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

appropriatness of feff model when central atom is not "embedded" (or only 1 layer embedded)
by Andrea L Foster 07 Mar '12

07 Mar '12

Hello All, can someone please help with this: (1) feff requires that the adsorbing atom be "embedded" (that is, surrounded by) other atoms in order to calculate potentials correctly, but how deeply does the atom need to be embedded? For example, if I construct a model of an adsorbate on a mineral surface, where that adsorbate has a full complement of 1st shell coordinating OH, O, and H2O groups as appropriate, but if I do not include all the uncoordinated f water atoms that would be nearby (so that I essentially have a surface in vacuum), will the potentials for my central atom be calculated correctly (or correctly enough for use in IFEFFIT)? a more specific example: the AsO4 tetrahedron bonded to the goethite surface, which is made of octahedrally-coordinated iron. The arsenate bonds to the goethite by sharing 1 edge of the tetrahedron with the apices of 2 adjacent Fe octahedra. a related question that comes to mind: if I just wanted to see the signal from the 2 adjacent Fe atoms, could I create a perfectly "useable" FEFF model (for IFEFFIT) by limiting my calculations to the small cluster of 1 arsenate tetrahedron and 2 Fe octahedra? thanks, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

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running ifeffit-1.2.11 under 64-bit Windows 7
by sameh 07 Mar '12

07 Mar '12

Hi, I have a new computer with 64-bit windows7. I have noticed that Artemis is running in a strange manner, it never produces the same results when the same data is fitted twice. I have uninstalled and then reinstalled the whole (ifeffit-1.2.11) package with the compatibility wizard which suggested to run the package in compatible mode to windows XP. After doing so, any of the programs is not running at all. My old laptop was 32-bit which runs 32-bit windows 7 and the ifeffit-1.2.11 package was running normally with this computer. Thank you very much and best regards Sameh Ibrahim Ahmed

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Coordination numbers using Artemis and sixpack
by Nicolae L. Aldea 05 Mar '12

05 Mar '12

Dear users, I ealized some XAS measurements regarding to supported gold catalysts as well as a standard sample on Au foil. 1. I like to a comparative analysis using Artemis and sispack. I have obtained some results using Artemis code. Unfortunately, for me is not so clear how to determine coordination numbers associated with each shells. I set dgen =1, I obtained S**2 values then I introduced S**2 in fist sample for fit step but I do not how to obtained values for different coordination shells. 2. Additionally, I like to use sixpack code. In this way I determined all steps up to |chi(r)| I tried to continue with make FEFF SS paths and FEFF exafs fitting. Unfortunately I could start the last steps. Are you so kind to indicate me how to do. Can you indicate me any tutorials or some examples to understand how to create SS paths and exafs fitting. Tanking you in advance Nick Aldea ******************************************************* * Dr. Nicolae L. Aldea * * National Institute for Research and Development * * for Isotopic and Molecular Technologies * * Donath Street 65-103, P. O. Box 700 * * 400293 Cluj-Napoca, Romania * * E-mail: naldea(a)itim-cj.ro * * Details: http://L30.itim-cj.ro/~naldea/index.htm * *******************************************************

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Fe K-Edge in Zirconium alloys and flattening effect
by adrien couet 01 Mar '12

01 Mar '12

Dear all, I am currently a PhD student working on the corrosion of zirconium alloys used in nuclear reactors. A very commonly used alloy in the industry is called Zircaloy-4 and has the following chemical formula in wt%: Zr-1.2Sn-0.2Fe-0.1Cr. The iron and chromium solubility limit in zirconium is very low. A large portion of the iron precipitates out as Zr(Cr,Fe) precipitates with approximately 40wt% of Fe, approximately 0.02wt% of Fe is left in solid solution in the zirconium matrix. Sn is completely soluble in zirconium. I am working on XANES of the Fe K-Edge absorption line in this material. To do so, I use the microbeam (0.2x0.2 microns) at the 2IDD beamline at the APS in fluorescence mode. To quantify my results, I needed proper standards of metallic Fe. I quickly realized that metallic Fe powder mixed with Zr powder did not give me the same XANES signal as the Zircaloy-4 metal (in which metallic Fe is embedded). Indeed, if you compare the "Fe powder in Zr" group to both Zircaloy-4 groups after normalization and flattening they look different. My thinking is that the Fe in precipitates and the Fe in solid solution, even if they are both metallic, could have different XANES patterns. So I decided to create a thin sample where I could probe either a precipitate or the matrix to get standards of metallic Fe in my Zircaloy-4 metal. Both signals (from Fe in a precipitate and Fe in solid solution) look similar once they are normalized and flattened (see in the attached project file). However, the data before flattening look significantly different! The post-edge of Fe in precipitates abruptly decreases whereas the post-edge of Fe in solid solution increases. I also acquired spectra in between these two extreme cases. When I scan in between the matrix and the precipitate, I see an evolution of the post edge, which looks more and more similar to the precipitate post-edge as I get closer to it. But after flattening they all look identical and the XANES spectra does not look too bad. I have some questions regarding this: - Is the flattening process changing anything such as the edge energy in a way that I should not use it when the post-edge slopes are significant as is the case here (even though my XANES spectra in solid solution and in the precipitate match after flattening)? - Have you ever seen this kind of post edge behavior before flattening? Do you think it could be due to a concentration effect since I am going from 0.02wt% of Fe in solid solution to 40wt% of Fe in the precipitate? I should mention that I have checked that no other elements present in the metal have edges that could potentially disturb the Fe post-edge. Thanks a lot for your help!!! -- Adrien Couet Graduate Student Dept of Nuclear Engineering, Penn State University +1 814 865 9709 axc1019(a)psu.edu

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Problem with creation of feff paths for americium in artemis
by Froehlich, Daniel 01 Mar '12

01 Mar '12

Dear Sir or Madam, We are looking forward to a beamtime investigating americium complexes and I wanted to create feff-paths for americium sulfate by using crystallographic data of europium sulfate and replacing Eu by Am. Atoms runs well and creates the feff.inp but when I then try tu run Feff I just get the error message Feff 6L.02 ? Eu H4 N O8 S2 Ruiz-Valero, Caridad New catalytically active neodymium sulfate Calculating potentials and phases... free atom potential and density for atom type 0 cannot remove an electron from this level Fatal Error: at GETORB-1 Their seems to be a problem with the atomic number because if I change Z=95 to 94 it runs without any problem. Is it possible to run it anyway with Z=95 or must I go for 94 instead which is the atomic number of Pu? Furthermore, I wanted to calculate the potentials with SCF approach but I read a lot of "google search results" without finding any helpful information.Or isn't it needed at all...? Many thanks in advance and best regards Daniel Fröhlich ______________________________________________ Dr. Daniel Fröhlich Physikalisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 253 D-69120 Heidelberg, Germany Institut für Nukleare Entsorgung (INE) Karlsruher Institut für Technologie (KIT) Campus Nord P.O. Box 3640 D-76021 Karlsruhe, Germany

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Single shell
by Anatoly I Frenkel 24 Feb '12

24 Feb '12

Dear subscribers: For your amusement, attached is a quintessential single-shell EXAFS spectrum. Second in simplicity, perhaps, after only mu_not. It is taken from a bulk metal oxide. The k-range in FT: from 2 to 15 A^-1. Can be used for teaching EXAFS basics. If anyone is interested I will send raw data. Anatoly

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AuPd CIF
by Kaiser, Julian 23 Feb '12

23 Feb '12

Dear ifeffit-list members, I'm looking for an AuPd CIF (crystal information file). I couldn't find one at the Crystallography Oben Database (www.crystallography.net<http://www.crystallography.net/>) or at the mailing-list archive. I've seen measurements at AuPd-foil published, so I think there meight also exist an CIF. Would be nice, if someone could give me a hint. Thanks for your kind help, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Corrupt .apj file
by Heinzel, John M CIV NSWCCD Philadelphia, 985 22 Feb '12

22 Feb '12

Hello, I was working on a number of different structures (Atoms pages and then FEFF input files), when one got "stuck" for some reason. While I've saved my file all the way through, the one structure that is causing an issue always makes Artemis get stuck (computer is totally fine but Artemis is unresponsive and CPU use goes to 100%) now, IF I click on it. Leave it alone and Artemis is fine, and I can work on the other theory sets. Since I cannot click on the one atoms/FEFF data set that I want to get rid of (without Artemis getting stuck, that is), is there an alternate way to edit .apj files so that I can remove the problem atoms/FEFF listing so that the file can remain functional? FYI, I'm running Artemis in iEXAFS 3.0.3 on OSX 10.7, if that helps. Thanks, John Heinzel

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Re: [Ifeffit] Ifeffit Digest, Vol 108, Issue 17
by 陈娟 15 Feb '12

15 Feb '12

Dear Bruce Thanks a lot for your suggestion. Yes, I did according your suggestion. I did the self-absorption correction and got the perfect spectrum as shown below. However, for the pure standards without dilution by BN, How to do the self-absorption correction? For example, I try one, but cannot get the credible spectra. ForDibenzyl Disulfide, the formula should be (C14H14S2)0.5435(BN)0, no dilution. I put (C14H14S2)0.5435(BN)0 in, but the spectrum I got is So can you tell me how to do the pure standards self-absorption correction using Athena? Much appreciated. Warm regards Juan Chen At 2012-02-15 02:00:01,ifeffit-request@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: fitting sulphur using standards by Athena (Bruce Ravel) > 2. Re: fitting sulphur using standards by Athena (Matthew Marcus) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 14 Feb 2012 09:07:45 -0500 >From: Bruce Ravel <bravel(a)bnl.gov> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] fitting sulphur using standards by Athena >Message-ID: <201202140907.45529.bravel(a)bnl.gov> >Content-Type: Text/Plain; charset="utf-8" > >On Tuesday, February 14, 2012 07:55:54 am ?? wrote: >> As I known, the spectra for standard diluted with BN and non-diluted are >> different. The peak of the non-diluted is low due to self-absorption, as >> shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur >> to about 3%. For dilution, the position of the peak is also changed. >> Therefore the non-diluted s1 spectra isnot the real spectra of >> dibenzothiophene. The question is what percentage should I dilute the >> standard to get the credible spectra for the standards?and how to explain >> the peak position change? > >Although this sort of thing can be approximated from tables of >absorption coefficients, the advice I usually give to my users is to >prepare a series of samples of diminishing concetrations and measure >then. > >Having a good intuition for sample preparation and the effects of poor >sample preparation is always important and even more so for low energy >edges. The best way to develop that intuition is by doing the >experiment yourself. > >> Can I use Athena to counteract the self-absorption and get the >> credible spectra for sdandards? > >Yes it can -- in principle. Doing a good job of self absorption >correction requires a lot of knowledge about your sample and its >matrix -- often more than one has. > >The use of the self absorption tool is explained in the Athena >document. I have also written a lecture on this topic. Go to > > https://github.com/bruceravel/XAS-Education/downloads > >and download the "selfabs.pdf" file. > >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/ifeffit/Demeter > > > >------------------------------ > >Message: 2 >Date: Tue, 14 Feb 2012 07:33:38 -0800 >From: "Matthew Marcus" <mamarcus(a)lbl.gov> >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] fitting sulphur using standards by Athena >Message-ID: <03B21711433A40B4AA45C3DE3410452A(a)als.lbl.gov> >Content-Type: text/plain; format=flowed; charset="utf-8"; > reply-type=original > >To reiterate a point which is often not understood - dilution won't fix overabsorption if the particles of the concentrated material >which are mixed in with the diluent are too big. For concentrated S compounds, "too big" is in the low microns. >When I run a S standard, I do it in total electron yield to avoid this problem. When I fit a S spectrum, I use a crude >oveabsorption model with a single parameter which is treated as an unknown fitting parameter, with the assumption >that the reference spectra were collected in a way which avoids overabsorption. > mam >----- Original Message ----- >From: "Bruce Ravel" <bravel(a)bnl.gov> >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> >Sent: Tuesday, February 14, 2012 6:07 AM >Subject: Re: [Ifeffit] fitting sulphur using standards by Athena > > >> On Tuesday, February 14, 2012 07:55:54 am ?? wrote: >>> As I known, the spectra for standard diluted with BN and non-diluted are >>> different. The peak of the non-diluted is low due to self-absorption, as >>> shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur >>> to about 3%. For dilution, the position of the peak is also changed. >>> Therefore the non-diluted s1 spectra isnot the real spectra of >>> dibenzothiophene. The question is what percentage should I dilute the >>> standard to get the credible spectra for the standards?and how to explain >>> the peak position change? >> >> Although this sort of thing can be approximated from tables of >> absorption coefficients, the advice I usually give to my users is to >> prepare a series of samples of diminishing concetrations and measure >> then. >> >> Having a good intuition for sample preparation and the effects of poor >> sample preparation is always important and even more so for low energy >> edges. The best way to develop that intuition is by doing the >> experiment yourself. >> >>> Can I use Athena to counteract the self-absorption and get the >>> credible spectra for sdandards? >> >> Yes it can -- in principle. Doing a good job of self absorption >> correction requires a lot of knowledge about your sample and its >> matrix -- often more than one has. >> >> The use of the self absorption tool is explained in the Athena >> document. I have also written a lecture on this topic. Go to >> >> https://github.com/bruceravel/XAS-Education/downloads >> >> and download the "selfabs.pdf" file. >> >> 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/ifeffit/Demeter >> >> _______________________________________________ >> 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 108, Issue 17 >****************************************

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fitting sulphur using standards by Athena
by 陈娟 14 Feb '12

14 Feb '12

Dear Sir, I face one quite confusing question. Hope to get your help about using Athena to do the fitting. What I am concerning is sulphur species in my char sample. However, I cannot get the good fitting results due to the standards i used. Please see the following figure. S1 in the figure means the dibenzothiophene standard, c26 is my char sample. I intend to fit the char sample by using the standards such as dibenzothiophene, dibenzyl disulfide, sulphate and so on, to get the sulphur species. However, because of the self-absorption, the pure standard spectra intensity is even lower than our char sample as shown in fig. 1. If I do like this, the fraction is higher than 1 in my sample, I cannot get the reasonable fitting data. So how to do the fitting? As I known, the spectra for standard diluted with BN and non-diluted are different. The peak of the non-diluted is low due to self-absorption, as shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur to about 3%. For dilution, the position of the peak is also changed. Therefore the non-diluted s1 spectra isnot the real spectra of dibenzothiophene. The question is what percentage should I dilute the standard to get the credible spectra for the standards?and how to explain the peak position change? Can I use Athena to counteract the self-absorption and get the credible spectra for sdandards? Waiting for your reply. Thank you very much. Best regards Juan Chen

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