On Friday 09 January 2009 12:34:01 pm Hashem Stietiya wrote:
I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr?
Hashem, There are two possible answers to your question -- the one you are probably looking for and the one that involves me getting up on my soapbox and lecturing. So.... in that order.... You are probably looking to use restraints. If you search the mailing list archives, you'll find some discussion of that topic. You might also find my explanation in this presentation useful: http://xafs.org/Workshops/APS2008?action=AttachFile&do=get&target=Ravel_Advanced.pdf In short, a restraint is a term that you add to the evaluation of the fitting metric which imposes a penalty on the fit when a parameter wanders away from a value that you have prior knowledge about. The next to last slide in that talk shows a screen shot that should make it clear how they get implemented in Artemis. I would caution you, though, against disregarding a fit that results in unphysical parameter values. That a parameter takes on an unphysical value is usually telling you something about your fitting model. If your delta R parameter is really large, perhaps your starting structure is not a very good representation of your real sample. If your sigma^2 parameter is negative, perhaps you have too much structural disorder in your model and the fit is compensating by inflating those paths with a negative sigma^2. Ifeffit and Artemis do not report things like negative sigma^2 parameters just to mess with your head. (Although that *would* be fun...!) The parameters reported are the parameters required to minimize the fit. Ifeffit doesn't know anything about science -- it just does what it can to make the fitting metric as small as possible. It's kinda stupid that way and Artemis isn't any smarter. Fortunately, _you_ are smarter. When a physically unreasonable parameter is reported, you can examine the assumptions made in your fitting model. If parameters are coming back in an unphysical state, it is almost certain that there is something unphysical about your fitting model. Thus, wonky values for the parameters of a bad fit are full of information that you need to interpret and use to refine your fitting model. Hope that helps, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/