeed you are 
> right that changing them to numbers results in different plots. But I 
> thought I should keep the default path parameters intact because they 
> are supposed to be from calculation . Moreover, many of these path 
> parameters do not have similar math expressions in (D)Artemis. See the 
> next paragraph.
> 
> Yes, I followed Bruce's suggestion to go through  the on line manual of 
> (D)Artemis with loading the Au foil data first then up to The Path Page, 
> aiming for fitting real data. I could generate paths from the Atoms and 
> Feff window and plot their chi(k) and so on, identical to the previous 
> project without loading in Au foil data. I could drag the selected paths 
> from the Atoms window into the Data window. By selecting each path the 
> associated parameters are displayed, but only N and (blank)=(S02)(?)=1, 
> the rest fields are empty. Are they supposed to be filled like in the 
> old Artemis? I then copied in math expression contents exactly the same 
> as in the old Artemis. The plotting shows only the Au foil data. Then I 
> pressed the yellow Fit button. A message box pops up: Fit cannot 
> continue: You have not defined any fitting parameters. Could you offer 
> more clues to continue? The (fit) project up to now is saved and attached.
> 
> There are more problems running (D)Artemis on my Windows 7 Professional 
> SP1. The program can load in the saved (fit) project described above but 
> always crashes on loading the first project without Au foil data, no 
> matter which compatibility mode I choose before starting. It may be 
> worth noting that only the (D)Artemis DOS window appears when choosing 
> None, Windows 7, Windows Vista SP2, Windows Vista SP1, Windows Vista, 
> Windows 2000, and Windows NT 4.0 SP5. On choosing Windows XP SP3, 
> Windows XP SP2, Windows 98 / Windows Me, and Windows 95 there appears 
> another DOS window on startup, D:\strawberry\perl\bin\perl.exe. I am not 
> sure if these information may help solving the cash problem of 
> (D)Artemis. On the other hand, the old Artemis can load in the project 
> file with no Au foil data without crashing.
> 
> Your help is greatly appreciated.
> 
> Ku-Ding
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Date: Mon, 24 Sep 2012 09:10:48 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Cc: bravel at bnl.gov
> Subject: Re: [Ifeffit] Why different installations of Atoms generate
> different results?
> 
> Dear Ku-Ding,
> 
> On Sat, Sep 22, 2012 at 8:13 AM, Tsuei, Ku-Ding <tsuei at nsrrc.org.tw> wrote:
>> 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
> 
> 
> The two results you show are quite different, but you don't tell us
> how you got them, expect to say the they were calculated by
> Artemis-Atom and D(Artemis)-Atoms.   This is an incomplete
> description, allowing many possible differences.   To be clear, Atoms
> only generates the feff.inp file.  These should be the same between
> the two versions, especially for as simple a case as fcc Au.  Next,
> Feff has to be run.   This will be the same, assuming the input files
> are the same.    Next, Artemis reads in the output files from Feff
> (you say you're using the first shell only, but I encourage you to
> verify that),  applies Path Parameters to these, and generates chi(k).
>  Are the number of Paths used, and the Path Parameters (N*S02, sigma2,
> e0, deltaR) the same in these two calculations?     I'd guess that
> they are not.
> 
> Providing plots of outputs is helpful, but as is said many times here,
> providing the project file is much more helpful as it shows not only
> the final result, but how you got there.
> 
> Cheers,
> 
> --Matt
> 
> 
> ------------------------------
> 
> 
>


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