[Ifeffit] Questions for Artemis fit

[Scott Calvin]

Hi Yanyun,

The shift observed in R-space is due to the effect of the potential of the absorbing and scattering atoms. 

You are asking a series of questions that, while thoughtful, are covered in basic tutorials and XAFS textbooks. I suggest you search for introductions to XAFS analysis, many of which are freely available and which come in many forms (videos, tutorial files, wikis, PowerPoints, chapters/books, etc.) and work through one or more of them.

Beginners are encouraged to use this list, but beginners and advanced users alike are also urged to see if the answer to their questions is readily and clearly available elsewhere first.

--Scott Calvin
Sarah Lawrence College

On Aug 20, 2014, at 1:11 AM, huyanyun at physics.utoronto.ca wrote:

> 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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