[Ifeffit] Ifeffit Digest, Vol 248, Issue 2

[bikov at phys.uni-sofia.bg]

Dear Edmund Welter, Dear Matt Newville,

Thank you for the answers and very informative explanations.

With best regards,
Konstantin

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> Today's Topics:
>
>    1. Fitting mechanism of Artemis (bikov at 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: bikov at phys.uni-sofia.bg
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Fitting mechanism of Artemis
> Message-ID:
> 	<1936f567bb85f017cc9aa404a2a49fda.squirrel at 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.welter at desy.de>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Fitting mechanism of Artemis
> Message-ID: <1ac7d9c6-e37f-2b17-82c5-bb382af973ba at 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, bikov at 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
>>
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> ------------------------------
>
> Message: 3
> Date: Fri, 6 Oct 2023 11:41:17 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Fitting mechanism of Artemis
> Message-ID:
> 	<CA+7ESbpV-FtSVhjEpoTdV72ntx4wAibjZHqZdeAq7ShpSZZiiw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Konstantin,
>
>
>
> On Fri, Oct 6, 2023 at 3:11?AM <bikov at 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
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> End of Ifeffit Digest, Vol 248, Issue 2
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>