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

Re: [Ifeffit] What does FEFF stand for?
by Scott Calvin 10 May '11

10 May '11

Right, Chris. There is a factor in the EXAFS equation, f(k). In different parts of the literature, f(k) sometimes has different meanings, but within the context of FEFF it refers to the effect of the potential of the scattering atom on both the scattering amplitude (the real part) and phase (the imaginary part). Thus, it stands for "f effective." My understanding, although I could be wrong is that the "effective" part came from an improvement of the theory to account for curved-wave effects. In other words, early theories approximated the photoelectron as a plane wave, but of course it spreads out radially from the absorbing atom. That change necessitated tweaking the definitions of the factors, so it became the "effective" f. --Scott Calvin Sarah Lawrence College On May 10, 2011, at 11:53 AM, Christopher Patridge wrote: > On 5/10/2011 2:49 PM, Francisco Garcia wrote: > > Dear all, > > I wish to ask a somewhat novice question: What does the acronym FEFF > stand for? > > Thank you. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > I am pretty sure it stand for the calculated Effective Scattering > factor F(eff)ective. > > buena salud, > > Chris Patridge > > > <ATT00001..txt>

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atoms possible bugs
by George Sterbinsky 10 May '11

10 May '11

Hello, I want to make everyone aware of some bugs that I think I have found in atoms, and pose some questions regarding the bugs, to anyone who may have seen them before. I have attached two atoms input files, generated using the Artemis atoms interface. The file A2n_atoms.inp is for a monoclinic structure in the A 2/n setting. On running atoms, one will find that there are six Ga atoms within a 4 A radius from the central Ga atom. If one reduces the the cluster size from 8 A in the .inp file to 6 A, one finds that now there are only two Ga atoms within 4 A of the central Ga atom. So it appears that atoms does not necessarily include all atoms within the cluster radius. The leads me to the question: how big should I make the cluster if I want to include all atoms within 6 A? An input file for the same structure converted to the C 2/c setting is also attached. When running atoms in the Artemis interface, the message "The axis lengths and angles specified are not appropriate for the given space group" is returned. Although, it appears that a Feff.inp file is still generated. It also appears to not have the same cluster size dependence as the A2/n structure. So can I trust this feff.inp file even though I received an error message? It seems to me that the answer would be yes, atoms did the calculations correctly and the error message being generated is just a bug, but I'm not certain about this. Thank you, George

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Re: [Ifeffit] Athena (Question about LC fitting)
by Bruce Ravel 10 May '11

10 May '11

Belay, I am CCing my response to the Ifeffit Mailing List, which is the appropriate venue for questions about the use fo the software. I encourage you to subscribe to and use the mailing list. On Tuesday, May 10, 2011 08:50:10 am you wrote: > Dear Dr. Ravel, > I am doing my PhD in title with identication of Fe-phases in cement > hydrates. I am using Athena for LC fitting. I use EXAFS spectra for the > fittings. My question is before LC fitting of EXAFS spectra , do I need to > calibrate the energy? I have normlized and alligned the spectra very well. > The problem is data calibration, when I calibrate the spectra, the energy > shifts and it destroys the fitting. Can you please give a clue why this > happens or do I make a mistake on the procedure? Thanks so much for your > cooperation. Alignment puts a group of spectra on the same relative energy scale. It is often necessary to do an explicit alignment when working at a beamline with an unstable and unencoded monochromator, as might be found at some older beamlines. Calibration intends to put a single spectrum on the correct absolute energy scale. That is, if you know what point in a spectrum represents a particular absolute energy, then calibration does as I said. LCF requires that the ensemble of data and standards all be aligned -- i.e. put on the same relative energy axis. Once that is done, you can proceed with LCF analysis. LCF does not require that the data be calibrated, only that they be aligned. That is, LCF requires that all the data+standards be on the same relative energy axis, but does not require that that energy axis be calibrated. The reason that is so is because LCF fitting is an abstract, numerical function that treats one data set (the "data") as a linear combination of two or more other data sets (the "standards"). No part of that mathematical process requires knowledge of the species of the absorber atom. Indeed, LCF does not require that the x-axis represent energy, only that it be the same for all data+standards. That said, the interpretation of your data might be easier to consider and easier to present in publcation if your data is calibrated. For instance, the Xray Data Booklet tells us that copper metal has an edge at 8979 eV. Calibration is the process of transforming your data such that its edge does, in fact, happen at 8979 eV. In Athena, using the calibration dialog both does an energy shift and sets the E0 value to 8979. If you want to calibrate your data as well as aligning your data, I find it less confusing to do the calibration first. I believe that the procedures can be commutative, but calibrating after aligning is confusing to me and more prone to error for me. Someone else might give you different advice. Finally, remember that calibration requires actual knowledge (as opposed to some assumption) about what point in a spectrum represents a particular absolute energy value. While you might reasonably assign the first big peak in the first derivative of copper metal to 8979 eV, you cannot correctly assign the first big peak in the first derivative of copper oxide to 8979 eV due to the upwards shift in threshold energy in the oxide. HTH, 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/

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Re: [Ifeffit] Linux command line ff2chi yields no output
by Francisco Garcia 09 May '11

09 May '11

Dear users, I posted a question on feff6 not yielding the any *.chi output. I was using the feff6 binary in ifeffit. However, I complied the feff6lite f77 code and run it and I got the chi.dat output file--which is exactly what I need. So kindly disregard my previous question. Thank you.

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ifeffit-first derivative fits
by Ganga Hettiarachchi 07 May '11

07 May '11

Bruce, Problem is that when we do the fit in derivative and, save the results, something other than first derivative is written to the file. Have you ever looked at the saved/written file of a first derivative fit? Thanks, Ganga -------------------- Ganga M. Hettiarachchi, Ph.D. Assistant Professor of Soil and Environmental Chemistry Department of Agronomy 2107 Throckmorton Plant Sciences Center Kansas State University Manhattan, KS 66506 USA 785-532-7209 (office) 785-532-6094 (FAX)

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Re: [Ifeffit] EXAFS on multi phase systems
by Rana, Jatinkumar Kantilal 06 May '11

06 May '11

Hi Scott, Hi Bruce, Thanks a lot for directing me to the available literatures. It will be of great help. With best regards, Jatin ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Thursday, May 05, 2011 7:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 99, Issue 1 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. EXAFS on multi phase systems (Jatinkumar Rana) 2. Re: EXAFS on multi phase systems (Scott Calvin) 3. Re: EXAFS on multi phase systems (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 05 May 2011 09:26:02 +0200 From: Jatinkumar Rana <jatinkumar.rana(a)helmholtz-berlin.de> To: Ifeffit users <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] EXAFS on multi phase systems Message-ID: <4DC2510A.7030907(a)helmholtz-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear ifeffit users, I was wondering if one could apply EXAFS to multi-phase systems (e.g. two phase systems) where both phases could be crystallographically different but contain same absorbing atom. Can anyone suggest any literature which dealt with such a problem ?? With best regards, Jatinkumar Rana Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Institut f?r angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583 ------------------------------ Message: 2 Date: Thu, 5 May 2011 07:46:33 -0700 From: Scott Calvin <dr.scott.calvin(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: Scott Calvin <scalvin(a)slc.edu> Subject: Re: [Ifeffit] EXAFS on multi phase systems Message-ID: <43612A83-383E-46DC-8182-4986C8C66FA1(a)gmail.edu> Content-Type: text/plain; charset="windows-1252"; Format="flowed"; DelSp="yes" Hi Jatinkumar, It's fairly common to do so. With linear combination analysis or principle component analysis, it's necessarily the case. But it's also done with modelling using FEFF. I personally have published many papers of this type. One early paper of mine that does this is: ?X-ray absorption spectroscopy of highly-cycled Li/CPE/FeS2 cells,? E. Strauss, S. Calvin, H. Mehta,* D. Golodnitksy, S. G. Greenbaum, M. L. denBoer, V. Dusheiko, and E. Peled, Solid State Ionics 164, 51 (2003). --Scott Calvin Sarah Lawrence College On May 5, 2011, at 12:26 AM, Jatinkumar Rana wrote: > Dear ifeffit users, > > I was wondering if one could apply EXAFS to multi-phase systems (e.g. > two phase systems) where both phases could be crystallographically > different but contain same absorbing atom. > > Can anyone suggest any literature which dealt with such a problem ?? > > With best regards, > > Jatinkumar Rana

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Re: [Ifeffit] EXAFS on multi phase systems
by Scott Calvin 05 May '11

05 May '11

Hi Jatinkumar, It's fairly common to do so. With linear combination analysis or principle component analysis, it's necessarily the case. But it's also done with modelling using FEFF. I personally have published many papers of this type. One early paper of mine that does this is: “X-ray absorption spectroscopy of highly-cycled Li/CPE/FeS2 cells,” E. Strauss, S. Calvin, H. Mehta,* D. Golodnitksy, S. G. Greenbaum, M. L. denBoer, V. Dusheiko, and E. Peled, Solid State Ionics 164, 51 (2003). --Scott Calvin Sarah Lawrence College On May 5, 2011, at 12:26 AM, Jatinkumar Rana wrote: > Dear ifeffit users, > > I was wondering if one could apply EXAFS to multi-phase systems (e.g. > two phase systems) where both phases could be crystallographically > different but contain same absorbing atom. > > Can anyone suggest any literature which dealt with such a problem ?? > > With best regards, > > Jatinkumar Rana

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EXAFS on multi phase systems
by Jatinkumar Rana 05 May '11

05 May '11

Dear ifeffit users, I was wondering if one could apply EXAFS to multi-phase systems (e.g. two phase systems) where both phases could be crystallographically different but contain same absorbing atom. Can anyone suggest any literature which dealt with such a problem ?? With best regards, Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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Bug in Athena merge preferences?
by Scott Calvin 28 Apr '11

28 Apr '11

Hi Bruce (and Ifeffiteers), I'm not positive this is a bug--maybe I'm just misunderstanding how the features are supposed to work. (It wouldn't be the first time!) In Athena 0.8.061 on a Mac running OS 10.5.8, I tried the following (I tried it in more than one project, to make sure it's not an intermittent bug): --Under Edit Preferences/Merge/Merge_Weight, choose "n" and apply to future sessions --Close Athena and reopen --Open a project --Mark two data sets. --Change the "importance" of one of them. --Under the merge menu, choose "weight by importance." --Under the merge menu, "merge marked data in chi(k)" The result for me is that the merged file ignores the importance I've assigned. I've also tried it in mu(E), with the same result. It seems that perhaps the "n" value in the preferences overrides the "weight by importance" option in the menu? If so, that's not the way I expect preferences and menu options to interact. Trying it with applying the "n" only to the current session also has an interesting behavior, although not necessarily the "wrong" one: it seems to just change the radio button in the menu. Also, if I change the radio button in the menu directly, the option under Preferences changes to match. For the current session, I can understand the argument that this is a reasonable behavior. But it is likely to cause confusion if a user changes it in the menu and then tries to use the preferences to check what the future sessions value is set to--if they haven't previously changed the preferences directly during the session, they might naturally assume that the value there is the value for future sessions, but in reality it just represents the most recent menu choice they made, and could be different in a future session. My suggested fix to both issues: the preferences should control what value the radio button takes on when Athena is first opened, and changes to the preferences should cause an immediate change to the status of the radio button. Subsequent changes to the radio button should not change the value under the preferences. And the behavior of the merge function should always reflect the current value of the radio button. --Scott Calvin Sarah Lawrence College

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GAANN Fellowships
by Carlo Segre 27 Apr '11

27 Apr '11

Dear All: Illinois Institute of Technology still has some GAANN Fellowships available in Physics and specifically for students interested in synchrotron radiation research. More information is available at http://www.iit.edu/research/undergraduate_research/news/gaan_award.shtml Note that the deadlines are not in force at this time, we will still accept applications. Carlo -- 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://phys.iit.edu/~segre segre(a)debian.org

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