[Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
Han Sen Soo
hssoo at lbl.gov
Thu Oct 7 13:21:43 CDT 2010
Hello Shelly and Scott,
Thank you both again for your suggestions. It seems that after making the MS path more linear in my cif file, the FEFF calculation increased the amplitude value of the path and dramatically increased the sigma^2 value in the fit. Strangely, the fit values for the distances remain pretty much the same and the statistical figures of merit have improved, but the sigma^2 values are now much more reasonable (about twice as large, but I have a more triangular than linear model, so you're right Scott, your explanation does not work for my case). I guess the increased amplitude made a difference?
Hello Abhijeet, I used a rudimentary geometrical way to get my bond angles. For a 3 atom triangle M-O-A, the effective MS path length (R_MOA) is twice the sum of the individual bond distances. So if you have the R_MOA, R_MO, and R_MA distances from your fits, you can use R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides of the triangle, you can use the geometrical Cosine Rule to get any of the 3 bond angles. This is just geometry so I don't know what the error propagation for this would be.
Thanks again everyone!
han sen
On Oct 7, 2010, at 6:36 AM, ifeffit-request at millenia.cars.aps.anl.gov wrote:
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> Today's Topics:
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> 1. Re: More than 256 paths on Mac OS 10.5? (Scott Calvin)
> 2. Re: sigma^2 values for multiple scattering paths (Scott
> Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Han Sen Soo)
> 3. Re: sigma^2 values for multiple scattering paths (Scott
> Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Scott Calvin)
> 4. Multiple scattering paths in fitting (Abhijeet Gaur)
> 5. schemes for delr and sigma2 for multiple scattering paths
> (Jatinkumar Rana)
> 6. Re: Multiple scattering paths in fitting (Frenkel, Anatoly)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 6 Oct 2010 10:01:27 -0700
> From: Scott Calvin <dr.scott.calvin at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] More than 256 paths on Mac OS 10.5?
> Message-ID: <6DD333D2-F58C-4E55-AB0D-430483EF97F4 at gmail.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Thanks, Matt!
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Oct 6, 2010, at 9:08 AM, Matt Newville wrote:
>
>> Hi Scott,
>>
>>
>> The attached zip file has dynamic libraries (and static program
>> ifeffit) built with 1024 paths and feff files. It contains the files
>>
>> lib/libifeffit.dylib
>> lib/libifeffit.so
>> bin/ifeffit
>>
>> The zip file should be unzipped under
>> /Applications/iXAFS.app/Contents/Resources/local/
>> to overwrite the above files. You should be able to open the iXAFS
>> Shell and type
>>
>> cd /Applications/iXAFS.app/Contents/Resources/local/
>> unzip ~/Downloads/iXAFS_1024paths.zip
>> athena
>>
>>
>> Athena and Artemis will automatically use the new dynamic library.
>>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 6 Oct 2010 10:36:25 -0700
> From: Han Sen Soo <hssoo at lbl.gov>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths
> (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
> Message-ID: <BC995EC7-578E-4256-9D62-DE5E73831893 at lbl.gov>
> Content-Type: text/plain; charset=us-ascii
>
> Hello Scott,
> Just to make sure I understand what you mean, are you saying that in your 3 atom system, the S1 and S2 atoms have relatively fixed locations but A may have large vibrational amplitudes in the A-S1 and A-S2 directions? So the round-trip 3 atom MS path has a small sigma^2 value since the variation in the A-S1-S2-A path is dictated by the more or less fixed S1 and S2 end-points (with minimal perpendicular contribution), whereas the 2 individual SS paths have large sigma^2 value due to the large A-S vibrations?
>
> I tried setting the sigma^2 value to a reasonable number for the MS path and it appears to increase the R factor slightly and tries to maximize the floating degeneracy I set (with a restrain to be physically reasonable based on my model). It does not look as good but at least it seems more plausible. I will try out Shelly's suggestions to see if they work too. I guess what I wanted to find out is whether the model I included is telling me that something is terribly wrong.
>
> Thank you all again for your responses!
> han sen
>
> On Oct 6, 2010, at 10:00 AM, ifeffit-request at millenia.cars.aps.anl.gov wrote:
>
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>> Today's Topics:
>>
>> 1. Re: sigma^2 values for multiple scattering paths (Scott Calvin)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 6 Oct 2010 09:39:49 -0700
>> From: Scott Calvin <dr.scott.calvin at gmail.com>
>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>> Cc: "Dr.Scott.Calvin at gmail.com" <Dr.Scott.Calvin at gmail.com>
>> Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths
>> Message-ID: <AB39966C-893D-4947-BED2-A26FC6534315 at gmail.edu>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> Although I agree with the main points that Bruce makes, I do want to
>> comment on one piece:
>>
>> On Oct 6, 2010, at 7:03 AM, Bruce Ravel wrote:
>>
>>> .
>>>
>>> In no case can I understand a physical explanation for the the MS
>>> sigma^2 being smaller than for the SS.
>>
>> Actually, there is a physical situation where something like that can
>> occur, although it sounds like it's not the one that Han Sen has.
>>
>> Consider an absorbing atom rattling around in a relatively fixed cage
>> or lattice. And then consider a linear (or near-linear) arrangement:
>>
>> S1 -- A -- S2
>>
>> One multiple scattering path that can sometimes have a sizable
>> contribution is A --> S1 --> S2 --> A. This path will have a sigma^2
>> that is a bit larger than the single-scattering path S1 --> S2 --> S1,
>> because of the perpendicular component of the motion of A.
>>
>> But it's quite frequently the case that S1 --> S2 --> S1 is not
>> modeled in a fit, because the S edge is not measured.
>>
>> On the other hand, the single scattering paths A --> S1 --> A and A --
>>> S2 --> A ARE included in the fit. Those two have high sigma^2's,
>> because A is rattling around a lot.
>>
>> Under that circumstance, a multiple-scattering path included in the
>> fit may indeed have a lower sigma^2 than the single-scattering paths
>> included in the fit.
>>
>> The moral, of course, is that it's not hard to think physically about
>> what sigma^2 means for a multiple scattering path. If one appears to
>> have an "unphysically" small sigma2, then the explanation is probably
>> one of the ones given by Bruce or Shelly.
>>
>> One more thought on this. How much does it change your fit, Han Sen,
>> if you set the sigma^2 for the multiple-scattering path to some
>> "reasonable" value. If the scientific information you want from your
>> fit is not sensitive to exactly what sigma^2 the MS path gets, and is
>> not significantly different when given a "reasonable" value than when
>> allowed to find its "best-fit" value, then there's probably no need to
>> resolve the issue. In my experience, this is often the case with low-
>> amplitude MS paths: the fit is improved by their inclusion, but may
>> not be particularly sensitive to the details of their path parameters.
>>
>> --Scott Calvin
>> Sarah Lawrence College
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
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>>
>>
>> End of Ifeffit Digest, Vol 92, Issue 4
>> **************************************
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 6 Oct 2010 10:51:59 -0700
> From: Scott Calvin <dr.scott.calvin at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths
> (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
> Message-ID: <CBC93BEC-49EA-40CB-B700-4CD1E421D1A5 at gmail.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On Oct 6, 2010, at 10:41 AM, Han Sen Soo wrote:
>
>> Hello Scott,
>> Just to make sure I understand what you mean, are you saying that in
>> your 3 atom system, the S1 and S2 atoms have relatively fixed
>> locations but A may have large vibrational amplitudes in the A-S1
>> and A-S2 directions? So the round-trip 3 atom MS path has a small
>> sigma^2 value since the variation in the A-S1-S2-A path is dictated
>> by the more or less fixed S1 and S2 end-points (with minimal
>> perpendicular contribution), whereas the 2 individual SS paths have
>> large sigma^2 value due to the large A-S vibrations?
>>
>
> Yes--you explained it far better than I did. :)
>
> --Scott Calvin
> Sarah Lawrence College
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 7 Oct 2010 12:51:01 +0530
> From: Abhijeet Gaur <abhijeetgaur9 at gmail.com>
> To: ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Multiple scattering paths in fitting
> Message-ID:
> <AANLkTim8q3nucice-cVa-F2jpqCR=abDbkKk=AJj2X87 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
> I just read the discussion on "sigma^2 values for multiple
> scattering paths ". One thing is clear that inclusion of multiple scattering
> path may increase the quality of fit. I have also some questions related to
> MS paths.
> 1. What else information can be obtained from multiple scattering paths?
> 2. What values of delr should be relevant for MS paths.
> 3. How can we determine the bond-angles from multiple-sacttering paths using
> Artemis fitting method.
>
> With thanks
> Abhijeet Gaur
> School of Studies in Physics
> Vikram University, Ujjain.
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 5
> Date: Thu, 07 Oct 2010 12:05:10 +0200
> From: Jatinkumar Rana <jatinkumar.rana at helmholtz-berlin.de>
> To: Ifeffit users <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] schemes for delr and sigma2 for multiple scattering
> paths
> Message-ID: <4CAD9B56.1070107 at helmholtz-berlin.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>
> It is reasonable to assign a constant fraction by which unit cell
> expands at a given temperature of XAFS measuremnt and so the variation
> in the path lengths for every single scattering paths could be assigned
> as delr = alpha * Reff. Similarly, one can assign sigma2 value for each
> single scattering path depending on both type of scatterer and its
> distance from the absorbing atom.
>
> Now coming to multiple scattering paths, Sigma2 for multiple scattering
> paths can be constrained based on the sigma2 of related single
> scattering paths and a definite path-geometry-dependent scheme
> (Triangle, collinear, reversed etc.) could be applied.
>
> Is there any such scheme for delr of multiple scattering paths ? or we
> can simply assume that all paths (single scattering and multiple
> scattering) undergo uniform expansion by a factor alpha.
>
> Thank you so much in advance for your valuable time...
>
> With best regards,
> Jatin Rana
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 7 Oct 2010 09:35:26 -0400
> From: "Frenkel, Anatoly" <frenkel at bnl.gov>
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Multiple scattering paths in fitting
> Message-ID:
> <CCBF39F82283424BBB90EA208CD9DE80014175C6 at exchangemb5.bnl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> For bond angles, this google search would be helpful:
>
> buckling angle multiple scattering xafs
>
> Anatoly
>
>
> ________________________________
>
> From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of Abhijeet Gaur
> Sent: Thu 10/7/2010 3:21 AM
> To: ifeffit
> Subject: [Ifeffit] Multiple scattering paths in fitting
>
>
> Hi all,
> I just read the discussion on "sigma^2 values for multiple scattering paths ". One thing is clear that inclusion of multiple scattering path may increase the quality of fit. I have also some questions related to MS paths.
> 1. What else information can be obtained from multiple scattering paths?
> 2. What values of delr should be relevant for MS paths.
> 3. How can we determine the bond-angles from multiple-sacttering paths using Artemis fitting method.
>
> With thanks
> Abhijeet Gaur
> School of Studies in Physics
> Vikram University, Ujjain.
> -------------- next part --------------
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> ------------------------------
>
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> End of Ifeffit Digest, Vol 92, Issue 5
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