Re: [Ifeffit] Self absorption Correction
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 farzana6...@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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] self absorption correction
On Wednesday, January 09, 2013 10:28:17 AM sum...@barc.gov.in wrote: Thanks Bruce. Till the time i look into the suggested works, here is the missing informations. That's kind of backwards. You should do your research *before* asking a question. One tends to ask better questions that way! Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data. The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04. Material: Eu(III) sorbed on silica. Again, you are not providing enough information so that your question can be answered well. Where did that stoichiometry come from? It would be useful to know how thick the Eu film is on the silica substrate and then compare that to the information depth (aorund 50 microns, if I understand correctly what the sample is) of Eu around its L3 edge. Judging from amount the data changes when applying the correction, it would seem as if your film is quite thin. The XANES changes very little and the EXAFS not at all when the correction is applied. Are you fretting about the change in edge jump? If so, why? Edge jump is, in most cases, a pretty arbitrary number for a fluorescence measurement [1]. If you change the gain on I0 by one order of magnitude, the edge jump changes by a factor of 10. If you change the gasses in IO or change the gains on your energy discriminating detectors, the edge jump again changes. This is in contrast to a transmission experiment where, by virtue of the natural log, the edge jump tells you something about the physical thickness of the absorbing part of the sample. By applying the self-absorption correction, you did some kind of linear transform to the data, changing the absolute scale of the numbers in some way. Comparing the normalized data (remember, the normalization algorithm is used explicitly to remove all of these arbitrary scling factors from the data) shows that the correction did very little to your data. Perhaps I don't quite understand what your concern is with these data, but I doubt that self-absorption should be among them. Cheers, B [1] Here's a counter example http://dx.doi.org/10.1021/ac060476m, but note that great care was taken in the work to make the ensemble of measurements in a consistent fashion. -- Bruce Ravel bra...@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] self absorption correction
Thanks Bruce. Till the time i look into the suggested works, here is the missing informations. Question: how to check the appropriateness of the self absorption correction? I don't have corresponding transmission data. The question came to my mind when i compared the uncorrected (of courese corrected for dead time) data and the corrected (with SiO2Eu0.002 formula; the formula corresponds to the mole (roughly atom)percentage. The edge jump enhanced after correction to ~1 from ~0.04. Material: Eu(III) sorbed on silica. Sumit -- Sumit Kumar Scientific Officer(E) Radioanalytical Chemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 4093/0644 (O). ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Self absorption Correction
Hi, In the J. Phys. III (France) paper you have the expression to calculate the information depth-magnitude. Self absorption will take place if this magnitude is smaller than your fine powder size. Typically, for a non-diluted material information depth-magnitude is (in microns) equal to one tenth of the measured edge energy (in keV) that should be compared to your powder grain size. Carlos Prieto At 08:51 03/02/2009, you wrote: Hi, Thanks Richard and Carlos for the the links. But is the Fluo-Algorithm for self absorption correction also valid if I have the concentrated sample (standard) applied as a fine powder to a carbon tape or is it only valid for much much thicker samples? thanks, Jens -- Message: 4 Date: Mon, 2 Feb 2009 09:51:10 -0500 From: Richard Mayes rtma...@gmail.com Subject: Re: [Ifeffit] Self absorption Correction To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: 5a2a54820902020651nfaf1af7q4ec435fc207fc...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Jens, Since no one has answered yet, I'll chime in. First let me direct you to a discussion of self-absorption and other sample-related distortions: http://www.xafs.org/Experiment/OverAbsorption (this is a link from the tutorials page of www.xafs.org). As for your questions: I think that you should use the non-normalized XANES data to perform the SA correction. for the angle-in and angle-out meanings, see Grant Bunker's paper on self-absorption here: http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf Now, how do you determine if you have self-absorption effects? I have to defer here to those with more experience. What you suggest sounds appropriate, but I'm not sure how you could determine this without studying multiple concentrations of your absorber and watch the signals, i.e. does a 10% increase in absorber concentration translate to a 10% increase in fluorescence yield (similar to what Matthew Marcus and Alain Manceau describe in their paper, from the over-absorption link above). HTH, -Rich On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse jens.kr...@uni-rostock.dewrote: Hi there, I have measured a pure reference compound with high absorber concentration in fluorescence mode (P K-edge XANES). I tried to use the Self absorption correction included in Athena but I don't really understand the results. Fist: Do I have to use the edge step normalized spectrum or the spectrum without normalization ? I tried both and the results of course a quite different. I would rather use the not normalized spectrum. Second: the value Angel in is this the angle between the incident beam and the sample surface and Angle out the angle between the sample surface and the detector position? Third: More general- How can I identify a spectrum suffering self absorption? Just comparing the relative peak intensities of total electron yield signal with the fluorescence yield signal ? thanks a lot for your comments, cheers, Jens -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090202/22fbb148/attachment-0001.html -- Message: 5 Date: Mon, 02 Feb 2009 16:59:19 +0100 From: Carlos Prieto cpri...@icmm.csic.es Subject: Re: [Ifeffit] Self absorption Correction To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: 20090202155915.dfcae9a...@estafeta.csic.es Content-Type: text/plain; charset=iso-8859-1; format=flowed Jens, Let me give you an old reference (but still usefull) for the self absorption treatment: R. Casta?er and C. Prieto, Fluorescence detection of EXAFS in thin film samples, J. de Phys. III (France), 7, 337-349 (1997). Best regards Carlos Prieto At 15:51 02/02/2009, you wrote: Jens, Since no one has answered yet, I'll chime in. First let me direct you to a discussion of self-absorption and other sample-related distortions: http://www.xafs.org/Experiment/OverAbsorptionhttp://www.xafs.org/Experiment/OverAbsorption (this is a link from the tutorials page of http://www.xafs.orgwww.xafs.org). As for your questions: I think that you should use the non-normalized XANES data to perform the SA correction. for the angle-in and angle-out meanings, see Grant Bunker's paper on self-absorption here: http://gbxafs.iit.edu/training
Re: [Ifeffit] Self absorption Correction
Jens, Let me give you an old reference (but still usefull) for the self absorption treatment: R. Castañer and C. Prieto, Fluorescence detection of EXAFS in thin film samples, J. de Phys. III (France), 7, 337-349 (1997). Best regards Carlos Prieto At 15:51 02/02/2009, you wrote: Jens, Since no one has answered yet, I'll chime in. First let me direct you to a discussion of self-absorption and other sample-related distortions: http://www.xafs.org/Experiment/OverAbsorptionhttp://www.xafs.org/Experiment/OverAbsorption (this is a link from the tutorials page of http://www.xafs.orgwww.xafs.org). As for your questions: I think that you should use the non-normalized XANES data to perform the SA correction. for the angle-in and angle-out meanings, see Grant Bunker's paper on self-absorption here: http://gbxafs.iit.edu/training/Self_Absorption_effects.pdfhttp://gbxafs.iit.edu/training/Self_Absorption_effects.pdf Now, how do you determine if you have self-absorption effects? I have to defer here to those with more experience. What you suggest sounds appropriate, but I'm not sure how you could determine this without studying multiple concentrations of your absorber and watch the signals, i.e. does a 10% increase in absorber concentration translate to a 10% increase in fluorescence yield (similar to what Matthew Marcus and Alain Manceau describe in their paper, from the over-absorption link above). HTH, -Rich On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse mailto:jens.kr...@uni-rostock.dejens.kr...@uni-rostock.de wrote: Hi there, I have measured a pure reference compound with high absorber concentration in fluorescence mode (P K-edge XANES). I tried to use the Self absorption correction included in Athena but I don't really understand the results. Fist: Do I have to use the edge step normalized spectrum or the spectrum without normalization ? I tried both and the results of course a quite different. I would rather use the not normalized spectrum. Second: the value Angel in is this the angle between the incident beam and the sample surface and Angle out the angle between the sample surface and the detector position? Third: More general- How can I identify a spectrum suffering self absorption? Just comparing the relative peak intensities of total electron yield signal with the fluorescence yield signal ? thanks a lot for your comments, cheers, Jens -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190 ___ Ifeffit mailing list mailto:Ifeffit@millenia.cars.aps.anl.govIfeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Carlos Prieto Instituto de Ciencia de Materiales de Madrid CSIC Cantoblanco, 28049 - MADRID (Spain) Tel.: 91 3349017 e-mail: cpri...@icmm.csic.es = ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Self absorption Correction
Hi, Thanks Richard and Carlos for the the links. But is the Fluo-Algorithm for self absorption correction also valid if I have the concentrated sample (standard) applied as a fine powder to a carbon tape or is it only valid for much much thicker samples? thanks, Jens -- Message: 4 Date: Mon, 2 Feb 2009 09:51:10 -0500 From: Richard Mayes rtma...@gmail.com Subject: Re: [Ifeffit] Self absorption Correction To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: 5a2a54820902020651nfaf1af7q4ec435fc207fc...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Jens, Since no one has answered yet, I'll chime in. First let me direct you to a discussion of self-absorption and other sample-related distortions: http://www.xafs.org/Experiment/OverAbsorption (this is a link from the tutorials page of www.xafs.org). As for your questions: I think that you should use the non-normalized XANES data to perform the SA correction. for the angle-in and angle-out meanings, see Grant Bunker's paper on self-absorption here: http://gbxafs.iit.edu/training/Self_Absorption_effects.pdf Now, how do you determine if you have self-absorption effects? I have to defer here to those with more experience. What you suggest sounds appropriate, but I'm not sure how you could determine this without studying multiple concentrations of your absorber and watch the signals, i.e. does a 10% increase in absorber concentration translate to a 10% increase in fluorescence yield (similar to what Matthew Marcus and Alain Manceau describe in their paper, from the over-absorption link above). HTH, -Rich On Fri, Jan 30, 2009 at 11:49 AM, Jens Kruse jens.kr...@uni-rostock.dewrote: Hi there, I have measured a pure reference compound with high absorber concentration in fluorescence mode (P K-edge XANES). I tried to use the Self absorption correction included in Athena but I don't really understand the results. Fist: Do I have to use the edge step normalized spectrum or the spectrum without normalization ? I tried both and the results of course a quite different. I would rather use the not normalized spectrum. Second: the value Angel in is this the angle between the incident beam and the sample surface and Angle out the angle between the sample surface and the detector position? Third: More general- How can I identify a spectrum suffering self absorption? Just comparing the relative peak intensities of total electron yield signal with the fluorescence yield signal ? thanks a lot for your comments, cheers, Jens -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20090202/22fbb148/attachment-0001.html -- Message: 5 Date: Mon, 02 Feb 2009 16:59:19 +0100 From: Carlos Prieto cpri...@icmm.csic.es Subject: Re: [Ifeffit] Self absorption Correction To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: 20090202155915.dfcae9a...@estafeta.csic.es Content-Type: text/plain; charset=iso-8859-1; format=flowed Jens, Let me give you an old reference (but still usefull) for the self absorption treatment: R. Casta?er and C. Prieto, Fluorescence detection of EXAFS in thin film samples, J. de Phys. III (France), 7, 337-349 (1997). Best regards Carlos Prieto At 15:51 02/02/2009, you wrote: Jens, Since no one has answered yet, I'll chime in. First let me direct you to a discussion of self-absorption and other sample-related distortions: http://www.xafs.org/Experiment/OverAbsorptionhttp://www.xafs.org/Experiment/OverAbsorption (this is a link from the tutorials page of http://www.xafs.orgwww.xafs.org). As for your questions: I think that you should use the non-normalized XANES data to perform the SA correction. for the angle-in and angle-out meanings, see Grant Bunker's paper on self-absorption here: http://gbxafs.iit.edu/training/Self_Absorption_effects.pdfhttp://gbxafs.iit.edu/training/Self_Absorption_effects.pdf Now, how do you determine if you have self-absorption effects? I have to defer here to those with more experience. What you suggest sounds appropriate, but I'm not sure how you could determine this without studying multiple concentrations of your absorber and watch the signals, i.e. does a 10% increase in absorber concentration translate to a 10% increase in fluorescence yield (similar to what Matthew Marcus and Alain Manceau describe in their paper
[Ifeffit] Self absorption Correction
Hi there, I have measured a pure reference compound with high absorber concentration in fluorescence mode (P K-edge XANES). I tried to use the Self absorption correction included in Athena but I don't really understand the results. Fist: Do I have to use the edge step normalized spectrum or the spectrum without normalization ? I tried both and the results of course a quite different. I would rather use the not normalized spectrum. Second: the value Angel in is this the angle between the incident beam and the sample surface and Angle out the angle between the sample surface and the detector position? Third: More general- How can I identify a spectrum suffering self absorption? Just comparing the relative peak intensities of total electron yield signal with the fluorescence yield signal ? thanks a lot for your comments, cheers, Jens -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
