Thanks Bruce for the quick response!I understood perfectly how to get from table 1 to table 2.I'm still a little lost on how to use that in Artemis.You said: "Artemis has compressed the three Feff calculations you would normally have to do into a single fuzzily degenerate path list."That's the thing I don't know how to do.How do I use Artemis to get the scattering paths listed in table 2 (Reff and degeneracy)What would be the step by step procedure in Artemis to get those paths so I can move them to the Path page?Thanks!Juan El Viernes, 19 de junio, 2015 14:44:47, Bruce Ravel escribió: On 06/19/2015 12:08 PM, Juan Manuel Conde Garrido wrote:

I'm somewhat new to EXAFS and this is my first question for the Ifeffit mailing list (which is a great source of information by the way). I was reading the excellent paper: "Path degeneracy and EXAFS analysis of disordered materials" and I have a "simple" question to ask: How do I get from table 1 to table 2?

Hi Juan, The easiest way to understand that is probably to run Atoms a few times.  Use this CIF file https://raw.githubusercontent.com/bruceravel/demeter/master/examples/recipes... and look at the clusters that come from each of the three Ti sites. You will find the nearest neighbor distances and degeneracies reported in Table 1. As I explain in the text near table one, the three Ti sites are not equally represented in the unit cell.  1/2 of the Ti atoms in the unit cell are Ti1.  Ti2 and Ti3 each represent 1/4 of the Ti population. The first column in Table 2 condenses the 12 near-neighbor distances given in Table 1 by taking into account the representation of each Ti site in the unit cell and by grouping paths with similar lengths into bins of a certain width.  The distances shown in the first column of table 2 are the weighted average of the paths that have been binned together.  The degeneracies reflect the proportional representation of each Ti site in the unit cell. The math for the paths at 2.050 and 2.498 is trivial.  The Ti2 site is the only one that contributes scatterers at those long distances.  The Ti2 site has two scatterers at, say, 2.050, but the Ti2 site only accounts for 1/4 of all the Ti scatterers.  2*1/4 = 1/2 --> row 3 of column 1 of Table 2.  The math for the two shorter distances is hardly more complicated.  I am sure you can work it out for yourself. I did not tablate the equivalent of Table 1 for the other kinds of scatterers, but if you let Artemis expand the zirconolite CIF file into feff.inp files for each of the three Ti sites, you can easily make the equivalent of Table 1 for each of the other scatterers.

Specifically, I think I know how to use fuzzy degeneracy in Artemis for the paths in one FEFF calculation, but in this case there are 3 sites for Ti, and that means 3 FEFF calculations (rigth?).

Sort of.  The magic cooked into Artemis manages the Feff calculations in a way that may be a bit surprising to you.  Artemis has Feff compute the scattering potentials for each of the equivalent sites. It then checks the muffin tin radii of the absorber from each Feff calculation and chooses the one whose absorber muffin tin radius is the median of all the calculations.  Artemis saves the file with those scsattering phase shifts and discards the others. Artemis then runs its own implementation of the pathfinder on each of the unique sites.  In the case of zirconolite, the pathfinder is run on each of the three Ti sites.  The paths found are all tossed onto a single heap (in the sense of http://dx.doi.org/10.1103/PhysRevB.52.2995) with degeneracies that are weighted by the population of the cite in the unit cell.  The degeneracy checker then runs, but with fuzzy degeneracy.  That is, paths with similar length are grouped together into bins of some width and presented to the user at their average distance. When one of these "fuzzy over sites" paths is used in a fitting model, Artemis uses the scattering functions from the Feff calculation it saved and the geometry of the fuzzily degenerate path to generate the feffNNNN.dat file. The idea of all of this machinery is to simplify the interaction with a structure having the sort of local disorder that we see in zirconolite.  My assertion is that the EXAFS data cannot possibly resolve all the details of the Ti-O partial pair distribution function.  This "fuzzy degeneracy over site" machinery provides a simplified way of approximating the contribution from a complex, highly non-Gaussian partial pair distribution.

So how do I use fuzzy degeneracy for paths from different FEFF calculations? And by the way, is it right if I imagine the material as having only 1 "fuzzy"/average site for Ti?

I don't think I quite understand this question, but I'll give it a shot. My intent is that you use fuzzy degeneracy over sites in the exact same way you usually use Feff in Artemis.  Artemis has compressed the three Feff calculations you would normally have to do into a single fuzzily degenerate path list. To say that another way, without "fuzzy degeneracy over sites", you would have to run (in the case of zirconolite) three Feff calculations then somehow figure out how to include all the possible Ti-O scatterers into your fitting model.  Any sensible approach would likely select one or a few representative O scatterers.  The parameters of the EXAFS equation would  then be parameterized to attempt to capture the full complexity of the Ti-O partial pair distribution.  "Fuzzy degeneracy over sites" is a tool that attempts to automate that tedious chore. HTH, B --   Bruce Ravel  ------------------------------------ bravel@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/