May 2012 - Ifeffit - millenia.cars.aps.anl.gov

Feff 9.0 CFAVERAGE
by Dreher Marian 05 Jun '12

05 Jun '12

Dear feff community, I'm aware that the issue of CFAVERAGE not creating a xmu.dat output file has already been discussed some years ago for feff 8.2; back then it was suggested to make some changes in the source code and recompile or wait for a newer version of feff in which this bug would be fixed. However, I'm running feff 9.0 and I still seem to have this issue. When using the CFAVERAGE card, no xmu.dat or chi.dat output is being created. Do I still need to manipulate the source code do fix that? Many thanks, Marian. Marian Dreher, Dipl. Chem. PhD Student, Catalytic Process Engineering Group Paul Scherrer Institut General Energy Research (ENE) Laboratory for Bioenergy and Catalysis Office: OLGA/221 CH-5232 Villigen PSI Switzerland Phone: +41 (0)56 310 2937 email: marian.dreher(a)psi.ch

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how to obtain average vacancy files?
by María Elena Montero Cabrera 31 May '12

31 May '12

Dear friends, I am trying to fit with Artemis, not very successfully, a maghemite structure. The main difficulty seems to be the vacancies in the structure. My idea, following a recently given Bruce’s advice to a person in this list, is to obtain “average vacancies” FEFF files and to work with the fully occupied magnetite structure. I wanted to obtain each file for a given vacancy configuration in the first coordination sphere and then to multiply the obtained functions by the weight of each configuration and summ them all. I had the hope of doing this by using the feff00nn.dat files that I have used when working with SixPack, some years ago. Surprisingly, I couldn’t find the Artemis’ corresponding feff00nn.dat files at any folder. What can I do? -- María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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atoms file of Zr-foil
by JeongEunSuk 26 May '12

26 May '12

Hello everyone Does anybody know atoms file of Zr-foil? I checked it in atoms.inp archive but it is no there. so I made it as following: title name: Zirconium title formula: Zr title sites: Zr1 title refer1: title refer2: title schoen: title notes1: metal, hexagonal close packed space p 63/ m m c a = 3.232 b = 3.232 c = 514.7 alpha= 90 rmax = 6.00 core = Zr1 atom Zr 0.33333 0.66667 0.25000 Zr1 ------ is it right?

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problem with Demeter- Artemis/Atoms
by Matt Frith 24 May '12

24 May '12

I was attempting to import a .cif file into Artemis to use for a FEFF calculation and I am getting the following error message: "Atoms is currently unable to use crystal data which has sites of partial occupancy. Sorry." These .cif files work fine with the old version of Artemis/Atoms. Is there currently a way around this problem, or is this something that will be addresses in later version. Thank you for your help. Sincerely, Matt Frith

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Question: About using polarization and ellipticity cards in FEFF
by xu dongbin 13 May '12

13 May '12

Hi, I would like to ask a question which has confused me for a few days. In my current case, I'm dealing with samples with c texture in the film normal. The sample was measured with linear polarized x-ray in both directions with the surface of sample parallel/perpendicular to the electrical field of x-ray. During measurement, the sample was always rotated around the film normal. Therefore, I think the parallel direction data can be treated with random orientated grains in the film plane. In order to describe this, I need use POLARIZATION and ELLIPTICITY cards in FEFF calculation. However, I'm not sure which case below is the correct one I should include in FEFF calculation for my case: a. POLARIZATION 1 1 0 ELLIPTICITY 1 0 0 1 b. ELLIPTICITY 1 0 0 1 I think these two cases should give the same calculation results, however, when I sum the paths in these two cases respectively using the same parameters(S02, E0, delR, sigma^2). The results give substantial difference. Can anyone help me to figure out this? Thanks&Regards!

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Debye function model, Math expression
by NIRAWAT THAMMAJAK 11 May '12

11 May '12

Hello, May I add more questions to this. I do a research on magnetic materials. Bond lenghts and geometries are really important to understand the magnetic interactions and I think EXAFS is the promising tool for this. I have measured the EXAFS spectra for quite a complex material system. There are 3 sites of absorbing atom (Fe) in the crystal structure, therefore I created 3 FEFF models to fit the data with different amplitudes. Closest neighbours are oxygen atoms, and then Li. The strongest scatterers are La atoms sitting ~4.26 angtrom away from the absorbing atom, which contribute a significant 3rd shell. Yes, there are many paths to include. Math expressions together with bulk structure details obtained from neutron diffraction help to minimise the parameters somewhat. However, there are thermal factorss, very small but too many of them. I measured my sample at 1.5 K, then sigma^2 are quite small. Could you please suggest any papers, models, or math expressions constraining these factors at low temperature. Would it be sensible to constrain them as 0, or a range of small numbers obtained from the significant shells? Thank you very much, Nirawat. On 24 August 2010 18:25, Frenkel, Anatoly <frenkel(a)bnl.gov> wrote: > Just to add: > These procedures, described in that article, can be easily implemented in > Mathematica. > Anatoly > > > ------------------------------ > *From:* ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Ravel, > Bruce > *Sent:* Tue 8/24/2010 1:23 PM > *To:* XAFS Analysis using Ifeffit > *Subject:* Re: [Ifeffit] debye function > > On Tuesday 24 August 2010 12:23:18 pm Kleber Daum Machado wrote: > > Hi, > > > > I'd like to know the explicit mathematical expressions that are > > represented by the functions debye(temp,thetad) and eins(temp,thetae). > > Are they given in some documentation file or article? > > See > > "Extended x-ray absorption fine structure Debye-Waller > factors. I. Monatomic crystals" > E. Sevillano, H. Meuth, J. J. Rehr > Phys. Rev. B 20, 4908–4911 (1979) > http://link.aps.org/doi/10.1103/PhysRevB.20.4908 > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > _______________________________________________ > 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 > >

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Problem with Ifeffit 1.2.11 on Windows XP
by 최선희(Sun Hee Choi) 08 May '12

08 May '12

Dear XAFS colleagues, I use Ifeffit 1.2.11 on Windows 7 machine with no difficulty, but that version bothers me when applied to Windows XP. One of useful tips is to select a value from the plot, that is the use of Pluck Button. When I try to select a value with pluck button, a wrong value is grabbed. Hardly a right value is grabbed! This problem also occurs in point finder. And, ‘Indicator’ does not work at all…I cannot see vertical lines…. Please help me to resolve the problem. Sunny ------------------------------------------------------------ Pohang Accelerator Laboratory (PAL) / POSTECH San 31, Hyojadong, Namgu, Pohang 790-784 Republic of Korea -------------------------------------------------------------

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Re: [Ifeffit] Ifeffit Digest, Vol 111, Issue 5
by Christopher Thomas Chantler 07 May '12

07 May '12

Hi All There has been much discussion of this at the recent Q2XAFS meeting. Proceedings are I believe being reviewed at the moment. >From I think some consensus of those attending, the most critical and most portable data was [mu/rho] versus E, with uncertainties; or mu versus E. Secondary data such as k^2chi vs k or chi vs r etc remains valuable of courseŠ I hope this helps. With luck there will be much discussion of this in Beijing [if we can all get visas!] Chris ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Secretary, Steering Committee, International IUCr Commission on XAFS Vice-President (Australasia) International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html On 8/05/12 3:00 AM, "ifeffit-request(a)millenia.cars.aps.anl.gov" <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: Writing a paper (Bruce Ravel) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 07 May 2012 12:32:16 -0400 >From: Bruce Ravel <bravel(a)bnl.gov> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] Writing a paper >Message-ID: <3694643.vNiDHMscfl@lachesis> >Content-Type: text/plain; charset="us-ascii" > >On Monday, May 07, 2012 04:10:35 PM mattie.peck(a)huskers.unl.edu wrote: >> Hello Everyone, >> >> I am in the process of fitting XAFS data for a paper and I was wondering >> what type of information should should be included. I remember coming >> across a website that had this information on it awhile ago but I can't >> seem to find my way back. We would like to publish a qualitative XANES >> paper and an EXAFS paper. Any suggestions on the type of information >> (plots, tables, R-factor, etc.) that should be included in each paper >> separately would be appreciated. > >Was this the page you were looking for? > > http://xafs.org/Reporting_EXAFS_Analysis > >Incomplete, but useful. > >B > > >-- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > Homepage: http://xafs.org/BruceRavel > Software: https://github.com/bruceravel > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 111, Issue 5 >*************************************** >

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Peak fitting in Excel
by Luanga Nchari 07 May '12

07 May '12

Hi folks, Does anybody know how to plot data for Gaussian and arctangent step peaks (from Athena) in Excel. I can't find the data after peak fitting. I've also searched in the Ifeffit mailing list archive. Cheers, Luanga

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Writing a paper
by mattie.peck＠huskers.unl.edu 07 May '12

07 May '12

Hello Everyone, I am in the process of fitting XAFS data for a paper and I was wondering what type of information should should be included. I remember coming across a website that had this information on it awhile ago but I can't seem to find my way back. We would like to publish a qualitative XANES paper and an EXAFS paper. Any suggestions on the type of information (plots, tables, R-factor, etc.) that should be included in each paper separately would be appreciated. Thanks, Matthea Peck

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