Re: [Ifeffit] Questions for Artemis fit

Hi Dr. Newville, I had similar situation and questions as with choosing Path Parameters. My goal is to identify the occupancy sites for a doped element in my sample. We have a rough guess of two possible sites, part of the doped atoms are filling a void site of the unit cell, the other part is to substitute an existing atom sites. I was being able to writing two ATOM files and run FEFF twice to calculate all possible PATH. But when I was going to define/guess the parameters ('N','amp', 'enot', 'delr','ss')for EACH path, I totally lost idea how to group all those paths, or how to guess all those five parameters for each path. Of course, I couldn't get a good fit as I don't know how to build the model and to refine parameters in this step. Here I post my understanding of the five parameters: 'N', path degeneracy, or coordination number; 'amp', usually close to 1, but as I have doping elements, I am expecting small partial numbers in some of the 'amp' to adjust for partial occupancy; 'enot', I think it is just the energy shift of your spectra, and as I believe my spectra are well aligned, I will SET 'enot' to zero. 'delr' is the variation of the real atom-atom distances from the calculated ones (I think I need to group paths to refine 'delr' but I don't know what's the criteria to group paths). 'ss' is to consider about the disorder effect and typically I use the Debye model. Let me know if I am wrong in any way. Could you please give me some suggestion how did you get started? I am looking forward to hearing from you. Best regards, Yanyun Quoting Matt Newville :

On Mon, Aug 18, 2014 at 7:45 PM, 이국승 wrote:

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Dr Newville,

Thank you for your reply.

My first question is that I did not find the atoms.inp file in the demeter installer. If that is true, where can I get the atoms.inp file?

You might find what you're looking for at http://cars9.uchicago.edu/~newville/adb/search.html Metallic Au (fcc) is there.

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Anyway, I did copy and paste the atoms.inp file of an old version of Artemis from my colleague's PC. I followed the Artemis intruction video for fitting Au foil data.

Hmm, it seems likely that you missed a step.

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I filled the crystal lattice information, run atoms, and Feff calculation.

Did you import and define a Path after doing this calculation? Did you define Path Parameters and variables for this fit?

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Finally I clicked the Fit button and I got the error message that I attached. Now here is my second question. What can I do to successfully Fit without errors? Do you have any idea from the error message?

It indicates that you have defined variables to refine in the fit ('amp', 'enot', and so forth) but not explained how those variables should alter the EXAFS signal. You'll probably want to use these in the Path Parameters for the first shell Au-Au scattering. But, you are doing the analysis, so the most important thing is that you understand how the variables you are asking to be refined actually effect the EXAFS signal. These error messages are a feature of the program to remind you that you need to understand the model you are using for the EXAFS signal.

So, what do you intend 'amp', 'enot', 'delr', and 'ss' to do? If you don't know, go back and review the tutorial information. The goal is not to get a fit, the goal is to understand what the fit results mean.

Another question (it might seem random, but it is not): what is your fitting range?

--Matt

PS: to be clear, these are not rhetorical questions. If you feel the need to respond, please actually think about and answer all questions above.