[Ifeffit] Question about fuzzy degeneracy

[Bruce Ravel]

The tool for computing fuzzy degeneracy over sites that is currently 
implemented in Artemis is specifically for multiple sites occupied by 
the same atomic species in a crystal structure.

As I stated in the paper, the same concept can be implemented by looping 
over positions in any kind of structural data -- your MD simulation 
would be a fine example.  That, however, is not implemented at this time 
in Artemis.

If you are so motivated to implement your solution in Larch, then I 
would recommend that you adopt the same strategy I described in the 
paper.  Bin your paths together, count them up and compute the average 
distance, write out a paths.dat file describing a path at the average 
distance, run the genfmt part of feff6 using your bespoke paths.dat 
file, and use that result.

Or skip the binning step and write out a paths.dat file that generates 
all the paths for all the absorber-scatterer pairs in your MD 
simulation.  Whatever works best for you.....

B


On 06/09/2016 10:32 AM, Mirko wrote:
> Hey,
>
> I am quite new to EXAFS and therefore very glad about this mailing list,
> it helps a lot.
>
> My question is about the fuzzy degeneracy mentioned in the paper "Path
> degeneracy and EXAFS analysis of disordered materials" (Ravel, B. J
> Synchrotron Radiat. <http://www.ncbi.nlm.nih.gov/pubmed/25343794>2014
> Nov;21(Pt 6):1269-74.)
>
> I investigate disordered systems like aqueous salt solutions and would
> like to use the method on my FEFF calculation. However, I obtained my
> structure for the FEFF calculation from a MD-Simulation and would like
> to average over several hundreds of FEFF calculations. To handle this
> amount of data I use LARCH, which doesn’t have the feature to degenerate
> similarpaths to one. I would like to use the method by myself to
> degenerate the first coordination shell of my oxygen atoms around the salt.
>
> How do you merge the FEFF parameters from each scattering paths after
> they are grouped together in a bin with the extended pathfinder
> algorithm (I think, you can’t just make an average of for example the
> phase shift or the mean free path … right?)
>
> Best regards and thanks a lot!
>
> Mirko
>
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-- 
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/