[Ifeffit] [EXT] Ifeffit Digest, Vol 222, Issue 6

Sat Aug 28 17:46:17 CDT 2021

Just a little comment.
If you propagate uncertainties, there is mathematically no difference between the weightings and expected fits for k powers times chi, so differences will mainly be in correlated parameters. Without propagating uncertainties you can get different answers in different regions of k fitting but the differences do not reflect physical parameters.

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Christopher Chantler, Professor, FAIP, Fellow American Physical Society
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS; CIT, CCN
IPP, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
chantler at unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40unimelb.edu.au> chantler at me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40me.com>
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Subject: [EXT] Ifeffit Digest, Vol 222, Issue 6

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Today's Topics:

   1. Manuscript comments regarding EXAFS modeling (Peng Liu)
   2. Re: Manuscript comments regarding EXAFS modeling (Matthew Marcus)

----------------------------------------------------------------------

Message: 1
Date: Sat, 28 Aug 2021 10:40:37 +0800
From: Peng Liu <liupeng5182 at gmail.com>
To: Ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Manuscript comments regarding EXAFS modeling
Message-ID:
        <CAJniE5J7VBPfTkKjU01fWUUzYoFR-DqarJmwNuLuDfK5GO2Niw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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 (??) and coordination
number (CN), so any chosen value will be compensated by CN and ??. 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 (??). 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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Message: 2
Date: Fri, 27 Aug 2021 22:11:32 -0700
From: Matthew Marcus <mamarcus at lbl.gov>
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Manuscript comments regarding EXAFS modeling
Message-ID: <f15a72c7-231a-c6ec-f9ce-873b5d4003e9 at lbl.gov>
Content-Type: text/plain; charset=utf-8; format=flowed

Was there a standard measured that's chemically similar to the unknown?
  If so, S0^2 could be set by requiring that the CN of the standard be
what it's known to be.  Often, the d?? is mostly relevant in terms of
differences or changes so an error in the absolute value isn't very
important.  If valence and ligands make such a big difference then it
would be impossible to measure CNs on samples for which no
extremely-similar model compounds are available.

Also, it's never been clear to me how doing the fit at three different
k-powers is better than doing it at just one intermediate value.  The
idea that it somehow gets you low-k and high-k information in a better
way seems like an attempt to pull out more independent data points than
actually exist.  OTOH, proving that you get the same answers, within
error bars, at different exponents would be a confidence-builder.
        mam

On 8/27/2021 7:40 PM, Peng Liu 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 (??) and coordination number (CN), so any chosen value will be
> compensated by CN and ??. 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 (??). 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
> <https://scholar.google.com/citations?user=qUtyvokAAAAJ&hl=en>
>
> http://grzy.cug.edu.cn/049121/zh_CN/index.htm
> <http://grzy.cug.edu.cn/049121/zh_CN/index.htm>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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