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

Large Enot values
by Paul Bingham 08 Jun '10

08 Jun '10

Hi, I have been struggling with a tricky problem and cannot resolve it - hopefully someone out there can help! I have collected fluorescence XANES and EXAFS at the Se K-edge and I'm currently trying to fit the EXAFS (see attached files). The XANES agrees very well with a number of my standards and shows that the vast majority, if not all, of the Se is present in this material (an amorphous oxide-based system) as Se4+. I have tried to fit the EXAFS using a single Se-O path from a range of cif files (the simplest being SeO2). Other ions than O present incorrect bond lengths and I am convinced the first shell is oxygen. I can obtain a decent fit in terms of most parameters, as long as I disregard the consistently high value of Enot. Guidelines indicate that Enot should be less than about 5(ish), but I consistently get values of 10-12 when I try to fit my spectra, of which one is present in the attached files. I have checked my background subtraction and tried as many different options, changes and tweaks that I know or can find suggested (too many to list here) but I cannot obtain a fit with Enot below about 10 and so I ask my colleagues out there who are more experienced than I with EXAFS - can anyone shed any light on (a) the potential cause/s and (b) any potential solution/s? Thanks in advance for your time. Best Regards Paul Bingham -- Dr. Paul Bingham Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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Re: [Ifeffit] Ifeffit Digest, Vol 88, Issue 4
by Jatinkumar Rana 08 Jun '10

08 Jun '10

Dear Dominik, Thank you so very much for your detailed explanation about the effects of particle size on XAFS spectra. Warm wishes, Rana On 07.06.2010 19:00, 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. particle size effects on XAFS spectra (Jatinkumar Rana) > 2. Re: particle size effects on XAFS spectra (Dominik Samuelis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 07 Jun 2010 14:49:33 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: Ifeffit users<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] particle size effects on XAFS spectra > Message-ID:<4C0CEADD.8040600(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Users, > > I am working with the EXAFS technique for the characterization of my > powder sample. I must admit that i am very much new to the technique and > its analysis. I have read many tutorials on preparing sample for XAFS > measurement (both transmission and fluoroscence). However, i am dealing > with the powder having particle size much more smaller than one > absorption length. > > I would like to know will it create any destructive effect on my XAFS > spectra ?? > > Many thanks in advance... > > Warm wishes, > Rana > > > ------------------------------ > > Message: 2 > Date: Mon, 07 Jun 2010 15:21:14 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] particle size effects on XAFS spectra > Message-ID:<4C0CF24A.10407(a)fkf.mpg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Rana, > > yes, it will have effects on your XAFS spectra, but not really > destructive. EXAFS only really vanishes if you have isolated atoms. As > long as your particles still have several hundred atoms with some > coordination shell-like ordering, EXAFS oscillations will show up. > > However, the amplitude of the XAFS signals will be smaller than in bulk > material, due to the lower average coordination number of the central > atoms. If you e.g. have 5 nm particles (some 2000 atoms), already almost > half of the atoms (~800) is sitting on the particle surface and > therefore has a reduced coordination number. > > There's a wealth of information in literature where people actually use > this effect for determining the particle size from XAFS. > > Another thing to keep in mind is that often it's not really clear how > the surfaces of a particle looks like chemically - there might be > adsorbates, or even passivation layers. If you're e.g. doing EXAFS on > untreated 5nm Si particles, you can't really expect to see anything > close to bulk Si, because the top layer might be SiO2 > > Best regards, > Dominik > > > > On 07.06.2010 14:49, Jatinkumar Rana wrote: > >> Dear Users, >> >> I am working with the EXAFS technique for the characterization of my >> powder sample. I must admit that i am very much new to the technique and >> its analysis. I have read many tutorials on preparing sample for XAFS >> measurement (both transmission and fluoroscence). However, i am dealing >> with the powder having particle size much more smaller than one >> absorption length. >> >> I would like to know will it create any destructive effect on my XAFS >> spectra ?? >> >> Many thanks in advance... >> >> Warm wishes, >> Rana >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >

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particle size effects on XAFS spectra
by Jatinkumar Rana 07 Jun '10

07 Jun '10

Dear Users, I am working with the EXAFS technique for the characterization of my powder sample. I must admit that i am very much new to the technique and its analysis. I have read many tutorials on preparing sample for XAFS measurement (both transmission and fluoroscence). However, i am dealing with the powder having particle size much more smaller than one absorption length. I would like to know will it create any destructive effect on my XAFS spectra ?? Many thanks in advance... Warm wishes, Rana

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1st North American Core Shell Spectroscopy Conference
by Carlo Segre 04 Jun '10

04 Jun '10

Hello All: Please share this announcement with anyone whom you feel might be interested. I am positive that I am not getting this out to the entire core shell spectroscopy community. The abstract deadline has been extended until June 1 for oral presentations. ---- Conference Announcement ---- 1st North American Core Shell Spectroscopy Conference to be held jointly with the 59th Denver X-ray Conference 2-6 August 2010 Ι Denver Marriott Tech Center Hotel, Denver, CO <https://resweb.passkey.com/Resweb.do?mode=welcome_ei_new&eventID=1454471> The first North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-Ray Conference, 2-6 August 2010. The conference will feature poster sessions as well as oral presentations and students, in particular are encouraged to participate with oral presentation submissions. All topics relating to core shell spectroscopy are welcome, including: · X-ray Absorption Spectroscopy · X-ray Fluorescence Spectroscopy / Fluorescence Mapping · Resonant Inelastic X-ray Scattering / X-ray Raman Scattering · X-ray Magnetic Circular Dichroism The conference will feature a special session and dinner in honor of Ed Stern. The list of invited speakers for this special session includes Dr. Mali Balasubramanian, Argonne National Laboratory Prof. Jerry Seidler, University of Washington Prof. Anatoly Frenkel, Yeshiva University Dr. Ken Kemner, Argonne National Laboratory Prof. John Rehr, University of Washington Prof. Michael Paesler, North Carolina State University The other invited speakers are: Dr. Corwin Booth, Lawrence Berkeley National Laboratory Prof. James Penner-Hahn, University of Michigan Prof. Daryl Crozier - Simon Fraser University Prof. Bruce Bunker - University of Notre Dame Prof. Trevor Tyson - New Jersey Institute of Technology Dr. Joshua Kas - University of Washington Dr. Simon Bare - UOP LLC Participants will be able to attend Denver X-Ray Conference Sessions being held in adjacent rooms. Details of the oral presentation sessions will be posted on the DXC web site <http://www.dxcicdd.com/default.htm> as they are available. Students are able to register for a reduced cost, are eligible for special student room rates <http://www.dxcicdd.com/10/details.htm#studentrooms>, and may apply for funding <http://www.dxcicdd.com/10/files/2010-DXC-Student-Travel-Grant-application.p…> to attend the conference. Abstract submissions for oral presentations will be open until June 1 and can be made on the Denver X-Ray Conference web site by selecting the "Submit Abstract for the Joint Meeting with the North American Core Shell Spectroscopy Conference" link on the left side of the page (the 8th button down) or directly at the abstract submission page <http://www.dxcicdd.com/cssc/cssc_abstract.asp>. For more information, visit http://www.dxcicdd.com or contact: Denise Flaherty, Conference Coordinator flaherty(a)icdd.com<mailto:flaherty@icdd.com> ICDD 12 Campus Boulevard Newtown Square, PA 19073 -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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plots from athena
by Saugata Datta 31 May '10

31 May '10

Hello, if you can help me with this question: I am trying to plot directly from athena via powerpoint for a publication/manuscript quality plot., I read a message posted that " "If you want to adjust things like fonts and line sizes on the plot for publication, then you have the option to save the plot as a metafile from the PGPlot window and import it into PowerPoint. Then convert the metafile into a drawing object with the "ungroup" feature. From this point you can change fonts, line shapes, colors, etc. to get the plot how you want it to look for publication. You can then re-save that slide as a picture (gif, tiff, metafile, etc) to be imported into the manuscript. This can get time intensive, but it's an alternative if all you want to do is adjust fonts and line colors/sizes. One caveat though, don't change the data! You can easily and unknowingly change the data if you're not careful (performing an action on one part of the drawing object without realizing another is highlighted for example) so always compare the final product to the original to make sure it's the same"... But I cannot find where the PGPlot window is., if you can kindly help. Say I want to plot six standards plotted /stacked one on top of the other in one figure, with correct seuqnce of legend? Can I do this without exporting to excel??? Thanks again... Saugata _________________________________________________________________ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID2…

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Exporting derivative data
by Paul Bingham 31 May '10

31 May '10

Hi, I wonder if you can help: I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window. Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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the use of constraints
by Kellie Aldi 28 May '10

28 May '10

Hi, I have a question on the use of constraints and restraints in EXAFS data fitting. I am using SixPack to build a model for the EXAFS of some synthetic layered transition metal (TM) oxides with relatively large amounts of layer vacancies. I am refining the occupancy of the layer TM site, from which I can determine the amount of layer vacancies. I want to include a parameter in this model that refines the number of these vacancies that are capped by interlayer TM (something that can happen in these structures), but I am having difficulty in deciding a responsible way to define the parameters of this variable. I am modifying the intensity of the interlayer TM scattering paths with a parameter fcap = (1-focc)*percap where focc is the refined occupancy of the layer TM site, and percap is the percentage of vacancies, "1-focc", that are capped by interlayer TM. However, just letting percap float, the value goes greater that 1... which, as a percentage, does not make much sense physically in my model. So I want to keep the value of this between 0 and 1. I have tried what was suggested on the IFEFFIT frequently asked questions page regarding constraints and restraints. I don't feel comfortable simply using a constraint and forcing the value to be between 0 and 1 using the suggested min/max idiom. I like better the idea of penalizing a fit when percap is outside of a defined range and thus "encouraging" the fit to settle percap somewhere inside this range. But in trying to use the restraint idea, including the fix suggested by Matt Newville for only penalizing the fit outside of the min/max range, percap still goes slightly above 1 (about 1.02) and in my results I get a value for the "penalty" that I am unsure how to interpret. Can this value be used to understand why the restraint still allows the value of percap to be outside of the defined "ideal" range? I am trying to understand how the restraint that Matt Newville defined in the link in the restraints/constraints FAQ works, but I am relatively new to EXAFS modeling and thus shaky on my skills at defining these parameters and knowing how certain math functions can be used. Are there any other help sections or guides that might address the use of such restraints? Or any suggestions on how to re-define this restraint? I would greatly appreciate any suggestions/input! Thanks, Kellie Aldi

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athena an widows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Inst. f. Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) - Campus Süd Engesserstrasse 18 76131 Karlsruhe email: matthias.bauer(a)kit.edu phone: +49 721 608 4320

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athena an windows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Karlsruhe Institute of Technologie - Campus Süd Inst. für Technische Chemie und Polymerchemie Engesserstrasse 18 76128 Karlsruhe email: matthias.bauer(a)kit.edu phone: 0049 721 608 4320

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fitting
by mohamed sobhy 26 May '10

26 May '10

----- Forwarded Message ---- From: mohamed sobhy <bakhshwan1981(a)yahoo.com> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Thu, May 20, 2010 4:14:18 PM Subject: [Ifeffit] fitting Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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