[Ifeffit] Manuscript comments regarding EXAFS modeling

[Matt Newville]

Hi Peng,

This will echo much of what Matthew Marcus wrote:

For comment 1 on S02, picking a value of 0.85 seems reasonable. I think the
reviewer is asking you to explain how you got that value.  Saying something
like "we chose that value so that the data from a simple metal foil (or
simple metal oxide, etc) gave the expected first shell coordination number"
should be enough.   Typically, S02 is determined once for a given set of
data with the same beamline conditions and *not* varying from sample to
sample.

For comment 2 on correlation, I would emphasize that N and sigma2 are
well-known to be correlated and that this correlation cannot be
eliminated.  The correlation is "managed" as all correlations are managed -
by a statistical analysis of that correlation.  The uncertainties reported
for all fitting variables always take those correlations into account.
That is just a normal part of the analysis.

There is a common misconception that using multiple k-weights "eliminates"
correlations between variables.  It does not.  It is available in
ifeffit/artemis/larch to try to help find more robust solutions.  In my
experience,  simultaneously using k-weights of 1, 2, and 3 does not
actually givr very results compared to using a k-weight of 2 or 3 alone,
though I'm willing to believe that there are cases where it can help find a
solution for a fit with both low-Z and high-Z scatterers.  That is, using
multiple k-weights is a fine thing to do but it does not lower correlations
between N and sigma2 (or E0 and R) by very much.

Cheers,


On Fri, Aug 27, 2021 at 7:41 PM Peng Liu <liupeng5182 at gmail.com> wrote:

> Dear Ifeffit members,
>
> I received the following two comments.
>
> "
> Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a
> fixed value (0.85). This factor is specific to particular chemical compound
> and sample preparation and quality (mostly homogeneity), measurement method
> (e.g. absorption, fluorescence). Authors can find in literature [e.g.
> Rehr2000] that SO2 for ideal samples (having no other effects) represent
> multielectron effects, which by definition depend on valence and ligands.
> Even more, SO2 is correlated with Debye-Waller factor (σ²) and coordination
> number (CN), so any chosen value will be compensated by CN and σ². As
> coordination numbers are used as quantitative indicators in discussion and
> following conclusions. I would request to clarify the selection criteria
> for SO2 values and advise to revise this approach (i.e. not to fix SO2 as
> the same value for all samples). I do not expect drastic changes in
> obtained CN values, but this should be tested.
>
> Comment 2: As I mentioned previously, coordination number (CN) is
> correlated with Debye-Waller factor (σ²). My question is: how this
> correlation is managed (eliminated)? Most probably (in FEFFIT) this is done
> by using 3 separate values for n (1,2,3), where n is a power in expression
> chi(k)*(k^n).
> "
> I used Artemis for the calculation. 1) Because S02 and CN are
> multiplication relations in the EXAFS equation, as we usually do, we fixed
> S02 to obtain CN for unknown samples. 2) there are outputs regarding the
> correlation between different fitting parameters from Artemis. Is there a
> way to manage or eliminate the correlation as the reviewer mentioned using
> Artemis or Larch?
>
> If you also could give me some suggestions to answer the comments, that
> would also be greatly appreciated.
>
> --
> Best Regards,
>
> Peng Liu
>
> School of Environmental Studies
>
> China University of Geosciences, Wuhan, Hubei Province, PR China
>
> https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en
> http://grzy.cug.edu.cn/049121/zh_CN/index.htm
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