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 ------------------------------------------------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
-- Bruce Ravel ------------------------------------ bra...@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/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
