[Ifeffit] Questions for Artemis fit

[huyanyun at physics.utoronto.ca]

Hi all,

Does Feff take into account of the radius of the each atom when it  
calculates atom-pair distance? I am wondering if the calculated  
atom-pair distance (Reff) in each SS path has already excluded the  
radius size of absorber and scatterer atoms? In the R-space spectra, I  
always have a big peak at R smaller than any of the calculated path  
distances, in other words, I feel there is no possible path  
contributing to this peak.

My goal is trying to understand where the filler atom is in a unit  
cell, so if the above question is 'yes', the true position of the  
filler atoms is very likely to be far away from the site I input in  
the ATOM file ?

Best regards,
Yanyun


Quoting Scott Calvin <scalvin at sarahlawrence.edu>:

> Hi Yanyun,
>
> This topic has been dealt with multiple times on the mailing list.  
> Please search the archive:
>
> http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/
>
> For example, searching for "sites" will give you several discussions  
> of the topic.
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Aug 19, 2014, at 2:49 PM, <huyanyun at physics.utoronto.ca>  
> <huyanyun at physics.utoronto.ca> wrote:
>
>> Hi all,
>>
>> How would you deal with the case that the absorber atoms are occupying
>> two different crystallography sites? Should I still use/guess the same
>> 'S02' for paths calculated from two sites?
>>
>> Best,
>> Yanyun
>>
>>
>> Quoting huyanyun at physics.utoronto.ca:
>>
>>> Hi Scott,
>>>
>>> Thank you for giving me detailed examples. I will go with your
>>> suggestion and try to reduce free parameters.
>>>
>>> Best,
>>> Yanyun
>>> Quoting Scott Calvin <scalvin at sarahlawrence.edu>:
>>>
>>>> Hi Yanyun,
>>>>
>>>> On Aug 19, 2014, at 12:05 PM, huyanyun at physics.utoronto.ca wrote:
>>>>>
>>>>> But my question is, for each path there are a set of Path Parameters,
>>>>> does that mean we have to fit this set of path parameters independent
>>>>> from those used in other paths?  For instance, if I am going to
>>>>> include 30 paths in my fitting, do I need to guess about 150
>>>>> (30*5=150) parameters (except guess the same 'enot' for all paths)?
>>>>
>>>> No. One of the great principles of Ifeffit (and thus Artemis) is
>>>> that the path parameters do not have to be the same as the fit
>>>> parameters.
>>>>
>>>> As a simple example, it's good to start with the model that all
>>>> paths have the same value for E0. So you can guess a single
>>>> parameter and then use that parameter for the E0 for all paths.
>>>>
>>>> As another simple example, a cubic crystal might be modelled as
>>>> having a uniform thermal (or Vegard's law) expansion. Then there
>>>> could be a single guessed parameter indicating the fractional
>>>> expansion (called, for example, alpha) while the delr for each path
>>>> could then be entered as alpha*reff.
>>>>
>>>> Much more complicated constraint schemes are possible, but for fits
>>>> with large number of paths, the number of guessed parameters is
>>>> almost always much much lower than the number of path parameters.
>>>>
>>>>>
>>>>> As shown on the fit Log file, the Correlation value between two fit
>>>>> parameters is the bigger the better, or the smaller the better?
>>>>
>>>> Not necessarily. Correlations are provided to help understand the
>>>> relationship between guessed parameters, but there's nothing
>>>> inherently wrong with a high correlation...the uncertainty
>>>> associated with that relationship is already represented in the
>>>> uncertainties reported with the fit. In other words, it is more
>>>> direct to focus on getting the uncertainties to be lower, rather
>>>> than the correlations.
>>>>
>>>> --Scott Calvin
>>>> Sarah Lawrence College
>>>>
>>>>
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>>>
>>>
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>>
>>
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