- Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 22 Mar '15

22 Mar '15

Hi Matt, Thanks a lot for your prompt reply. The method I am referring to is not the multiple k-weight fits by constraining N*S02. My apologies for not being clear enough. Let's do it again. I am actually referring to an approach where we take an advantage of a different k-dependence of various parameters to breakdown correlations between them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. In this case, to breakdown correlation between S02 and sigma2, one can assume a series of S02 values and perform fits using a single k-weight each time (say k-weight 1,2 and 3) and record corresponding sigma2 values. Let us say for k-weight =1, a series of preset S02 values will result in a series of corresponding sigma2 values refined in fits, which can be plotted as a straight line in sigma2 vs. S02 plot. Similar straight lines can be obtained for fits using k-weight = 2 and then 3. Now, these three lines may intersect at or near some point, which will determine the "true" value of parameters independent of k-weight. One can then constrain S02 to a value obtained from the point of intersection of three lines and vary sigma2 in a fit. In this particular case, however, the advantage is, S02 does not depend on changes inside sample and we have very good estimate of its range (say 0.7 - 1.0). Now suppose instead of S02 (which i now set to a reasonable value), I am interested in determining N, but it is highly correlated with sigma2. Each time when disorder in the sample increases, the sigma2 increases and due to its high correlation, N is also overestimated. On the other hand, when the disorder in the sample decreases, the sigma2 decreases and I can have a "true" estimation of N in the sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" estimation of N, even if disorder is high in my samples ? or it is simply not possible due to the fact that both N and sigma2 varies with changes inside the sample. Best regards, Jatin ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Saturday, March 21, 2015 3:14 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 38 Send Ifeffit mailing list submissions to ifeffit(a)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-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Re: amplitude parameter S02 larger than 1 (Scott Calvin) 2. Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) 3. Re: Breaking down correlationships between parameters (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Mar 2015 18:53:06 -0400 From: Scott Calvin <scalvin(a)sarahlawrence.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 Message-ID: <D2ADF788-9BC6-41E2-BD6B-794BD2E59DBC(a)slc.edu> Content-Type: text/plain; charset="utf-8" Hi Yanyun, Good. So here's the procedure for a Hamilton test. We're comparing the fit with S02 guessed to the one with S02 set to 0.90, because that was your a priori best guess at S02. I take the ratio of the first R-factor to the second. You didn't actually say the R-factor for the fit with S02 guessed, but it's clearly around 0.0055 based on the other information you gave. The R-factor for the 0.90 fit is 0.021. So the ratio is 0.0055/0.021 = 0.26, which we'll call x. For the first fit the degrees of freedom is 31.2 - 24 = 8.2. Take half of that and call that a. So a is 4.1. The first fit guesses 1 parameter that the second one doesn't. Take half of 1 and call that b. So b is 0.5. Find a regularized lower incomplete beta function calculator, like this one: http://www.danielsoper.com/statcalc3/calc.aspx?id=37 Enter x, a, and b. The result is 0.001. This means that there is a 0.1% chance that the fits are actually consistent, and that the difference is just due to noise in the data. So in this case, we can't just explain away the high S02 as insignificant. Of course, you could pretty much eyeball that once you gave me the uncertainties; since your fit said 1.45 +/- 0.14, that's likely to be quite incompatible with S02 = 0.9. Still, it's nice to put that on a firmer statistical basis, and I've personally found the Hamilton test quite helpful for answering "do I need to worry about [X]?" type questions. But in your case, you do need to worry about it. This discussion has generated several suggestions; hopefully one of them is a good lead! --Scott Calvin Sarah Lawrence College > On Mar 20, 2015, at 4:30 PM, huyanyun(a)physics.utoronto.ca wrote: > > Hi Scott, > > In all situations, 31.2 independent data points and 24 variables were > used. In the case of setting S02 to a value, 23 variables were used. > > Let me know if there is any other info needed. > > Best, > Yanyun > > > Quoting Scott Calvin <scalvin(a)sarahlawrence.edu>: > >> Hi Yanyun, >> >> To actually do a Hamilton test, the one other thing I need to know >> the number of degrees of freedom in the fit...if you provide that, >> I'll walk you through how to actually do a Hamilton test--it's not >> that bad, with the aid of an online calculator, and I think it might >> be instructive for some of the other people reading this list who >> are trying to learn EXAFS. >> >> --Scott Calvin >> Sarah Lawrence College >> >> >>> On Mar 20, 2015, at 3:46 PM, huyanyun(a)physics.utoronto.ca wrote: >>> >>> Hi Scott, >>> >>> Thank you so much for giving me your thought again. It is very helpful >>> to know how you and other XAFS experts deal with unusual situations. >>> >>> The floating S02 is fitted to be 1.45+/-0.14, this just means the fit >>> doesn't like the idea of an S02 in a typical range. Instead of setting >>> S02 to 0.9, I have to figure out why it happens and what it might >>> indicate. >>> >>> I guess a Hamilton test is done by adjusting one parameter (i.e., S02) >>> while keeping other conditions and model the same. Is that right? So >>> I record this test as following: >>> >>> 1) Floating S02: S02 fits to 1.45+/-0.14, R=0.0055, reduced >>> chi^2=17.86, Percentage=0.53+/-0.04 >>> 2) Set S02=0.7, R=0.044, reduced chi^2=120.6, percentage=0.81+/-0.2 >>> 3) set S02=0.8, R=0.030, reduced chi^2=86.10, percentage=0.77+/-0.07 >>> 3) set S02=0.9, R=0.021, reduced chi^2=60.16, percentage=0.72+/-0.06 >>> 4) set S02=1.0, R=0.017, reduced chi^2=49.5, percentage=0.67+/-0.05 >>> 5) set S02=1.1, R=0.012, reduced chi^2=35.1, percentage=0.62+/-0.03 >>> 6) set S02=1.2, R=0.009, reduced chi^2=24.9, percentage=0.59+/-0.02 >>> 7) set S02=1.3, R=0.007, reduced chi^2=18.9, percentage=0.57+/-0.02 >>> 8) set S02=1.4, R=0.0057, reduced chi^2=16.1, percentage=0.55+/-0.02 >>> 9) Floating S02 to be 1.45+/-0.14 >>> 10) set S02=1.6, R=0.006, reduced chi^2=17.8, percentage=0.53+/- 0.02 >>> 11) set S02=2.0, R=0.044, reduced chi^2=120.7, percentage=0.37+/-0.06. >>> >>> Therefore, I will say S02 falling in the range 1.2~1.6 gives >>> statistically improved fit, but S02=0.9 is not terrible as well. I >>> agree with you that I could always be confident to say the percentage >>> is 0.64+/-0.15, but I do want to shrink down the uncertainty and think >>> about other possibilities that could cause a large S02. >>> >>> I did double-check the data-reduction and normalization process. I >>> don't think I can improve anything in this step. By the way, I have a >>> series of similar samples and their fittings all shows floating S02 >>> larger than one based on the same two-sites model. >>> >>> Best, >>> Yanyun >>> >>> >>> >>> >>> Quoting Scott Calvin <scalvin(a)sarahlawrence.edu>: >>> >>>> Hi Yanyun, >>>> >>>> Lots of comments coming in now, so I?m editing this as I write it! >>>> >>>> One possibility for why you're getting a high best-fit S02 is that >>>> the fit doesn't care all that much about what the value of S02; i.e. >>>> there is broad range of S02's compatible with describing the fit as >>>> "good." That should be reflected in the uncertainty that Artemis >>>> reports. If S02 is 1.50 +/- 0.48, for example, that means the fit >>>> isn't all that "sure" what S02 should be. That would mean we could >>>> just shrug our shoulders and move on, except that it correlates with >>>> a parameter you are interested in (in this case, site occupancy). So >>>> in such a case, I think you can cautiously fall back on what might >>>> be called a "Bayesian prior"; i.e., the belief that the S02 should >>>> be "around" 0.9, and set the S02 to 0.9. (Or perhaps restrain S02 to >>>> 0.9; then you're really doing something a bit more like the notion >>>> of a Bayesian prior.) >>>> >>>> On the other hand, if the S02 is, say, 1.50 +/- 0.07, then the fit >>>> really doesn?t like the idea of an S02 in the typical range. An S02 >>>> that high, with that small an uncertainty, suggests to me that >>>> something is wrong?although it could be as simple as a normalization >>>> issue during data reduction. In that case, I?d be more skeptical of >>>> just setting S02 to 0.90 and going with that result; the fit is >>>> trying to tell you something, and it?s important to track down what >>>> that something is. >>>> >>>> Of course, once in a while, a fit will find a local minimum, while >>>> there?s another good local minimum around a more realistic value. >>>> That would be reflected by a fit that gave similarly good >>>> quantitative measures of fit quality (e.g. R-factors) when S02 is >>>> fit (and yields 1.50 +/- 0.07) as when its forced to 0.90. That?s >>>> somewhat unusual, however, particularly with a global parameter like >>>> S02. >>>> >>>> A good way to defend setting S02 to 0.90 is to use the Hamilton test >>>> to see if floating S02 yields a statistically significant >>>> improvement over forcing it to 0.90. If not, using your prior best >>>> estimate for S02 is reasonable. >>>> >>>> If you did that, though, I?d think that it would be good to mention >>>> what happened in any eventual publication of presentation; it might >>>> provide an important clue to someone who follows up with this or a >>>> similar system. It would also be good to increase your reported >>>> uncertainty for site occupancy (and indicate in the text what you?ve >>>> done). I now see that your site occupancies are 0.53 +/- 0.04 for >>>> the floated S02, and 0.72 +/-0.06 for the S02 = 0.90. That?s not so >>>> bad, really. It means that you?re pretty confident that the site >>>> occupancy is 0.64 +/- 0.15, which isn?t an absurdly large >>>> uncertainty as these things go. >>>> >>>> To be concrete, if all the Hamilton test does not show statistically >>>> significant improvement by floating S02, then I might write >>>> something like this in any eventual paper: ?The site occupancy was >>>> highly correlated with S02 in our fits, making it difficult to >>>> determine the site occupancy with high precision. If S02 is >>>> constrained to 0.90, a plausible value for element [X] [ref], then >>>> the site occupancy is 0.53 +/- 0.04. If constrained to 1.0, the site >>>> occupancy is [whatever it comes out to be] To reflect the increased >>>> uncertainty associated with the unknown value for S02, we are >>>> adopting a value of 0.53 +/- [enough uncertainty to cover the >>>> results found for S02 = 1.0]. >>>> >>>> Of course, if you do that, I?d also suggest tracking down as many >>>> other possibilities for why your fit is showing high values of S02 >>>> as you can; e.g., double-check your normalization during data >>>> reduction. >>>> >>>> If, on the other hand, the Hamilton test does show the floated S02 >>>> is yielding a statistically significant improvement, I think you >>>> have a bigger issue. Looking at, e.g., whether you may have >>>> constrained coordination numbers incorrectly becomes more critical. >>>> >>>> ?Scott Calvin >>>> Sarah Lawrence College >>>> >>>> >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ------------------------------ Message: 2 Date: Sat, 21 Mar 2015 13:06:39 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Breaking down correlationships between parameters Message-ID: <DA4C7D90F90BC249A03505C87F2EB8AB230EE6D1@didag1> Content-Type: text/plain; charset="iso-8859-1" Dear All, I have stumbled upon a question regarding correlationships between various parameters in EXAFS fitting. As we know, the parameters S02*N and sigma2 are highly correlated (where N is the number of nearest neighbors). I would like to determine the number of nearest neighbors for a series of sample subjected to some treatment. I can do this by simply setting S02 to a value for a given absorber (based on the literature or my own measurements of some reference compounds) and letting N and sigma2 vary in a fit. However, the problem is the physical process which changes the number of nearest neighbors, also introduces structural disorder in samples. Thus, I always get the values of N overestimated due to its correlationship with sigma2. I know of a method which can be used to breakdown the correlationship between S02 and sigma2 by setting a series of S02 values at different k-weights and refining the corresponding sigma2 as discussed in several literature. However, in this approach the explicit assumption is, S02 is the property of absorbing atoms and thus is independent of changes occurring inside the sample. In my case, however, both sigma2 and N vary with changes inside samples. Is there any way to break this correlationship ? I look forward to your valuable suggestions and comments. Best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Breaking down correlationships between parameters
by Rana, Jatinkumar Kantilal 21 Mar '15

21 Mar '15

Dear All, I have stumbled upon a question regarding correlationships between various parameters in EXAFS fitting. As we know, the parameters S02*N and sigma2 are highly correlated (where N is the number of nearest neighbors). I would like to determine the number of nearest neighbors for a series of sample subjected to some treatment. I can do this by simply setting S02 to a value for a given absorber (based on the literature or my own measurements of some reference compounds) and letting N and sigma2 vary in a fit. However, the problem is the physical process which changes the number of nearest neighbors, also introduces structural disorder in samples. Thus, I always get the values of N overestimated due to its correlationship with sigma2. I know of a method which can be used to breakdown the correlationship between S02 and sigma2 by setting a series of S02 values at different k-weights and refining the corresponding sigma2 as discussed in several literature. However, in this approach the explicit assumption is, S02 is the property of absorbing atoms and thus is independent of changes occurring inside the sample. In my case, however, both sigma2 and N vary with changes inside samples. Is there any way to break this correlationship ? I look forward to your valuable suggestions and comments. Best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] amplitude parameter S02 larger than 1
by Joshua Kas 20 Mar '15

20 Mar '15

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(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. 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(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 > Message-ID: > < > 545F89325F51764C902D37B42C9F4D530148FDA88C(a)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(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of > huyanyun(a)physics.utoronto.ca [huyanyun(a)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(a)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(a)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.ht… > >> > 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 > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 145, Issue 31 > **************************************** >

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Re: [Ifeffit] amplitude parameter S02 larger than 1
by Joshua Kas 20 Mar '15

20 Mar '15

On Fri, Mar 20, 2015 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. 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(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] amplitude parameter S02 larger than 1 > Message-ID: > < > 545F89325F51764C902D37B42C9F4D530148FDA88C(a)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(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of > huyanyun(a)physics.utoronto.ca [huyanyun(a)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(a)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(a)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.ht… > >> > 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 > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 145, Issue 31 > **************************************** >

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Data being overwritten in Artemis history window
by Godfrey, Ian 18 Mar '15

18 Mar '15

?Dear All, Sorry... another bug report! Hopefully the last one for a while! In the history window some, but not all, data from previous fits seems to get overwritten when running a new fit. Specifically I've noticed this happening with the information in the "Data set" section. To reproduce run a QFS fit with some R-space fitting windows (say 2-4); at this point the log will be displayed correctly in the history window. Now change the R window (say 1.5-3.5) and run the fit again. When you go to the history window the R window information will be displayed correctly for the most recent fit but, for the previous fit it will have been overwritten by the newer fit. Some of the other info, such as R-factor by k-weight seems to get overwritten too. A video of this behaviour can be found here: https://wwwa-e.ucl.ac.uk/cgi-bin/dropbox/dropbox.cgi?state=pickup_info&id=2… password: 54c8545f System info: Win 8.1 Enterprise x64 running Demeter 0.9.22 pre release x64; log attached. All the best, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] (D)Artemis shutting down automatically
by Raj kumar 11 Mar '15

11 Mar '15

Dear Bruce, Thanks for the reply. Please see the attachment for the files which i have used. Regards, Raj On Wed, Mar 11, 2015 at 6:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Re: Increase in uncertainty of Eo and fitting mismatch > (Matt Newville) > 2. Re: Data being overwritten in Artemis history window (Bruce Ravel) > 3. (D)Artemis shutting down automatically (Raj kumar) > 4. Re: (D)Artemis shutting down automatically (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Mar 2015 12:08:24 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Increase in uncertainty of Eo and fitting > mismatch > Message-ID: > < > CA+7ESbot-UZAgz3WM9EqaNROc7io+KnBE5NbEoMvxVoixPWGcw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Raj, > > Some comments and suggestions. > > On Tue, Mar 10, 2015 at 11:11 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > Dear All, > > > > Recently, I recorded Copper foil EXAFS as a reference in (Dispersive > EXAFS) > > transmission mode at Soleil, Paris. For understanding the data quality > (of > > my sample), i started fitting copper EXAFS through Artemis. After the > DATA > > extraction, i fitted copper in Artemis and found a shift in energy. For > this > > reason, i have modeled with and without corrected Copper EXAFS in > Artemis. > > What does "with and without corrected Copper EXAFS" mean? > > > Initially, i started with first shell and progressed to three shell fit > > through step by step. During the course of fitting, some of the following > > troubles have been faced. Please help me to rectify it. > > > > For first shell fit: Everything goes well and converged to reasonable > > physical values of copper foil. Whereas for further increment in copper > > shells leads to increase in Debye-waller factor for all three shells and > > By itself would not worry me too mcuh. > > > increase in uncertainty value of E0 than the actual value. > > What actual value? You mean the uncertainty in E0 increases when you > go from 1 to 3 shells? That increase in uncertainty could easily be > due to a worse overall fit. > > > Moreover, i have noticed that the (increase of shells in the fit) not > only > > changes the physical parameters and also modifies the Fourier transform. > > The Fourier transform of the data depends only on the k-space data, > and the weighting and windowing applied. It doesn't depend on the > values of the fitting parameters -- those affect only the Fourier > transform of the model. > > > The inference are the following: A shift in first and third shell of > Cu-Cu > > are observed, respectively, to larger and shorter distance than the > > experimental spectrum with diminished second shell amplitude. > > Not sure what you mean.... larger and shorter than what? > > I would recommend fitting one spectrum first -- I don't quite > understand why you have 2 spectra with an obvious E0 shift between > them, and no (unless I missed something) shared parameters. > > > --Matt > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Mar 2015 13:50:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data being overwritten in Artemis history > window > Message-ID: <54FF2F03.8060708(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/09/2015 04:17 AM, Godfrey, Ian wrote: > > In the history window some, but not all, data from previous fits seems > > to get overwritten when running a new fit. Specifically I've noticed > > this happening with the information in the "Data set" section. To > > reproduce run a QFS fit with some R-space fitting windows (say 2-4); at > > this point the log will be displayed correctly in the history window. > > Now change the R window (say 1.5-3.5) and run the fit again. When you go > > to the history window the R window information will be displayed > > correctly for the most recent fit but, for the previous fit it will have > > been overwritten by the newer fit. Some of the other info, such as > > R-factor by k-weight seems to get overwritten too. > > I just pushed a fix for this to github and posted new windows installer > candidates at > > http://bruceravel.github.io/demeter/#windows > > If you see any other questionable behavior in the history window let me > know. I think I understood the ramifications of the fix I made, but I am > not 100% certain. > > The windows installers also include the most recent version of gnuplot. > Hopefully that will address your problem regarding zooming and > scrolling. > > If it does not, try changing the gnuplot->terminal configuration > parameter to "qt". qt is one of the other terminal options in the new > version of gnuplot. It makes a pretty plot, but I like the controls on > the wxt terminal more. If you are unsatisfied with that, try setting it > to "windows", which is the third (and to my eye, the worst) of the three > plot terminal options. Hopefully one of them will work for you. > > Cheers, > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Wed, 11 Mar 2015 09:59:54 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] (D)Artemis shutting down automatically > Message-ID: > < > CAAW7+QMAn0kbe0udnpMzyPpqsb0X_t632Qwk7bWuMhtbzY96WQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i have faced automatic shutting down of artemis during the import > of chi file. For more clarification, please see the first log file. > > Also, i observed emptying of .fpj files. This happens during the saving of > old .apj to .fpj or/and during the frequent saving of .fpj files after .apj > conversion. Please see the second log file for this problem. > > > Regards, > Raj >

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Re: [Ifeffit] Increase in uncertainty of Eo and fitting mismatch
by Raj kumar 11 Mar '15

11 Mar '15

Dear matt and Bruce, Thanks for the reply. Bruce i am working in new version (facing some problem) and will write to you soon >>"What does "with and without corrected Copper EXAFS" mean? For more clarity, in the new file, i have presented single copper EXAFS fit and showed the result. Please see the attachment for that. >>What actual value? You mean the uncertainty in E0 increases when you go from 1 to 3 shells? That increase in uncertainty could easily be due to a worse overall fit. Here i am mentioning *final fit* value as *actual value* and their *error bar *is uncertainty. If you look at the Eo value from 1 shell (fit 1) to 3 shell (fit 3), it decreases and close to zero whereas the corresponding uncertainty tending to reach more than or equal to 1. This is what i am mentioning here by saying Eo uncertainty increases for the inclusion of shells. >>>The Fourier transform of the data depends only on the k-space data, and the weighting and windowing applied. It doesn't depend on the values of the fitting parameters -- those affect only the Fourier transform of the model. I am really sorry, aforementioned sentence has been written in wrong and misleading way. The point i would like to make here is about the fit in R-space. The trouble i am facing is the following: I*f you look at the fit in R-space, similarly, * from 1 shell (fit1) to 3 shell (fit3) fit, the first shell theoretical shape shifts to larger distance (*for three shell fit (fit 3) in R-space*) compared to the only first shell fit (*fit 1*). If you look the third shell theoretical shape, it is shifted towards the shorter distance than the experimental spectrum (in *fit 3*), while the amplitude of second shell fit is always less than the experimental observation. Why it is occurring so? and what i am missing here? I hope i have conveyed the problem in right way. With regards, Raj On Wed, Mar 11, 2015 at 6:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Re: Increase in uncertainty of Eo and fitting mismatch > (Matt Newville) > 2. Re: Data being overwritten in Artemis history window (Bruce Ravel) > 3. (D)Artemis shutting down automatically (Raj kumar) > 4. Re: (D)Artemis shutting down automatically (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Mar 2015 12:08:24 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Increase in uncertainty of Eo and fitting > mismatch > Message-ID: > < > CA+7ESbot-UZAgz3WM9EqaNROc7io+KnBE5NbEoMvxVoixPWGcw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Raj, > > Some comments and suggestions. > > On Tue, Mar 10, 2015 at 11:11 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > Dear All, > > > > Recently, I recorded Copper foil EXAFS as a reference in (Dispersive > EXAFS) > > transmission mode at Soleil, Paris. For understanding the data quality > (of > > my sample), i started fitting copper EXAFS through Artemis. After the > DATA > > extraction, i fitted copper in Artemis and found a shift in energy. For > this > > reason, i have modeled with and without corrected Copper EXAFS in > Artemis. > > What does "with and without corrected Copper EXAFS" mean? > > > Initially, i started with first shell and progressed to three shell fit > > through step by step. During the course of fitting, some of the following > > troubles have been faced. Please help me to rectify it. > > > > For first shell fit: Everything goes well and converged to reasonable > > physical values of copper foil. Whereas for further increment in copper > > shells leads to increase in Debye-waller factor for all three shells and > > By itself would not worry me too mcuh. > > > increase in uncertainty value of E0 than the actual value. > > What actual value? You mean the uncertainty in E0 increases when you > go from 1 to 3 shells? That increase in uncertainty could easily be > due to a worse overall fit. > > > Moreover, i have noticed that the (increase of shells in the fit) not > only > > changes the physical parameters and also modifies the Fourier transform. > > The Fourier transform of the data depends only on the k-space data, > and the weighting and windowing applied. It doesn't depend on the > values of the fitting parameters -- those affect only the Fourier > transform of the model. > > > The inference are the following: A shift in first and third shell of > Cu-Cu > > are observed, respectively, to larger and shorter distance than the > > experimental spectrum with diminished second shell amplitude. > > Not sure what you mean.... larger and shorter than what? > > I would recommend fitting one spectrum first -- I don't quite > understand why you have 2 spectra with an obvious E0 shift between > them, and no (unless I missed something) shared parameters. > > > --Matt > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Mar 2015 13:50:59 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data being overwritten in Artemis history > window > Message-ID: <54FF2F03.8060708(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/09/2015 04:17 AM, Godfrey, Ian wrote: > > In the history window some, but not all, data from previous fits seems > > to get overwritten when running a new fit. Specifically I've noticed > > this happening with the information in the "Data set" section. To > > reproduce run a QFS fit with some R-space fitting windows (say 2-4); at > > this point the log will be displayed correctly in the history window. > > Now change the R window (say 1.5-3.5) and run the fit again. When you go > > to the history window the R window information will be displayed > > correctly for the most recent fit but, for the previous fit it will have > > been overwritten by the newer fit. Some of the other info, such as > > R-factor by k-weight seems to get overwritten too. > > I just pushed a fix for this to github and posted new windows installer > candidates at > > http://bruceravel.github.io/demeter/#windows > > If you see any other questionable behavior in the history window let me > know. I think I understood the ramifications of the fix I made, but I am > not 100% certain. > > The windows installers also include the most recent version of gnuplot. > Hopefully that will address your problem regarding zooming and > scrolling. > > If it does not, try changing the gnuplot->terminal configuration > parameter to "qt". qt is one of the other terminal options in the new > version of gnuplot. It makes a pretty plot, but I like the controls on > the wxt terminal more. If you are unsatisfied with that, try setting it > to "windows", which is the third (and to my eye, the worst) of the three > plot terminal options. Hopefully one of them will work for you. > > Cheers, > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Wed, 11 Mar 2015 09:59:54 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] (D)Artemis shutting down automatically > Message-ID: > < > CAAW7+QMAn0kbe0udnpMzyPpqsb0X_t632Qwk7bWuMhtbzY96WQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i have faced automatic shutting down of artemis during the import > of chi file. For more clarification, please see the first log file. > > Also, i observed emptying of .fpj files. This happens during the saving of > old .apj to .fpj or/and during the frequent saving of .fpj files after .apj > conversion. Please see the second log file for this problem. > > > Regards, > Raj >

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Re: [Ifeffit] wavelet transformed XAS in Larch-0.9.24
by Danilo Oliveira de Souza 11 Mar '15

11 Mar '15

On Tue, Mar 10, 2015 at 10:43 AM, Matthias Filez <Matthias.Filez(a)ugent.be> wrote: > Dear mailing list user, > > I am currently trying to use the cauchy_wavelet.py plugin of Larch-0.9.24 to > wavelet transform some k-space EXAFS data. In principle, everything works > properly, but I would like to adjust the order of the Cauchy wavelet to 50. > However, a view inside the script does not make clear what changes are > necessary. How can this be done? > > Please provide me your suggestions, > Many thanks, > > Matthias Filez Hi, Matthias You should check the MATLAB script made by Manuel MUÑOZ, François FARGES and Pierre ARGOUL. I think you have such freedom of choice you looking for. It works pretty well! Try this link http://perso.univ-mlv.fr/farges/wav/ Regards, -- *Danilo OLIVEIRA DE SOUZA* (PhD fellow) Université de Sciences et Technologies de Lille (Université Lille 1) UCCS - Unité de Catalise et Chimie du Solid, Bat. C3, 110. Cité Scientifique, 59655, VIlleneuve d'Ascq CEDEX. danilo.olsouza(a)gmail.com d.oliveira-de-souza(a)ed.univ-lille1.fr tel: +33 06.63.55.86.12

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(D)Artemis shutting down automatically
by Raj kumar 11 Mar '15

11 Mar '15

Dear All, Recently, i have faced automatic shutting down of artemis during the import of chi file. For more clarification, please see the first log file. Also, i observed emptying of .fpj files. This happens during the saving of old .apj to .fpj or/and during the frequent saving of .fpj files after .apj conversion. Please see the second log file for this problem. Regards, Raj

2 1

Increase in uncertainty of Eo and fitting mismatch
by Raj kumar 10 Mar '15

10 Mar '15

Dear All, Recently, I recorded Copper foil EXAFS as a reference in (Dispersive EXAFS) transmission mode at Soleil, Paris. For understanding the data quality (of my sample), i started fitting copper EXAFS through Artemis. After the DATA extraction, i fitted copper in Artemis and found a shift in energy. For this reason, i have modeled with and without corrected Copper EXAFS in Artemis. Initially, i started with first shell and progressed to three shell fit through step by step. During the course of fitting, some of the following troubles have been faced. Please help me to rectify it. For first shell fit: Everything goes well and converged to reasonable physical values of copper foil. Whereas for* further increment in copper shells* leads to *increase in Debye-waller factor for all three shells* and *increase in uncertainty value of E0 than the actual value*. Moreover, i have noticed that the (increase of shells in the fit) *not only changes the physical parameters and also modifies the Fourier transform*. The inference are the following: A shift in first and third shell of Cu-Cu are observed, respectively, *to larger and shorter distance than the experimental spectrum* with diminished second shell amplitude. Although Copper foil EXAFS is standard and well known sample, i am stuck with fitting. Please help me to overcome these problems. For your reference, project file of Copper file is attached with this email. Regards. Raj

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