Hello, You said you averaged in E(k)? Is this reciprocal space? Are calculating XANES or EXAFS spectra with Feff? You said you would transform the data to real space so I assume it is EXAFS. I don’t think there is flattened mode in EXAFS. If you clarify what you are calculating that might help. Are you comparing intensities between theory and experimental? The intensities would be very different given that there was no noise in the calculations. Sorry I don’t have answers just questions. Chris Sent from my iPhone

On Jan 28, 2019, at 3:57 AM, FonsPaul wrote:

Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions! _______________________________________________ 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

I thought I would add that perhaps the only way forward is to average the already normalized chi(k) spectra that feff also outputs, however, it still would be nice to be able to see simulated that that can be compared to experimental E(k). From: Ifeffit on behalf of FonsPaul Reply-To: XAFS Analysis using Ifeffit Date: Tuesday, January 29, 2019 8:13 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting flattened feffit simulation results Thank you for reply. I am calculating structures (aka coordinates that are used for input to feff) in DFT and ultimately I simply wish to transform the k-space plot to r-space. However, I would like to plot the E(k) data for “cosmetic” reasons and the flattening is an issue there. An improper “pre-edge” subtraction will also affect the relative intensities of the Χ(R)(r) data as well so I guess my request is not entirely for cosmetic reasons. Presumably the E(k) data in feff is already normalized (I didn’t check). From: Ifeffit on behalf of Chris Patridge Reply-To: XAFS Analysis using Ifeffit Date: Monday, January 28, 2019 20:18 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting flattened feffit simulation results Hello, You said you averaged in E(k)? Is this reciprocal space? Are calculating XANES or EXAFS spectra with Feff? You said you would transform the data to real space so I assume it is EXAFS. I don’t think there is flattened mode in EXAFS. If you clarify what you are calculating that might help. Are you comparing intensities between theory and experimental? The intensities would be very different given that there was no noise in the calculations. Sorry I don’t have answers just questions. Chris Sent from my iPhone On Jan 28, 2019, at 3:57 AM, FonsPaul mailto:paul-fons@aist.go.jp> wrote: Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions! _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto: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

Hi Matt, I think the “turn of the pre-edge baseline” option would be useful in cases like mine where one would like to plot the “experimental” E(k) as well as its Fourier transform. If it’s easy to do, why not offer a checkbox to run off the pre-edge subtraction? In any case, thanks for thinking about the problem. Cheers, Paul From: Ifeffit on behalf of Matt Newville Reply-To: XAFS Analysis using Ifeffit Date: Tuesday, January 29, 2019 13:21 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Plotting flattened feffit simulation results Hi Paul, On Mon, Jan 28, 2019 at 2:57 AM FonsPaul mailto:paul-fons@aist.go.jp> wrote: Hi All, I have a rather simple question and a reply for either Larch or athena would be welcome. I have calculated a number of structures using DFT and have run feff on each of the appropriate sites and have then averaged the E(k) results. I have no problem reading in the data to athena, however, due to the lack of a pre-edge baseline, it is typically not possible to choose a reasonable “pre-edge” baseline so that I can plot the data for the different structures in “flattened” mode. The “post-edge” baseline works very well with the default values (as there is literally no noise in the spectra). My question is how can I induce athena to plot the E(k) data for the different structures in “flattened” mode. Ultimately, I will end up taking a Fourier transform into real space so I would also like to have a proper baseline so I can compare intensities as well. In effect, the data from feff9 is already normalized. Thanks for any suggestions! Sorry for the trouble. Perhaps we should add a routine that adds a more realistic preedge to the Feff XANES calculations, so that the "normal" pre-edge and normalization steps work better? I would think that simply add a segment of 0s for value below the main edge might wok well enough..... That would be easy enough to do.... --Matt