Hi Ava, OK, thanks - that sounds good.
On Wed, Oct 18, 2023 at 12:12 AM Ava Rajh <ava.r...@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 <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 > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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