[Ifeffit] Problem with large so2: Updated

[Raj kumar]

Dear all,


Earlier, I have posted few questions on large so2 value and got valuable
suggestions from Scott and Bruce. Here i am presenting my summary of
earlier emails and the present views. Could you please tell me whether am i
going in right direction.


I have been trying to fit EXAFS signal of YbVO4 both in bulk and
nanoparticles form. Here, I would like to estimate so2 from bulk
(reference) and subsequently use the number, as normalization parameter, to
calculate the co-ordination number in all nanoparticles. Nanoparticles were
synthesized by solution route. First, I have modelled my reference (bulk
YbVO4) with two so2, N and R as free parameters. So2-1 is for first two
shell and so2-2 is for rest other shells. If I use single so2, the value is
obtained to be around 0.9 with unsatisfactory fit whereas second so2-2
incorporation leads to satisfied fit with large uncertainty on the obtained
number i.e., (2.04 +/- 0.9). Using the same strategy, I could successfully
fit the nanoparticles again with large so2-2 (1.79). From literature and
IFEFFIT earlier discussion, i understood that so2 should be between 0.8-1.2
value.  Further, so2-2 is found to well correlated with ss1 and delc (a
parameter to define the movement of atoms in c direction). Among two, the
former parameter (ss1) strongly correlate with so2 and take value of 0.8
and 1.9  for fixed and varying ss1, respectively, during the fit. This
large value of  so2 cannot be controlled with the used model. Also, I have
tried to fit the curve with fixed so2 i.e., below 1 but leads to
unsatisfactory fit. For your info, i have tabulated various strategy and
the resultant parameters. After considering Scott suggestions *(and
previous posts),* i have concluded the following: Since, so2 is used as a
normalization parameter and with the estimated uncertainty, i would
like to consider
the obtained number as reasonable value to normalize the unknown to
calculate the CN in other systems. Is this strategy good to calculate the
CN in unknown? and later to describe the trend on obtained parameters?

Regards,
Raj


Parameters comparison vs So2.docx
Description: MS-Word 2007 document
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Re: [Ifeffit] about sigma2 for exafs fitting

[Scott Calvin]

Hi Shaofeng,

The parameter b does not have to do solely with the difference in N_var between 
the two fits! As I say in the book,

“Changes in the theoretical standards used by the model can often be accounted 
for as if they were changes in parameters. For example, if fit A assumed that 
the nearest neighbors were oxygen and included coordination number, bond 
length, and MSRD for those oxygen atoms as free parameters, while fit B assumed 
the nearest neighbors were sulfur and used the same three parameters, then a 
Hamilton test could be applied with the assumption that those three parameters 
were “changed”—instead of applying to oxygen, they now apply to sulfur. If E0 
and S02 were also free parameters, they would not be considered to be changed, 
as they are primarily a property of the absorber, not the scatterer.”

In your case, it looks to me like two or three parameters are changed between 
models (I count four free parameters in your table, one of which is E0, so I’m 
not sure why you say there are only three…is there another constraint?) Suppose 
there are two free parameters changed. b = 2/2 = 1.

x is the ratio of R-factors between the fits.

Using the values you list below, then, gives a result of 0.64, which indicates 
such variation is quite likely to have taken place by chance.

You chose the worst case of your three, though; the pH 3 case. The pH 10 case 
shows the most improvement in the R-factor with x = 0.007/0.012 = 0.58. The 
probability of getting that much improvement by chance drops to 0.30—less 
likely, but still pretty close to a coin flip.

Even the fact that you got all three to show improvement doesn’t quite reach 
the 95% confidence level, although it’s becoming suggestive.

Why, then, are fits that seem to have much lower R-factors not attaining 
statistical significance? The main culprit is that you have a relatively small 
number of independent points for studying this kind of system.

So where’s that leave you?

I’ll stand by the results of the Hamilton test…there’s not quite enough data 
here, on its own, for me to decide in favor of your second model. If you have 
other evidence pointing in that direction, these results could be used as 
supporting evidence. But with the combination of the closeness of fit not 
improving to a statistically significant degree and the sigma2 taking on an 
unusual (but not impossible) value, there needs to be more to the argument, in 
my opinion.

Best,
Scott Calvin
Lehman College of the City University of New York

On Jan 5, 2017, at 12:19 AM, Shaofeng Wang 
mailto:wangshaof...@iae.ac.cn>> wrote:

Dear Scott,

I have learned the Hamilton test. However, this method seems not suitable to 
distinguish our results because the Nvar are same for the two fittings (3 when 
S02 was fixed). So the b value should be zero and the calculator on the website 
 http://www.danielsoper.com/statcalc/calculator.aspx?id=37 can not carry on.

In addition, I am not sure the value x. Is it the ratio of R-factors between 
two fits? I calculated the results using a=2.18 (Nidp and variables (Nvar) were 
7.35 and 3), b=0.1, and x=0.818 (the ratio of two R-factors) and got the 
Regularized lower incomplete beta function of 0.0807. Does it mean 
something?

Cheers,

Shaofeng

--
Shaofeng Wang, Ph.D of Geochemistry
Environmental Molecular Science Group
Institute of Applied Ecology, Chinese Academy of Sciences
Shenyang, 110016, China
wangshaof...@iae.ac.cn
www.iae.cas.cn


From: Scott Calvin
Sent: Thursday, January 05, 2017 11:50 AM
To: XAFS Analysis using Ifeffit
Cc: Shaofeng Wang
Subject: Fwd: about sigma2 for exafs fitting

Shaofeng has given me permission to repost her question here on the ifeffit 
mailing list. It is quoted below my response.

Dear Shaofeng,

As Bruce and I said before, a sigma2 of 0.0007 A^2 is not impossible, although 
it indicates less disorder than is typically present. Your attached table does 
seem to show some improvement by using the model from the hydrogen-containing 
structure as compared to the arsenate. A more rigorous test for statistical 
improvement can be conducted using the Hamilton test (you mentioned you’ve 
consulted XAFS for Everyone; full details of the Hamilton test are given there).

It’s also encouraging that the uncertainties on your sigma2 determinations 
using the hydrogen-containing model are quite small; it appears that the fit is 
not getting confused by correlations even though it’s fitting both coordination 
number and sigma2, as that would generally also cause high uncertainties in the 
correlated parameters.

Is such a stiff sigma2 reasonable in this case? I have no idea. I just don’t 
know enough about this particular system; perhaps someone else on the list 
does. Oh, and one other question—was the data collected at room temperature

Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 3

[Raj kumar]

Hi Scott and Bruce,

In continuation with earlier email, here, I am just briefing the
observation on the analyzing systems. In my case, reference sample (bulk
YbVO4) itself takes large second so2 with huge uncertainty(2.04 +/- 1.36) to
get a satisfactory fit. Further, this parameter is found to correlate with
ss1 and delc (a parameter to define the movement of atoms in c direction).
Among two, the former parameter (ss1) strongly correlate with so2 and take
value below 1 and large so2, for using ss1 as fixed and free parameter,
respectively. This large value of  so2 cannot be controlled with the used
model. Also, I have tried to fit the curve with fixed so2 i.e., below 1 but
leads to unsatisfactory fit. After considering your suggestion and closely
look into second so2, i have concluded the following: Since, so2 is used as
a normalization parameter and with the available uncertainty, i would
consider the obtained number as reasonable value to normalize the unknown
to calculate the CN in other systems. Is this good strategy to proceed to
calculate the CN? and later to describe the trend on obtained parameters?

Regards,
Raj

On 4 January 2017 at 12:38, 
wrote:

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>1. Re: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar)
>2. Re: Ifeffit Digest, Vol 167, Issue 2 (Bruce Ravel)
>3. Re: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar)
>
>
> --
>
> Message: 1
> Date: Tue, 3 Jan 2017 21:32:51 +0100
> From: Raj kumar 
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Scott,
>
> Thank you very much for your prompt response. EXAFS measurement was done
> after the XRD characterization. From XRD, it is confirmed that there is no
> side phase formation and contamination. Hence, i guess the heavier element
> role could be avoided here.
>
> Split distances could be the reason??. The following is the method, i have
> opted for modelling the obtained curve. Since YbVO4 is zircon structure, i
> have constrained distance in paths 3, 8 and 9 with the pre-structural info
> and let other distances vary with regular mathematical expression
> alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for
> all paths but fit failed miserably for multi-shells.
>
> Regards,
> Raj
>
> On 3 January 2017 at 19:00, 
> wrote:
>
> > Send Ifeffit mailing list submissions to
> > ifeffit@millenia.cars.aps.anl.gov
> >
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> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > or, via email, send a message with subject or body 'help' to
> > ifeffit-requ...@millenia.cars.aps.anl.gov
> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Ifeffit digest..."
> >
> >
> > Today's Topics:
> >
> >1. Re: Problem with large so2 (Scott Calvin)
> >
> >
> > --
> >
> > Message: 1
> > Date: Tue, 3 Jan 2017 09:59:18 -0600
> > From: Scott Calvin 
> > To: XAFS Analysis using Ifeffit 
> > Subject: Re: [Ifeffit] Problem with large so2
> > Message-ID: <3ef5e209-7681-49c6-9713-4bbf34c61...@gmail.edu>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Raj,
> >
> > I haven?t looked at your files, but the kinds of results you are
> > describing often indicate the model you are using beyond the first shell
> is
> > incorrect. It may be that it has the wrong elements (e.g., heavier
> elements
> > are present than what you modelled) or that the model includes split
> > distances when in reality the compound is more symmetric.
> >
> > In short, no, the high second S02 does not make sense (although it would
> > be good to know the uncertainties).
> >
> > Best,
> > Scott Calvin
> > Lehman College of the City University of New York
> >
> > > On Jan 3, 2017, at 9:38 AM, Raj kumar  wrote:
> > >
> > > Dear All,
> > >
> > >
> > >
> > > I have been trying to fit EXAFS signal of YbVO4 both in bulk and
> > nanoparticles form. Here, I would like to estimate so2 from bulk
> > (reference) and subsequently use the number, as normalization parameter,
> to
> > calculate the co-ordination number in a