[Ifeffit] Questions for Artemis fit
huyanyun at physics.utoronto.ca
huyanyun at physics.utoronto.ca
Tue Aug 19 09:55:56 CDT 2014
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 <newville at cars.uchicago.edu>:
> On Mon, Aug 18, 2014 at 7:45 PM, 이국승 <lks3006 at postech.ac.kr> wrote:
>
>> 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.
>
>> 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.
>
>> 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?
>
>> 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.
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