[Ifeffit] amplitude parameter S02 larger than 1
Scott Calvin
scalvin at sarahlawrence.edu
Fri Mar 20 12:51:50 CDT 2015
Hi again,
I'm not sure about your structure overall, but including more distant scattering shells can help reduce that particular correlation, if the data supports it and if you enough confidence in what the lattice looks like to introduce more distant shells in to your model without having to fit lots of new free parameters.
--Scott Calvin
Sarah Lawrence College
> On Mar 20, 2015, at 1:44 PM, huyanyun at physics.utoronto.ca wrote:
>
> Hi Josh and Anatoly,
>
> Thank you for bringing up this point.
>
> I agree that P would be 100% correlated with S02 if we assume both
> sites have the same first-shell distance. In my fit, the correlation
> between the percentage parameter P and S02 is -0.73.
>
> Do you have any good idea on how to break this kind of correlation, or
> alternative way to find the 'true S02' and 'true P'?
>
> Best,
> Yanyun
>
>
> Quoting Joshua Kas <joshua.j.kas at gmail.com>:
>
>> Anatoly makes a very good point, and his example can also be used to show
>> that there could be very large correlation between s02 and your percentage
>> parameter. For example, if you assume that the first shell distances are
>> the same for the two sites, and take Anatoly's example of 4 and 6 nearest
>> neighbors, then your parameter P is 100 percent correlated with s02, i.e.,
>> all it does is change the coordination smoothly from 4 to 6. In a real
>> system this probably won't happen, but the correlation could still be
>> large. Have you looked at it?
>>
>> Josh
>>
>> On Fri, Mar 20, 2015 at 10:00 AM, <ifeffit-request at millenia.cars.aps.anl.gov
>>> wrote:
>>
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>>> Today's Topics:
>>>
>>> 1. Re: amplitude parameter S02 larger than 1 (Anatoly I Frenkel)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Fri, 20 Mar 2015 16:57:02 +0000
>>> From: Anatoly I Frenkel <afrenke2 at yu.edu>
>>> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>>> Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1
>>> Message-ID:
>>> <
>>> 545F89325F51764C902D37B42C9F4D530148FDA88C at YUWEXCPM11.yuad.uds.yu.edu>
>>>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> One possible scenario: If one site has 6 nearest neighbors and the other -
>>> 4, and if you choose the site with 4 neighbors to construct FEFF to model
>>> your EXAFS data; and if you set your degeneracy equal to 4 and make your
>>> amplitude factor as S02*x of one site + S02*(1-x) of another site, then
>>> your S02 will come out larger than it should be because it will compensate
>>> for the fact that you underestimate the degeneracy of the 6-coordinated
>>> site.
>>>
>>> Anatoly
>>>
>>> ________________________________________
>>> From: ifeffit-bounces at millenia.cars.aps.anl.gov [
>>> ifeffit-bounces at millenia.cars.aps.anl.gov] on behalf of
>>> huyanyun at physics.utoronto.ca [huyanyun at physics.utoronto.ca]
>>> Sent: Friday, March 20, 2015 12:04 PM
>>> To: XAFS Analysis using Ifeffit
>>> Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1
>>>
>>> Hi Chris,
>>>
>>> Thank you for your suggestion. But I don't have a standard. Also, I
>>> wonder whether a multiple-site situation could be different from the
>>> normal one-site case with respect to S02.
>>>
>>> Best,
>>> Yanyun
>>> Quoting Chris Patridge <patridge at buffalo.edu>:
>>>
>>>> Hi,
>>>>
>>>> One thing that could be considered is transferring the SO2 factor
>>>> from a reliable source such as a standard and then use that value in
>>>> the fit. Chemical transferability of SO2 to similar systems is often
>>>> acceptable. You could also try constraining the value in the fit as
>>>> well. SO2 and Debye are also correlated so this may also affect the
>>>> value.
>>>>
>>>> Hope that helps,
>>>>
>>>> Chris
>>>>
>>>>
>>>>
>>>> Sent from my iPhone
>>>>
>>>>> On Mar 19, 2015, at 6:32 PM, huyanyun at physics.utoronto.ca wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I know this question has been asked for many times. S02 is expected
>>>>> to be around, but smaller than 1, a fact that has been explained,
>>>>> such as in the following previous emails, in our mailing list.
>>>>>
>>>>>
>>> http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg02237.html
>>>>>
>>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2003-February/000230.html
>>>>>
>>>>> However, I am continually get S02 value larger than 1 for a series
>>>>> of similar samples when I fit data in Artemis. I think my fit is
>>>>> very good, because my suspected model(based on other technique)
>>>>> could be verified in XAFS analysis (i.e., defensible in physics),
>>>>> the statistics is good ( R=0.01, reduced chi-square=31.4,
>>>>> fit-range:1.5~6 Angstrom, k-range: 3~14 angstrom-1) and all the
>>>>> parameters such as the bond length, sigma2 are physically
>>>>> reasonable. The only thing makes me uncomfortable is that parameter
>>>>> S02 keeps between 1.45 to 1.55 during the fitting.
>>>>>
>>>>> In my system, the absorber atom occupies two crystallographic
>>>>> sites. So I built a model with paths generated from two FEFF
>>>>> calculations. For paths generated from the 1st and 2nd FEFF
>>>>> calculation, the amplitude parameters are set to be S02*P% and
>>>>> S02*(1-P%) respectively, where P% is the first site occupancy
>>>>> percentage. Both S02 and P are free parameters during the fit, and
>>>>> P is an important conclusion I want to extract from XAFS fitting.
>>>>>
>>>>> However, the fit result gives me S02=1.45 ~ 1.55 and P=0.51 ~ 0.56
>>>>> all the time (i.e., for each path the 'total amplitude' S02*P% or
>>>>> S02*(1-P%) are about 0.7~0.8, smaller than 1). It looks to me that
>>>>> I got a 'perfect' fit but I am not sure if S02 larger than one is
>>>>> defensible. So I have to ask:
>>>>>
>>>>> 1) Is my current fit with S02 larger than one reasonable? If not,
>>>>> what could be suggested to get around it?
>>>>>
>>>>> 2) What's the meaning of S02? It is interpreted in physics that it
>>>>> is a reduced electron excitation parameter, but is it possible that
>>>>> S02 will be affected by any experimental condition?
>>>>>
>>>>> 3) Can anyone share whether you had the multiple site system that
>>>>> gets S02 larger than one?
>>>>>
>>>>> Looking forward to your help.
>>>>>
>>>>> Best,
>>>>> Yanyun
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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