Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5

7 Oct 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@millenia.cars.aps.anl.gov wrote:
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Today's Topics:
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 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] More than 256 paths on Mac OS 10.5?
Message-ID: <6DD333D2-F58C-4E55-AB0D-430483EF97F4@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 
To: ifeffit@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: 
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@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 
To: XAFS Analysis using Ifeffit 
Cc: "Dr.Scott.Calvin@gmail.com" 
Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths
Message-ID: 
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
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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 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths
  (Scott	Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
Message-ID: 
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 
To: ifeffit 
Subject: [Ifeffit] Multiple scattering paths in fitting
Message-ID:

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.