Dear Edmund Welter, Dear Matt Newville, Thank you for the answers and very informative explanations.
With best regards, Konstantin > Send Ifeffit mailing list submissions to > ifeffit@millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-ow...@millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Fitting mechanism of Artemis (bi...@phys.uni-sofia.bg) > 2. Re: Fitting mechanism of Artemis (Edmund Welter) > 3. Re: Fitting mechanism of Artemis (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Oct 2023 11:09:55 +0300 > From: bi...@phys.uni-sofia.bg > To: ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] Fitting mechanism of Artemis > Message-ID: > <1936f567bb85f017cc9aa404a2a49fda.squir...@mail.phys.uni-sofia.bg> > Content-Type: text/plain;charset=utf-8 > > Dear all, > I have a general question regarding the mechanism employed in the fitting > procedures implemented in Artemis. > How exactly is performed a fit? Do we have a fixed > central atom (absorbing/emitting atom) and only the distances to the > neighbors included in the probed pathways are varied, i.e. by varying the > coordinates of the corresponding neighbor atoms, or during > the fitting process Artemis can vary the position of the absorption center > too? Could the procedure be constrained in such a way that the scattering > pathways are adjusted by only varying the coordinates of the central atom? > > With kind regards, > Konstantin Bikov > PhD Student at the Physics Department > of the University of Sofia, Bulgaria > > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Oct 2023 11:05:26 +0200 > From: Edmund Welter <edmund.wel...@desy.de> > To: ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Fitting mechanism of Artemis > Message-ID: <1ac7d9c6-e37f-2b17-82c5-bb382af97...@desy.de> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Dear Konstantin, > > why would you want to do that? If you change the distance between A-B > you the distance between B-A changes by the same amount. If you move the > absorber away from let's say the centre of an octaeder you would split > the (next) nearest neighbours shell into different shells with different > distances. If the differences are large enough and the resolution of > your EXAFS spectrum sufficient you would see more than one (first > neighbours) peak in the FT of your EXAFS spectrum. But that would be > another model that you would feed into FEFF before you start your second > fit. Technically you would fneed to define the position of all atoms in > your model in world-coordinates. So the absorber would no longer be at > 0,0,0. I would guess that this would make the computation and the model > more complex or at least less intuitive. > > Best regards, > > Edmund > > > On 06.10.23 10:09, bi...@phys.uni-sofia.bg wrote: >> Dear all, >> I have a general question regarding the mechanism employed in the >> fitting >> procedures implemented in Artemis. >> How exactly is performed a fit? Do we have a fixed >> central atom (absorbing/emitting atom) and only the distances to the >> neighbors included in the probed pathways are varied, i.e. by varying >> the >> coordinates of the corresponding neighbor atoms, or during >> the fitting process Artemis can vary the position of the absorption >> center >> too? Could the procedure be constrained in such a way that the >> scattering >> pathways are adjusted by only varying the coordinates of the central >> atom? >> >> With kind regards, >> Konstantin Bikov >> PhD Student at the Physics Department >> of the University of Sofia, Bulgaria >> >> _______________________________________________ >> 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 > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Oct 2023 11:41:17 -0500 > From: Matt Newville <newvi...@cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Fitting mechanism of Artemis > Message-ID: > <ca+7esbpv-ftsvhjepotdv72ntx4waibjzhqzdeaq7shpszz...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Konstantin, > > > > On Fri, Oct 6, 2023 at 3:11?AM <bi...@phys.uni-sofia.bg> wrote: > >> Dear all, >> I have a general question regarding the mechanism employed in the >> fitting >> procedures implemented in Artemis. >> How exactly is performed a fit? > > > > That is a pretty open-ended question to be able to answer with precision. > Is the question more about how fitting works in general, or about what is > modeled and allowed to change in the mode for EXAFS? > > There are plenty of writeups and resources on both topics, including > program documentation. > > Do we have a fixed central atom (absorbing/emitting atom) and only the >> distances to the >> neighbors included in the probed pathways are varied, i.e. by varying >> the >> coordinates of the corresponding neighbor atoms, or during >> the fitting process Artemis can vary the position of the absorption >> center >> too? > > > > Within the context of the software here, the answer is sort of that the > central atom is fixed. > > The way we model EXAFS is effectively (more below, as some might object > to > this) as a 1-dimensional problem. Single scattering EXAFS depends only on > the scalar distance between the atoms (or path length for the > photo-electron). Now, some aspects of EXAFS scattering definitely depend > on more than just distance. The Z of the scattering atom definitely has a > large effect. The angle of the X-ray polarization vector with the > three-dimensional bond direction can also have an effect. These are > folded into the scattering amplitude and phase shift. But even the > disorder terms, sigma^2, and so on, are really capturing the disorder in > R, > not the 3-D disorder. > > For sure, multiple-scattering paths will have 3D information baked into > them. With Feff and the way we use it, this 3D info *is* folded into the > scattering amplitudes and phase shifts calculated for a path and all we > really vary is the distribution of path lengths for those paths. > > In 1-D, it does not matter whether the absorber or scatterer moves, the > only thing that matters is the distance. In fact, to the extent that > neighboring atoms move together in the same direction, there is no effect > on the EXAFS -- an atom in a solution or melt will have EXAFS (it might be > weak, but it does not fall to 0 at a phase transition). EXAFS is much > more > sensitive to "optical phonons" (neighboring atoms moving in opposite > direction) than to "acoustic phonons" (neighboring atoms moving in the > same > direction). > > Now, one can take a reverse-monte-carlo approach: calculate a lot of > different local structures, sum the EXAFS for each calculation, and see > which is best. One can also do something sort of in-between: calculate > a > set of "undistorted paths" and one or more sets of "distorted paths" and > then do a linear (or for some multiple-scattering case, quadratic) model > to > combine these. > > > Could the procedure be constrained in such a way that the scattering >> pathways are adjusted by only varying the coordinates of the central >> atom? >> > > Yes. In fact, this has been done several times. If you imagine a metal > ion > (let's say Ti) surrounded by six neighbors (let's say O) in an octahedron, > a common thing to try to model is if that Ti atom moves away from the > center of the octahedron, say in a perovskite-like structure. > > For the simplest case (ie, what I would start with ;)), you could > calculate > the EXAFS with Ti at the center of a perfect octahedron and get 6 > equivalent paths, and add those to give the EXAFS. If the octahedron is > distorted, you might have 2, 3, 4, or 6 paths. Let's go all the way to > "general" 6 paths. Each path would use a different Feff calculation (or > a > copy). You would not be limited to varying the change in each of the six > path lengths (our 'delr' parameter) to have the same delr for all paths. > Instead, you could define 3 new fitting variables, let's say "dx", "dy", > and "dz" for the displacement of the absorbing Ti from the position used > in > the Feff calculation (let's just call that "origin"). > > If you only have "dz", then one path gets shorter by dz, one gets longer > by > dz, and the other four get longer by sqrt(reff*2 + dz**2), where "reff" is > the magic "R used for each path Feff calculation. I'll leave the more > general case for you ;). > > Hope that gets you started, > > --Matt > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20231006/3e5dbf97/attachment.htm> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 > > > ------------------------------ > > End of Ifeffit Digest, Vol 248, Issue 2 > *************************************** > _______________________________________________ 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