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

[Matt Newville]

Hi Ava,

OK, thanks - that sounds good.

On Wed, Oct 18, 2023 at 12:12 AM Ava Rajh <ava.rajh at ijs.si> wrote:

> 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 <newville at cars.uchicago.edu>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Differences between Larch and Artemis when
> >       performing FEFF calculations
> > Message-ID:
> >       <
> CA+7ESbrWm5UoBYggLmi+-WZRU6mn4Y_-z1OBVg57pAu4rsXM7w at 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.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 Newville <newville at cars.uchicago.edu> 630-327-7411
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