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

[Matt Newville]

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.rajh at 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_______________________________________________
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--Matt
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