On 05/31/2016 01:23 PM, sb2c08@gmail.com wrote:
To be clearer, can I make the excited state and ground state models in Artemis, take the data and difference (which can be done in Athena) and use that as a direct comparison, perhaps as you would with XANES data? I understand my data but I do not understand the best method to try get at least a first shell fit from the EXAFS region, collected by taking the difference of the ground state from the excited state, and can this be done in anyway via Artemis through some data analysis.
While it seems like Artemis specifically wants traditional EXAFS data as its input, that's not really the case. It just wants something wiggly that can be Fourier transformed. While it seems like Artemis wants a full Feff calculation and all the path files that come from it with all the degeneracies that Feff thinks it has, that also is not really the case. I don't know what your data are or what they look like (you haven't told us), so I will make up a scenario off the top of my head. Hopefully that will still be instructive. Suppose that our ground state is a pure metal -- say iron metal. Iron metal has a near neighbor at about 2.5A. Suppose that our secondary state includes some iron oxide -- that has a neighbor at about 1.9A and a correspond peak at a much shorter distance. Suppose we can guess the amount of pure metal in the secondary state. Then we could do some simple arithmetic to isolate (approximately!) the oxide contribution. This will resemble an iron oxide standard, but with much smaller amplitude. Seems to me that this difference spectrum could be fit in Artemis by running Feff on the oxide, parameterizing the fit much like a conventional spectrum, but giving the model enough freedom to have a much smaller amplitude. That is, you cannot force the fit to have an S02 of around 0.9 -- like a normal fit -- and the full coordination number of the normal oxide. Something in the fitting model must be introduced to allow the amplitude to be small enough to fit the difference data properly. You, then, need to have a way of interpreting this much smaller amplitude in a way that makes sense for the problem at hand. To say all that another way ... your difference data has Fourier components ... Feff provides Fourier components ... you supply a model (and an interpretation!) that fits Feff's Fourier components to the Fourier components in your data. If your data can be described by Feff, Artemis can do the describing. 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/