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

[Tsuei, Ku-Ding]

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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