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

Create Atoms input with just coordinates
by M Ferrier 01 Jun '15

01 Jun '15

Hi, I am trying to create an Atoms input file for actinium. Since not a lot is known about this element we run some DT calculations. One molecule of Ac acetate in a box surrounded by water. I have the coordinate of each elements. I was told the symmetry was P1 (I guess for the box) but unfortunately their is no symmetry in liquid and thus we cannot input the cell parameters (distances a, b, c and angles alpha, beta, gamma). I was wondering if their were a way to make Atoms run to obtain the Feff calculations. Or we should use a different model with a known solid? Thank you for your help Maryline Ferrier

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low and negative ss2 and bug in the log file of fit history
by Raj kumar 01 Jun '15

01 Jun '15

Dear All, I am trying to fit the first shell FT of bulk YbVO4 (measured in dispersive EXAFS) with the reference YbVO4. The resultant SS2 value for the first shell is found to be low for wide k-range selection, whereas approaching negative for the relatively short k-range window. While approaching negative value (of ss2), i have tried to constraint the ss2 value using expression abs(ss). In that case, ss2 value is found to take value 0. Please help me to figure out the problem. Further i have found a small bug in the fit history window. After each fit, earlier data set in the log file of fit history is found to overwritten with the latest fitting parameters (like k range, dk, etc..). Here in my log file window, all fit data set contain the same data set value as like the last fit (fit9). Regards, Raj

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by fred.mosselmans＠diamond.ac.uk 01 Jun '15

01 Jun '15

Dear Kug-Seung Your main initial problem is you didn't understand the structure of Mn3O4. It is a spinel with two Mn sites one octahedral and one tetrahedral. You need to consider both sites to have a chance of fitting, and set multiplication factors on the relative amps in the ratio. It has 1/3 tetrahedral sites and 2/3 octahedral. You need to do the feff calculation twice with each site as the core atom. In the attached project I have done this. You then end up with a lot of paths so to try to restrict the no of variables I have made several of sigma squared to be the same. I am sure this model could be improved upon but I wanted to show you how to get going in fitting the structure. In theory as the Mn tetrahedral site and octahedral sites are different oxidations states they might (should) have different E0s as well but with a limited data range this gets hard to test properly. Best wishes Fred Mosselmans Message: 1 Date: Mon, 01 Jun 2015 15:59:40 +0900 From: ??? <lks3006(a)postech.ac.kr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Mn3O4 EXAFS fitting Message-ID: <1433141980110.23146.postech(a)postech.ac.kr> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150601/4ec…>

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Re: [Ifeffit] _Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

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Re: [Ifeffit] Ifeffit Digest, Vol 147, Issue 20
by Raj kumar 29 May '15

29 May '15

Hi Bruce, The comments are very helpful to assure my data processing and for future experiments. Yes, all measurements were obtained in Dispersive EXAFS mode. As for i know (at least until my preparation time) the bulk sample (first one) doesn't contain the Hf impurities. However, i will double check that point. Regards, Raj On Fri, May 29, 2015 at 7:00 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: Peak at short distance in FT - YbVO4 nanoparticles > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 29 May 2015 12:52:38 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Peak at short distance in FT - YbVO4 > nanoparticles > Message-ID: <55689956.8040302(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 05/29/2015 11:54 AM, Raj kumar wrote: > > Recently, i have performed EXAFS for YbVO4 bulk (prepared through > > sintering process) and nanoparticles (at room temperature). > > Nanoparticles were synthesized by co-precipitation technique and their > > EXAFS was measured by passing the prepared solution using peristaltic > > pump. After all subtraction (background and solvent), nanoparticles XAS > > data were recovered and processed for the fitting. After Fourier > > transform, it was observed that both nanoparticles posses an additional > > short peak (or shoulder) at about 1.2 A from bulk. Since the peak > > appears much closer to 1 A, i suspect this may due to artifact or bad > > background subtraction. Hence, i would like to know the way to eliminate > > this peak at short distance. > > Hi Raj, > > A few comments: > > 1. Your bulk sample (the first one in the list) may have a bit of Hf > in it it. It's hard to tell, but the mu(E) seems to be trending > upward right at the end of the data, which is the approximate edge > energy of Hf L3. I got a slightly better background removal by > changing the end of the spline range to 600. But this a minor > detail. The real story seems to be that .... > > 2. You data are pretty noisy. If you plot chi(R) out to 10 Angstroms > (which is, presumably, well beyond where you should expect to see > good signal in your data), you get a sense of how the level of > noise manifests itself in chi(R). To my eye, the peak/shoulder at > about 1.2 that you are asking about is of about the same size as > the level of noise in your data. > > You are asking how to get rid of a feature in the data that is > aesthetically unpleasing. I don't think that's the right question. > > Your data are what they are. Your data are noisy and measured over a > rather short energy range. That doesn't give you a lot of choices > about how aesthetically appealing you can make the Fourier transform > be. > > You seem to be operating Athena correctly and there aren't any magic > buttons that will make your short, noisy data longer or less noisy. I > don't see anything obviously wrong in how you are processing your data > and -- short of using PhotoShop ;) -- I don't see any defensible way of > making the feature at 1.2 go away. > > > > Am I correct in thinking that these data are measured in the > dispersive geometry? If so, my suggestion is to reconsider how you > make your samples. This kind of experiment is VERY sensitive to the > homogeneity of the sample. You have to take extraordinary care to make > your samples as homogeneous as possible. I suspect most of the > glitchy little points in your data are indicative of sample > inhomogeneity. > > You also should worry about purity of your source material. Granted, > it canbe very difficult to obtain rare earth metal samples that are > elementally pure. But if your data range is short because of other > edges, then you need samples that are more pure. > > HTH, > 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/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 147, Issue 20 > **************************************** >

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Peak at short distance in FT - YbVO4 nanoparticles
by Raj kumar 29 May '15

29 May '15

Dear All, Recently, i have performed EXAFS for YbVO4 bulk (prepared through sintering process) and nanoparticles (at room temperature). Nanoparticles were synthesized by co-precipitation technique and their EXAFS was measured by passing the prepared solution using peristaltic pump. After all subtraction (background and solvent), nanoparticles XAS data were recovered and processed for the fitting. After Fourier transform, it was observed that both nanoparticles posses an additional short peak (or shoulder) at about 1.2 A from bulk. Since the peak appears much closer to 1 A, i suspect this may due to artifact or bad background subtraction. Hence, i would like to know the way to eliminate this peak at short distance. Regards, Raj

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Output of data fit in k-space from current version of Artemis
by Rosalie Hocking 27 May '15

27 May '15

Hi Guys, I am embarrassed to ask this question, but I am fairly new to Artemis (moving over from the dark side of EXAFSPak) Could anyone advise me how to export a fit in k-space? If I go to the Artemis data window and go Data “save data and fit as” it doesn’t seem to match up with the simulations on the window. Exports in R-space seem sensible, but no amount of repetition and changes alternation, of fits etc seems to result in similarly sensible output in k-space. If anyone could help I would appreciate it- I can email you my fit file if it would help. kind regards, Rosalie

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polarization in Artemis
by Bruce Ravel 25 May '15

25 May '15

Hi, Everything in the discussion between Eugenio and Matt is stuff I agree with, except ... When I rewrote Artemis, one of the motivations was that I wanted to write my own pathfinder rather than to continue using the one in Feff. My main motivation was fuzzy degeneracy (http://bruceravel.github.io/demeter/artug/extended/fuzzy.html) plus I wanted to correct a few other things I saw as shortcomings. When I was writing it years ago, I didn't immediately see an easy way to consider polarization correctly while also doing fuzzy degeneracy correctly. I have since figured that out, but years went by and only one person ever asked me about polarized feff calculations in Artemis. So I never implemented it. It's a funny thing, when you wait for a bus, none comes, then two show up at once. A month ago, I was asked about polarization in Artemis, and now Eugenio brings it up! Polarization works (although it needs testing) in the very latest code in github. But I did that work since the last time I built a Windows installer. Ellipticity does not yet work (in Artemis -- it works just fine in Feff, but Artemis does not deliver the ellipticity-dependent calculation to the user). Anyway, I will try to find a few hours this week to build a new Windows installer, which will included the ability to consider linear polarization. > Artemis used to make this very easy (sum paths without fitting), but > I don't recall how to do this in the latest version. Still is easy. Well, I think it is. YMMV :) http://bruceravel.github.io/demeter/artug/plot/vpaths.html 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/

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