Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations
Hi Ava, OK, thanks - that sounds good. On Wed, Oct 18, 2023 at 12:12 AM Ava Rajh 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 > > To: XAFS Analysis using Ifeffit > > 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 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? > &
Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations
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 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations Message-ID: 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 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
Re: [Ifeffit] Differences between Larch and Artemis when performing FEFF calculations
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 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 ___ 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
