Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations

[Ava Rajh]

Hello Matt!

thank you for the response. In putting together all the project files 
for the minimal working example I tested a bunch more .cif files of 
various materials including different graphite file, and there was no 
difference in Larch and Athena in any of them (as long as the same FEFF 
version and input settings are used) as expected.

Looking closely at the feff input file for the C.cif I was having 
trouble with, there were some differences which I haven't noticed when 
looking through them before. So as far as I am concerned, this was a 
user error on my part, as the generated input files weren't exactly the 
same. If I save the input feff file from Larch and use that in Artemis 
or the other way around, as you suggested, the results match exactly. 
The compared spectra in my previous message were calculated separately, 
exported and plotted together.

thank you for very much for the help and kind regards, Ava



Message: 1
Date: Mon, 16 Oct 2023 15:24:26 -0500
From: Matt Newville <newvi...@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Differences between Larch and Artemis when
        performing FEFF calculations
Message-ID:
        <ca+7esbrwm5uobygglmi+-wzru6mn4y_-z1obvg57pau4rsx...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Ava,

I think you'll have to give us more details about what you have done.  
The
figures you show are all in R-space, so after at least some 
processing...
 So, yes, project files and/or scripts would be helpful.  Yes, there 
can be
subtle changes in the background subtraction (and in the normalization
process too) between Larch and Ifeffit/Athena/Artemis.

By default, Artemis uses Feff 6.10 and Larch uses Feff 8.  For the C K
edge, that could have a noticeable difference, especially in the 
placing of
the k=0 value, though I do not know how big that effect would be for C
(graphite?).   But also, Artemis and Larch can both read the inputs 
from
the other calculations:  it might be that this is what you have done to
make the plots, but that wasn't 100% clear to me.




On Mon, Oct 16, 2023 at 2:08?PM Ava Rajh <ava.r...@ijs.si> wrote:

Dear all!

I haven't been able to find a similar question/issue in the previous
threads, so I hope someone can help me figure out what is going on.

I am trying to fit a Carbon EXAFS spectra, using graphite as a model. 
I
am first focusing on just the first two single scattering paths, so I
calculated the theoretical paths with FEFF in Larch and tried using 
them
to fit the spectra. I was consistently getting slightly lower 
distances
than expected, but otherwise an OK fit.

The issue is, I tried to compare the analysis with a colleague who is
using Athena. At first glance the EXAFS spectra, using the exact same
parameters, looked very similar (but not exactly the exactly the same,
this I attributed to Larch using a different autobk procedure). I 
would
have however expected the theoretical paths to match exactly, if they
were calculated and plotted with the same parameters. But they were 
also
slightly different.  I then downloaded Athena and spent time trying to
find where the differences come from. If I compare the first two
calculated shells from Larch with the ones from Athena, with exactly 
the
same set of test parameters (S02 = 1, E0 = 0, dr1 = 0, s2_1 = 0, dr2 =
0, s2_2 = 0), the resulting models do not match. I made sure the paths
are calculated from the came .cif file in both cases, use FEFF6, have
the same calculated reference distances, same FT...

So, my main question is, am I missing something important in regards 
to
calculations, why would the calculated paths be different and which 
one
would be the "correct" one to use for the fit? And the other question
would be about the fact that EXAFS spectra of experimental data look
slightly different using Larch and Athena, am I right in disregarding
this, or should I dig deeper and find the source of discrepancy?

I am enclosing a plot of just the calculated first two shells from
Athena and Larch (FT: kmin =  2, kmax = 7.5, Fittting in R space, kw =
3, kWindow = Hanning, dk = 1.0, Rmin = 0.6, Rmax = 2.1) along with the
cif file I ended up using for testing the differences. If it would be
helpful, I can also provide the project files and larch script I used
for the dataset, but I am mainly interested in understanding the
differences seen in the theoretical parts first. I tested this using
Larch v 0.9.72 and Demeter 0.9.26

Thank you ver much for the help, and If I need to provide any 
additional
info please let me know.
kind regards, Ava

--
Ava Rajh_______________________________________________
_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit