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

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 21 May '15

21 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 11 May '15

11 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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Ca EXAFS with Ge220 or InSb111
by Lisa Bovenkamp 11 May '15

11 May '15

Hello. After having some troubles recording a good EXAFS spectrum with some old InSb111 crystals I started wondering if it might be better to use Ge220 instead. Anybody have some experience with that? Lisa

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Scatter Plot in Athena
by Shoaib Muhammad 05 May '15

05 May '15

Dear All, In Athena documentation section I can see data plotted as scatter instead of line type plot (for example the plot shown in the attached file). This feature seems to be helpful in deglitching the bad data points but I could not figure out how to do it! Can anybody guide me how to plot data as scatter in Athena? My platform is Windows8 x64. Thanks, /Shoaib

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Re: [Ifeffit] Self absorption Correction
by Richard Mayes 04 May '15

04 May '15

Farzana, I'm copying the IFEFFIT mail list, they may have the information buried in the archives somewhere. That link points to Grant Bunker's webpage containing his XAFS tutorials and it will not open for me at the moment either. However, there are several very good books that have come out lately on XAFS that explain self absorption quite well. If you're not interested in getting a copy of the books, there is a discussion thread from when I was a newbie to overabsorption that is found on the XAFS.org tutorials page. I suggest going through it as several contributed substantial knowledge in that thread (http://www.xafs.org/Experiment/OverAbsorption) Cheers, -Rich On Mon, May 4, 2015 at 7:47 PM, Farzana Nasreen <farzana6109(a)gmail.com> wrote: > Dear Rich, > > http://cars9.uchicago.edu/pipermail/ifeffit/2009-February/008631.html > > I was looking at this above link to find out similar information that Jen > had. Unfortunately, I couldn't open the link in the reply that you gave to > her. > Do you know where I can download this paper by > > *http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf <http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf>* > > I am working on some PFY-XAS data on some uranium compounds. > > Thanks > > Farzana > > > > >

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