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Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 4
by Pierre Lecante 09 Feb '16

09 Feb '16

Hi Pinit, here is what you can expect from a SDD: "At X-ray energies greater than silicon K absorption edge, which we have measured for crystalline silicon to be 1839 eV, the response function of the device shows two distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is due to the silicon fluorescent photons that have escaped far enough from the original site of interaction to be detected as a separate event. The other peak centered at energy /E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an escape peak." So, indeed this shouldn't be a concern if you had a perfect rejection of harmonics on your beamline; if not, inelastic scattering of harmonic by the sample, even rejected by energy analysis, should likely induce internal fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy to check: presence or not of harmonic in your scattering. Pierre Le 02/02/2016 23:41, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Could you please give me some information? (Bruce Ravel) > 2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > 3. Re: Athena with IOS "El Capitan" (Bruce Ravel) > 4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2016 15:30:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: pinit <pinit(a)slri.or.th> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Could you please give me some information? > Message-ID: <56B111F5.7050108(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 02/01/2016 11:58 PM, pinit wrote: >> Dear Bruce, >> >> I am Pinit from SLRI, Thailand. I have some questions concerning the >> Si-drift detector. >> >> Could you give me some suggestions if Si-detector can detect the >> corrected Si K-edge or not? This is because I have seen a significant >> EXAFS signal (higher in amplitude in FT) measured by Si-drift detector >> differs from Lytle detector or ionization chambers (TM mode). > Hi Pinit, > > Nice to hear from you. I am CCing my answer to the Ifeffit Mailing > List. Someone else may have more insight into your question than I > do. You should CC the list in your response. > > I'd probably need to know more about the sample and the nature of the > measurement you made to understand why you are seeing a different > signal with the Si drift detector. > > Normally one would expect that he EXAFS would be /attenuated/ either > due to self-absorption or due to the energy dependence of the I0 > detector. That you are seeing a larger EXAFS signal with the Si-drift > seems surprising. > > One thing that occurs to me is that the Compton and elastic peaks > probably overlap the Si K alpha ROI quite a bit, even extending into > the EXAFS region. I would have thought that, too, would serve to > attenuate the EXAFS (but maybe I am thinking about that wrongly). > > Perhaps it would help to show us some of the data...? > > B > > > > -- Groupe MC2 CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/MC2 Full list of publications: http://www.researcherid.com/rid/A-8745-2011

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Re: [Ifeffit] Could you please give me some information?
by Pierre Lecante 09 Feb '16

09 Feb '16

Hi Pinit, here is what you can expect from a SDD: "At X-ray energies greater than silicon K absorption edge, which we have measured for crystalline silicon to be 1839 eV, the response function of the device shows two distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is due to the silicon fluorescent photons that have escaped far enough from the original site of interaction to be detected as a separate event. The other peak centered at energy /E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an escape peak." So, indeed this shouldn't be a concern if you had a perfect rejection of harmonics on your beamline; if not, inelastic scattering of harmonic by the sample, even rejected by energy analysis, should likely induce internal fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy to check: presence or not of harmonic in your scattering. Pierre Le 02/02/2016 23:41, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Could you please give me some information? (Bruce Ravel) > 2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > 3. Re: Athena with IOS "El Capitan" (Bruce Ravel) > 4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2016 15:30:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: pinit <pinit(a)slri.or.th> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Could you please give me some information? > Message-ID: <56B111F5.7050108(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 02/01/2016 11:58 PM, pinit wrote: >> Dear Bruce, >> >> I am Pinit from SLRI, Thailand. I have some questions concerning the >> Si-drift detector. >> >> Could you give me some suggestions if Si-detector can detect the >> corrected Si K-edge or not? This is because I have seen a significant >> EXAFS signal (higher in amplitude in FT) measured by Si-drift detector >> differs from Lytle detector or ionization chambers (TM mode). > Hi Pinit, > > Nice to hear from you. I am CCing my answer to the Ifeffit Mailing > List. Someone else may have more insight into your question than I > do. You should CC the list in your response. > > I'd probably need to know more about the sample and the nature of the > measurement you made to understand why you are seeing a different > signal with the Si drift detector. > > Normally one would expect that he EXAFS would be /attenuated/ either > due to self-absorption or due to the energy dependence of the I0 > detector. That you are seeing a larger EXAFS signal with the Si-drift > seems surprising. > > One thing that occurs to me is that the Compton and elastic peaks > probably overlap the Si K alpha ROI quite a bit, even extending into > the EXAFS region. I would have thought that, too, would serve to > attenuate the EXAFS (but maybe I am thinking about that wrongly). > > Perhaps it would help to show us some of the data...? > > B > > > > -- Groupe MC2 CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/MC2 Full list of publications: http://www.researcherid.com/rid/A-8745-2011

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Athena with IOS "El Capitan"
by Manuel Cossio Kohler 02 Feb '16

02 Feb '16

Hello, I am having some issues with the Athena software. After upgrading the OS of the macbook pro to "El Capitan" Version 10.11.3, Athena stopped working properly. Once the iXAFS icon was clicked nothing happened. I decided to do a bit of research and installed the latest verion of XQuartz version 2.7.8. I was able to launch athena by executting "athena" from the terminal. Up to that point, I figured that everything was running smoothly until I realized that I could prompt any plots. Something in the software or operating system was not allowing Athena to display plots. I would be really grateful if you could provide me with a solution to this problem (if there is any) or any advice that would allow me to process XAS data again. Thank you Regards, Manuel Cossio

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Re: [Ifeffit] Could you please give me some information?
by Bruce Ravel 02 Feb '16

02 Feb '16

On 02/01/2016 11:58 PM, pinit wrote: > Dear Bruce, > > I am Pinit from SLRI, Thailand. I have some questions concerning the > Si-drift detector. > > Could you give me some suggestions if Si-detector can detect the > corrected Si K-edge or not? This is because I have seen a significant > EXAFS signal (higher in amplitude in FT) measured by Si-drift detector > differs from Lytle detector or ionization chambers (TM mode). Hi Pinit, Nice to hear from you. I am CCing my answer to the Ifeffit Mailing List. Someone else may have more insight into your question than I do. You should CC the list in your response. I'd probably need to know more about the sample and the nature of the measurement you made to understand why you are seeing a different signal with the Si drift detector. Normally one would expect that he EXAFS would be /attenuated/ either due to self-absorption or due to the energy dependence of the I0 detector. That you are seeing a larger EXAFS signal with the Si-drift seems surprising. One thing that occurs to me is that the Compton and elastic peaks probably overlap the Si K alpha ROI quite a bit, even extending into the EXAFS region. I would have thought that, too, would serve to attenuate the EXAFS (but maybe I am thinking about that wrongly). Perhaps it would help to show us some of the data...? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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pi/2deltak
by Ritimukta Sarangi 01 Feb '16

01 Feb '16

Hello, I was recently asked about the accuracy of this formulation for obtaining EXAFS resolution and I did not have a good answer. Can someone point to a reference or explain here? Thank you for your time, Best, -Riti

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FW: Data summation - missing groups
by Godfrey, Ian 01 Feb '16

01 Feb '16

Sorry, I've just seen that this has already been reported. Ian From: Godfrey, Ian Sent: 27 January 2016 11:21 To: 'XAFS Analysis using Ifeffit' <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Data summation - missing groups Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? Thanks, Ian Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London, And School of Materials Science, Japan Advaned Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp> 02076 794864

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Re: [Ifeffit] pi/2deltak
by Avakyan L.A. 31 Jan '16

31 Jan '16

Hello Riti, the criterion of R-resolution of pi/2deltak can be drawn from the Nyquist theorem. The amount of information in the spectra is limited by Nidp = 2 deltak deltaR / pi. Then, in assumption of equal distribution of information over the R-interval, the minimal interval can be estimated as deltaR / Nidp = pi/2deltak. The problem is that exact formula for Nidp is not known. Sometimes it has addition of +1 or +2 to represent the fact that single point (deltak=0) still contains information. Moreover, information is not equally distributed: some k-regions are more rich, other are less... And when energy interval is very short (glass, liquid) this question becomes vital. Sometimes, this resolution limit can even be overcome as it is shown in [http://dx.doi.org/10.1103/PhysRevB.82.064204] Best regards, Leon Leon Avakyan PhDr, Physics Faculty, Southern Federal University laavakyan(a)sfedu.ru On 31.01.2016 21:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Message: 2 > Date: Sat, 30 Jan 2016 17:35:04 -0800 > From: Ritimukta Sarangi<ritimukta(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] pi/2deltak > Message-ID: > <CAMWiF7ymrKEDSZw31pcgwCzZH5tsFvFk+151gxfjRz9jUARH4w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I was recently asked about the accuracy of this formulation for obtaining > EXAFS resolution and I did not have a good answer. Can someone point to a > reference or explain here? > Thank you for your time, > Best, > -Riti

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Re: [Ifeffit] Ifeffit Digest, Vol 155, Issue 16
by Christopher Thomas Chantler 30 Jan '16

30 Jan '16

Dear Jason Good topic We have published a few papers discussing analysis with thickness distributions and roughness. Normally the XERT method will address this especially for small samples. Particularly see J. L. Glover, C. T. Chantler, M. D. de Jonge, ‘Nano-roughness in gold revealed from X-ray signature,’ Physics Letters A373 (2009) 1177-1180. The general topic of thickness effects is of course wider, and partially addressed in a couple of other papers. Hope this helps Chris ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, 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 ________________________________________ From: Ifeffit [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: Sunday, 31 January 2016 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 155, Issue 16 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: Effect of gradual thickness variation in beam (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Fri, 29 Jan 2016 14:32:43 -0500 From: Jason Gaudet <jason.r.gaudet(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Effect of gradual thickness variation in beam Message-ID: <CANMcWtOLubiomegk-GM6SMS6CSpw0B0Hg21rMe9-hV8uQEkxhw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Anatoly, Sorry, I meant to write 1000 um inner diameter. Energies will be V and Fe, 5465 & 7112 eV. Samples are roughly 1 absorption length thick for the metal (V, Fe) and about 2-2.5 absorption lengths for the entire sample. Bruce, I may just flip over the sample holder and have the sample tubes in plane with the storage ring to take advantage of the greater horizontal spread, rather than focusing on the vertical. Cutting the vertical slits down to 100-300 um while keeping the horizontal around 500 um ought to get me the most beam at the least variation in mu(E), especially if I go with 1500 um ID tubes. The samples are nice and concentrated so I can afford to give up a lot of photon flux. Bar-napkin calculations tell me with a 1500 um ID tube and 200 um V 750 um H slits I'll lose an acceptable amount of photon flux and have a <1% thickness variation. I'm fairly confident I've made pressed pellets with as much or more variation from one spot to another, without noticeable mu(E) changes from spot to spot, in the vicinity of this energy range. I'll go ahead and take your advice, and amend my setup procedure with some measurements of Io intensity and mu(E) reproducibility as a function of slit width. While a bit of a bother, it's still worth it to keep our sample prep simple and inexpensive. Thanks, Jason On Thu, Jan 28, 2016 at 9:12 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > On 01/27/2016 07:05 PM, Jason Gaudet wrote: > >> I'm planning on some transmission-mode XAS with smaller than usual >> sample tubes. I'm realizing I might be in danger of creating excessive >> non-uniformity in my samples by having the beam size on the same order >> of magnitude as the sample tube radius. >> >> For example, let's say I want to measure liquid in a sample tube with a >> 1000 micron outer diameter, with a beam 500 microns wide and centered on >> the sample tube. If the tube is orthogonal to the ring plane, the entire >> vertical portion of the beam will pass through the same length of >> liquid. But in the horizontal plane, the center of the beam will pass >> through 1000 microns of sample while the edges of the beam will pass >> through 866 microns of sample, due to the curvature of the sample cell >> across the horizontal plane. >> >> Most of what I know about the statistics of thickness effects are about >> leakage and pinholes - nonlinearity caused by a few spots having very >> low or negligible sample thickness. But I don't know how significant a >> "mild" thickness distribution might be. If this sort of thickness >> distribution is going to be an issue it would be great to know that >> beforehand and either go with larger samples, smaller beam size, or more >> creative orientation. >> > > > Jason, > > There may be some distortion to the data due to the varying thickness. > On the plus side, liquids tend to be very homogeneous. > > Probably the best solution to this situation, if it's available at the > beamline, is to focus the beam in the vertical, for example, using a > flat mirror on a bender. Focusing to a spot would also address the > thickness situation, but you need to be mindful that the intense beam > could generate radicals from the liquid, causing sample damage. > > If the sample is sufficiently concentrated, then you could simply slit > the beam down to 100 or 200 microns and still have enough for a > transmission measurement. In fact, that would be the way to decide if > you are seeing a big problem from the shape of the tube. Compare the > mu(E) with the slits at 500 to mu(E) with the slits at 100 (carefully > aligning the sample both times, of course). If they are the same, > then, then you're golden. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

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Effect of gradual thickness variation in beam
by Jason Gaudet 29 Jan '16

29 Jan '16

Sample cell Hi all, I'm planning on some transmission-mode XAS with smaller than usual sample tubes. I'm realizing I might be in danger of creating excessive non-uniformity in my samples by having the beam size on the same order of magnitude as the sample tube radius. For example, let's say I want to measure liquid in a sample tube with a 1000 micron outer diameter, with a beam 500 microns wide and centered on the sample tube. If the tube is orthogonal to the ring plane, the entire vertical portion of the beam will pass through the same length of liquid. But in the horizontal plane, the center of the beam will pass through 1000 microns of sample while the edges of the beam will pass through 866 microns of sample, due to the curvature of the sample cell across the horizontal plane. Most of what I know about the statistics of thickness effects are about leakage and pinholes - nonlinearity caused by a few spots having very low or negligible sample thickness. But I don't know how significant a "mild" thickness distribution might be. If this sort of thickness distribution is going to be an issue it would be great to know that beforehand and either go with larger samples, smaller beam size, or more creative orientation. Thanks, Jason

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Data summation - missing groups
by Godfrey, Ian 27 Jan '16

27 Jan '16

Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? Thanks, Ian Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London, And School of Materials Science, Japan Advaned Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp> 02076 794864

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