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

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

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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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wavelet transformed XAS in Larch-0.9.24
by Matthias Filez 10 Mar '15

10 Mar '15

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 PhD student Ghent University / Laboratory for Chemical Technology Technologiepark 914, B-9052 Ghent - Belgium http://www.lct.UGent.be<http://www.lct.ugent.be/> Disclaimer: http://helpdesk.UGent.be/email/disclaimer.php<http://helpdesk.ugent.be/email/disclaimer.php>

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Importing data with the new version of Athena
by Bruce Ravel 09 Mar '15

09 Mar '15

Hi, This question was sent to our mailing list by someone who is not subscribed. For some reason, it was not in the administration queue on the list server, so I couldn't forward it along in the normal fashion. Here is Sander Bruun's question: > For some reason I am unable to import data directly from *.dat files > in the new version of Athena. It says I may be needing a plugin, but > I do not know how to install it. Can anybody help. It worked fine in > some of the older versions of Athena, but I cannot find and install > them now. Sander, That's not enough information for me to answer the question. "*.dat" is not a file format. A file called "*.dat" can (and usually does!) contain almost anything. Without an example of the sort of file that is giving you trouble, I cannot possibly know what's going on. If your data comes from a particular beamline, it's possible that you simply need to enable that beamline's plugin. There are a couple plugins that come with the software related to specific beamlines at ESRF.... http://bruceravel.github.io/demeter/aug/other/plugin.html#athena%27spluginr… Cheers, B PS: If you subscribe to the mailing list (see http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) then you mail will be posted to the list without my intervention. -- 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/

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