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

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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polarization on FEFF calculation
by Eugenio Paris 24 May '15

24 May '15

Dear all, i have a question about polarization vector in performing the FEFF calculation in Artemis. I am studying the system CeOBiS2 using Bi L3-edge EXAFS. Starting from *.cif file i'm creating the *.inp file which atoms list come out as follows: ATOMS * this list contains 35 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 bi 0.00000 0.00000 0.00000 2.50509 4 s2.1 2.50509 2.81711 0.00000 -0.12006 4 s1.1 2.81967 -2.81711 0.00000 -0.12006 4 s1.1 2.81967 0.00000 2.81711 -0.12006 4 s1.1 2.81967 0.00000 -2.81711 -0.12006 4 s1.1 2.81967 0.00000 0.00000 -3.31180 4 s1.2 3.31180 ... Bismuth has a S atom sitting on top of him (s2) and it is square coordinated with other four S atoms (s1). I made measurements on single crystals using fluorescence yield. The experimental geometry consist of the x-ray beam coming at (almost) normal incidence which corresponds to electric field vector lying on the crystal's ab plane. If I perform the FEFF calculation without taking account of polarization I obtain the first scattering paths which are 1) @S2.1@, Degen = 1, Reff = 2.5051, Rank = 100 2) @S1.1@, Degen = 4, Reff = 2.8197, Rank = 100 3) @S1.2@, Degen = 1, Reff = 3.3118, Rank = 14.78 4) ...... When I insert the line "POLARIZATION 1 0 0" in the imput file i get 1) @S2.1@, Degen = 1, Reff = 2.5051, Rank = 100 2) @S1.1@, Degen = 4, Reff = 2.8197, Rank = 100 3) @S1.2@, Degen = 1, Reff = 3.3118, Rank = 3.67 4) ...... which is exactly the same result for the first 2 scatterings, even if the rank of higher shells is changed... Now, my question is: If the components of the polarization vector has to be written in the same reference frame of the atom list i'm expecting to see a strong suppression of the rank factor for the @S2.1@ scattering whose bond is along the z-direction, is it correct? the .cif file is attached Thank you in advance, Eugenio

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Plucking issue in the deglitching
by Shoaib Muhammad 23 May '15

23 May '15

Dear all, I am using Demeter Athena 0.9.21 on Windows 8.1 x64. Recently I measured some XAS data in which there are some glitches. Somehow pluck tool is working very inaccurate for me during deglitching. I can't select the point where I click, so I have to remove several points in order to get rid of one point. I have attached a short screen cast video along with sample XAS dataset in which I am trying to remove a point from pre-edge for demo purpose. I would be thankful if you could look into it. Regards, /Shoaib

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Re: [Ifeffit] Ifeffit Digest, Vol 147, Issue 10
by kakarla chandu 22 May '15

22 May '15

Dear all I am Dr. Chandrasekhar working on experimental condensed matter physics in NSYSU-Taiwan. As a part of my research, I am carrying XAS experiments for some multiferoic and strongly correlated systems. This is very new topic for me. As a part of my research I am studying one system. In that particular system, I face a situation where Cu2+ ions surrounded by five oxygen ligand atoms in different ligand geometries. That is CuIO5 is in square pyramid and CuIIO5 in trigonal bipyramid. So I did the EXAFS spectrum now how can I analyze the data, since XAS is element specific the Cu element scan I got one spectrum but I don’t know whether it is coming from CuIO5 or CuIIO5. So if you have any suggestion please help me Waiting for your reply. With Regards Dr. Chandu On Thu, May 21, 2015 at 6:31 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. Plucking issue in the deglitching (Shoaib Muhammad) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 22 May 2015 10:31:23 +0900 > From: "Shoaib Muhammad" <mshoaibce(a)gmail.com> > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Plucking issue in the deglitching > Message-ID: <002b01d0942f$05b44b60$111ce220$(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > > > Dear all, > > > > I am using Demeter Athena 0.9.21 on Windows 8.1 x64. Recently I measured > some XAS data in which there are some glitches. Somehow pluck tool is > working very inaccurate for me during deglitching. I can't select the point > where I click, so I have to remove several points in order to get rid of > one > point. I have attached a short screen cast video along with sample XAS > dataset in which I am trying to remove a point from pre-edge for demo > purpose. > > > > I would be thankful if you could look into it. > > > > Regards, > > /Shoaib > >

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help
by Jagadesh K Kesavan 12 May '15

12 May '15

Hi I have windows 8 (32 bit) operating system in my laptop. I am not able to istall the six pack software, It is not working in my pc. What is the problem? how could i resolve this problem? Do i get the proper six pack software for windows 8 (32 bit)? Kindly suggest me. Looking for your reply. Thank you. With Best Regards, ----------------------------- *JAGADESH KOPULA KESAVAN* PhD Research Scholar Material Science and Nanotechnology Department of Science University of Rome 3 Via della Vasca Navale 84, 00146, Rome, Italy. E-mail: jagadesh.kopulakesvan(a)uniroma3.it Tel: 06/57337054 Mob: +39 3207769588 -----------------------------

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Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)
by Lisa Bovenkamp 12 May '15

12 May '15

Hello. No, the resolution is fine. I can do XANES fine with InSb111. We use those for years. Just had problems with EXAFS because for this long range the flux has to be more stable from the crystals. Lisa

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