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.
-------------------------------------------------------------------------------------- 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 chant...@unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40unimelb.edu.au> chant...@me.com<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40me.com> http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=http%3a%2f%2foptics.ph.unimelb.edu.au%2f%7echantler%2fxrayopt%2fxrayopt.html> http://optics.ph.unimelb.edu.au/~chantler/home.html<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=http%3a%2f%2foptics.ph.unimelb.edu.au%2f%7echantler%2fhome.html> ________________________________ From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of ifeffit-requ...@millenia.cars.aps.anl.gov <ifeffit-requ...@millenia.cars.aps.anl.gov> Sent: Sunday, 29 August 2021 3:00 AM To: ifeffit@millenia.cars.aps.anl.gov <ifeffit@millenia.cars.aps.anl.gov> Subject: [EXT] Ifeffit Digest, Vol 222, Issue 6 External email: Please exercise caution Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit 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 You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." 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 <liupeng5...@gmail.com> To: Ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Manuscript comments regarding EXAFS modeling Message-ID: <cajnie5j7vbpftkkju01fwuuzyofr-dqarjmwnuludfk5go2...@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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20210828/5f68543c/attachment-0001.htm> ------------------------------ Message: 2 Date: Fri, 27 Aug 2021 22:11:32 -0700 From: Matthew Marcus <mamar...@lbl.gov> To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Manuscript comments regarding EXAFS modeling Message-ID: <f15a72c7-231a-c6ec-f9ce-873b5d400...@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@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ------------------------------ End of Ifeffit Digest, Vol 222, Issue 6 ***************************************
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