[Ifeffit] sigma^2 values for multiple scattering paths (Shelly Kelly/Bruce Ravel); Re: Ifeffit Digest, Vol 92, Issue 2

Wed Oct 6 10:44:27 CDT 2010

Hello Shelly and Bruce,
Thank you both for replying. I was wondering if there was some obvious reason that I missed. But you're both right, I think I will try to re-orientate the paths to make them more linear and then try the Debye and Einstein models. I may be back for more before I conclude that its bad data quality... Thank you again!
han sen

On Oct 6, 2010, at 7:02 AM, ifeffit-request at millenia.cars.aps.anl.gov wrote:

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> Today's Topics:
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>   1. Re: Ifeffit Digest, Vol 92, Issue 1 (Elsa Sileo)
>   2. sigma^2 values for multiple scattering paths (Han Sen Soo)
>   3. More than 256 paths on Mac OS 10.5? (Scott Calvin)
>   4. Re: sigma^2 values for multiple scattering paths (Shelly Kelly)
>   5. Re: sigma^2 values for multiple scattering paths (Bruce Ravel)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 5 Oct 2010 20:58:03 +0000 (GMT)
> From: Elsa Sileo <e_sileo at yahoo.es>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 92, Issue 1
> Message-ID: <532560.26796.qm at web27807.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Thanks Shelly,
> ?
> now atoms is running beautifully!!!
> ?
> Elsa
> ?
> 
> --- El s?b, 2/10/10, ifeffit-request at millenia.cars.aps.anl.gov <ifeffit-request at millenia.cars.aps.anl.gov> escribi?:
> 
> 
> De: ifeffit-request at millenia.cars.aps.anl.gov <ifeffit-request at millenia.cars.aps.anl.gov>
> Asunto: Ifeffit Digest, Vol 92, Issue 1
> Para: ifeffit at millenia.cars.aps.anl.gov
> Fecha: s?bado, 2 de octubre, 2010 14:00
> 
> 
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> Today's Topics:
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> ???1. Incorrect distances obtaines from Scorodite CIF file (Elsa Sileo)
> ???2. Re: Incorrect distances obtaines from Scorodite CIF file
> ? ? ? (Shelly Kelly)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 1 Oct 2010 17:06:28 +0000 (GMT)
> From: Elsa Sileo <e_sileo at yahoo.es>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Incorrect distances obtaines from Scorodite CIF
> ??? file
> Message-ID: <957578.81901.qm at web27807.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Shelly, thanks?for your answer to the Eo aligment.
> Now I am attaching the the scorodite CIF?file because I get incorrect As-Fe distances when I use it to obtain the feff path.
> I hope someone has the answer,
> ?
> Elsa
> ?
> 
> 
> ? ? ? 
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> ------------------------------
> 
> Message: 2
> Date: Fri, 1 Oct 2010 15:39:16 -0500
> From: Shelly Kelly <dr.sdkelly at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Incorrect distances obtaines from Scorodite CIF
> ??? file
> Message-ID:
> ??? <AANLkTinissMLx8GE6vM4LrdvK9X=n-qsnMe4u8k+m-vn at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Elsa:
> 
> If you open the scorodit.cif file you will find that the space group is "P c
> a b". When you read the file into Artemis the space group gets scrambled
> up.? If you fix the space group on the atoms page, it will work.
> 
> Shelly
> 
> On Fri, Oct 1, 2010 at 12:06 PM, Elsa Sileo <e_sileo at yahoo.es> wrote:
> 
>> Dear Shelly, thanks for your answer to the Eo aligment.
>> Now I am attaching the the scorodite CIF file because I get incorrect As-Fe
>> distances when I use it to obtain the feff path.
>> I hope someone has the answer,
>> 
>> Elsa
>> 
>> 
>> 
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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> ------------------------------
> 
> Message: 2
> Date: Tue, 5 Oct 2010 22:26:55 -0700
> From: Han Sen Soo <hssoo at lbl.gov>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] sigma^2 values for multiple scattering paths
> Message-ID: <C2181CEC-4451-47DB-B5D4-1926C3212752 at lbl.gov>
> Content-Type: text/plain; charset=us-ascii
> 
> Hello,
> I briefly read through the FAQ about this but I'm not sure if it answers my question. Are there situations where the sigma^2 for a multiple scattering path can be smaller than the direct paths? So small that they're on the order of 0.001-0.003 for a degeneracy of 12 such paths?
> I'm working on a fitting model that does not work well with additional shells but it looks almost perfect with a multiple scattering path included. I'm skeptical however, because of the small sigma^2 values. I am also not discounting the fact that the data quality may be poor. But I would appreciate any physical reasons for small sigma^2 values. Thanks!
> han sen
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 5 Oct 2010 17:28:02 -0700
> From: Scott Calvin <dr.scott.calvin at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] More than 256 paths on Mac OS 10.5?
> Message-ID: <E766085E-4695-44CD-A548-9B2B62DA7775 at gmail.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> Hi all,
> 
> Do any of you have a version of Ifeffit compiled for Mac OS 10.5 that  
> allows more than 256 paths?
> 
> --Scott Calvin
> Sarah Lawrence College
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 6 Oct 2010 09:02:21 -0500
> From: Shelly Kelly <dr.sdkelly 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
> Message-ID:
> 	<AANLkTimtGEaZknmeydZopnKihh0Cax5GitjRYXbYCdaY at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Han Sen:
> 
> I agree that the small sigma2 values for the MS paths is suspect. The
> data is saying that it wants more amplitude from these paths than is
> physically possible. One way to increase the amplitude of the paths is
> to make the scattering angle closer to 180deg for a linear path.  It
> is a bit tedious to edit the feffit input file to get that to run, but
> can be done with a bit of geometry.
> 
> This will not work for a triangle MS path. In that case I would look
> for additional contribution from other MS or SS paths at the same
> distance.
> 
> Another way to force sigma2 to be larger would be to use a Debye or
> Einstein Model to model both the SS and MS path.  That will make
> sigma2 for both of them at least reasonable. Although the fit will not
> be as perfect.
> 
> HTH,
> Shelly
> 
> On Wed, Oct 6, 2010 at 12:26 AM, Han Sen Soo <hssoo at lbl.gov> wrote:
>> Hello,
>> I briefly read through the FAQ about this but I'm not sure if it answers my question. Are there situations where the sigma^2 for a multiple scattering path can be smaller than the direct paths? So small that they're on the order of 0.001-0.003 for a degeneracy of 12 such paths?
>> I'm working on a fitting model that does not work well with additional shells but it looks almost perfect with a multiple scattering path included. I'm skeptical however, because of the small sigma^2 values. I am also not discounting the fact that the data quality may be poor. But I would appreciate any physical reasons for small sigma^2 values. Thanks!
>> han sen
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Wed, 6 Oct 2010 10:02:24 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths
> Message-ID: <201010061002.24587.bravel at bnl.gov>
> Content-Type: Text/Plain;  charset="iso-8859-1"
> 
> On Wednesday 06 October 2010 01:26:55 am Han Sen Soo wrote:
>> Hello,
>> I briefly read through the FAQ about this but I'm not sure if it answers my
>> question. Are there situations where the sigma^2 for a multiple scattering
>> path can be smaller than the direct paths? So small that they're on the
>> order of 0.001-0.003 for a degeneracy of 12 such paths? I'm working on a
>> fitting model that does not work well with additional shells but it looks
>> almost perfect with a multiple scattering path included. I'm skeptical
>> however, because of the small sigma^2 values. I am also not discounting
>> the fact that the data quality may be poor. But I would appreciate any
>> physical reasons for small sigma^2 values. Thanks! han sen
> 
> Han Sen,
> 
> It is always useful to remember the physical meanings of the
> parameters use in the EXAFS equation.  sigma^2 is a mean square
> variation in the distance between the absorber and a scatterer.
> 
> Suppose we have this configuration:
> 
>  X------O------Y
> 
> that is, absorber X, scatterer Y and a colinear O atom in between.
> 
> The path length for the path X-Y-X is the same as for X-O-Y-X and for
> X-O-Y-O-X.  If we just consider thermal motion of the atoms along that
> axis, then the mean square variation in paths lengths for those three
> paths must also me the same.  That's neither deep nor complicated --
> its just geometry.  
> 
> The argument in the last paragraph neglected the prospect of the O
> atom experiencing thermal motion perpendicular to that axis.  That
> effect means that 
> 
>   sigma^2(X-O-Y-O-X) > sigma^2(X-O-Y-X) > sigma^2(X-Y-X)
> 
> A common approximation made in data analysis is that this perpendiular
> effect is small compared to the uncertainties in sigma^2 and so those
> three sigma^2 values are constrained to be the same.
> 
> In no case can I understand a physical explanation for the the MS
> sigma^2 being smaller than for the SS.
> 
> That said, you have a fit and a result.  When you float the MS sigma^2
> it comes out smaller.  I would suggest that is telling you something
> about the fitting problem rather than something about the physics of
> the atomic configuration.
> 
> A smaller sigma^2 means that the contribution from those paths is
> being enhanced.  That might be due to a correlation with an amplitude
> parameter.  It might be due to a data quality problem.  It might be
> due to a mistake in the implementation of your fitting model.
> 
> This sort of thing happens all the time.  I frequently analyze data
> and come up with a curious, unphysical result like this.  It hasn't
> yet meant that I have discovered some wonderous new physics.  Very
> occassionally, it means that I have uncovered a shortcoming in Feff,
> but that is exceedingly rare.  Usually it means that I have a problem
> with my data or I have made a mistake filling in all the boxes in
> Artemis.  
> 
> B
> 
> 
> -- 
> 
> Bruce Ravel  ------------------------------------ bravel at bnl.gov
> 
> National Institute of Standards and Technology
> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
> 
> My homepage:    http://xafs.org/BruceRavel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
> 
> 
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