Re: [Ifeffit] Strange EXAFS oscillations, never seen before
Dear Carlo and Lorenzo, Many thanks for sharing your feedback. I agree, the only option is to remeasure the system. Best regards Jatin From: Ifeffit [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of ifeffit-requ...@millenia.cars.aps.anl.gov [ifeffit-requ...@millenia.cars.aps.anl.gov] Sent: Monday, March 20, 2017 6:00 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 169, Issue 19 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Strange EXAFS oscillations, never seen before (Carlo Segre) -- Message: 1 Date: Sun, 19 Mar 2017 12:00:14 -0500 (CDT) From: Carlo Segre <se...@iit.edu> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Strange EXAFS oscillations, never seen before Message-ID: <alpine.deb.2.20.1703191154500.17...@hydride.segre.home> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Hi Rana: I agree. The data is basically unusable as it is. You clearly have issues in the background (look at the oscillations in the pre-edge area) and the three data sets are different from each other which is another clue. It looks like you have transmission data with a very samll edge jump (0.09) which is sort of marginal for XANES much less EXAFS at 5BM). In addition, your sample probably has pinholes and is not uniform. You should be taking this data in fluorescence with such a small amount of sample unless you have an absolutely uniform sample. Carlo On Sun, 19 Mar 2017, Lorenzo Stievano wrote: > > Dear Rana, > > you seem to have real EXAFS oscillations up to k=9, then there are surely > some artefacts in your spectra, which are unusable from that point on. In > fact, if you limit your spline range to 9 in Athena, you get oscillations > that look real and seem to have some sense. > > These artefacts are probably of experimental origin (shit happens), I do not > think you can do much about them,with the exception of remesuring your > spectra. > > Yours sincerely, > > Lorenzo > > Le 19/03/2017 ? 17:13, Rana, Jatinkumar Kantilal a ?crit?: > > Dear all, > I observed strange EXAFS oscillations in my data up to about 1000 eV > beyond the K-edge, I would like to share this situation with you and > hope to get some feedback. Please find attached the athena project > file of the data. > > The chemical composition of the material is (Fe0.5Cu0.5)Sn5. The EXAFS > sample was prepared by taking the material equal to 2 absorption > lengths at the Cu K-edge, mixing it with graphite and pressing into > the pellet, which was sealed between the Kapton tape. > > The measurements were carried out at the Cu K-edge of the material in > the transmission mode at the beamline 5BM of APS. > > Here are my concerns: > > (1) In the athena project file, the data files "Cu_S1_scan003" > and?"Cu_S1_scan004" are the two scans of the same sample measured one > after the other. As can be seen, there are strong oscillations even at > 1000 eV from the Cu K-edge, which is strange because generally EXAFS > oscillations "wash out" as we go higher in energy. Nevertheless, the > two scans appear reproducible. > > (2) Once I removed the sample and remeasured it after some time > (because?I did not believe the previous 2 scans), I found completely > different data (i.e., data "Cu_S1_scan005").? > > (3) The Cu reference foil measured simultaneously along with the > sample for each of these scans appear quite reproducible. > > I am puzzled as to what can contribute to such effects. I have never > seen such effects before.? > > We can rule out the possibility of beam damage, since I have measured > up to 3 scans (25 min per scan) and they all look reproducible. > However, once I remove the sample and remeasure it after some time to > reproduce the previous 3 scans, the scan looks totally different. > > Also, we can rule out the chemical instability of the material, since > the material is quite air-stable. > > I have measured a series of samples with this composition and all of > them have the same effect.? > > I would very much appreciate your feedback! > > Best regards >
[Ifeffit] Strange EXAFS oscillations, never seen before
Dear all, I observed strange EXAFS oscillations in my data up to about 1000 eV beyond the K-edge, I would like to share this situation with you and hope to get some feedback. Please find attached the athena project file of the data. The chemical composition of the material is (Fe0.5Cu0.5)Sn5. The EXAFS sample was prepared by taking the material equal to 2 absorption lengths at the Cu K-edge, mixing it with graphite and pressing into the pellet, which was sealed between the Kapton tape. The measurements were carried out at the Cu K-edge of the material in the transmission mode at the beamline 5BM of APS. Here are my concerns: (1) In the athena project file, the data files "Cu_S1_scan003" and "Cu_S1_scan004" are the two scans of the same sample measured one after the other. As can be seen, there are strong oscillations even at 1000 eV from the Cu K-edge, which is strange because generally EXAFS oscillations "wash out" as we go higher in energy. Nevertheless, the two scans appear reproducible. (2) Once I removed the sample and remeasured it after some time (because I did not believe the previous 2 scans), I found completely different data (i.e., data "Cu_S1_scan005"). (3) The Cu reference foil measured simultaneously along with the sample for each of these scans appear quite reproducible. I am puzzled as to what can contribute to such effects. I have never seen such effects before. We can rule out the possibility of beam damage, since I have measured up to 3 scans (25 min per scan) and they all look reproducible. However, once I remove the sample and remeasure it after some time to reproduce the previous 3 scans, the scan looks totally different. Also, we can rule out the chemical instability of the material, since the material is quite air-stable. I have measured a series of samples with this composition and all of them have the same effect. I would very much appreciate your feedback! Best regards Jatin Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de athena.prj Description: athena.prj ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Breaking down correlationships between parameters
Hi Chris, The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ? Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 23 March, 2015 12:16 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 42 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) 2. Re: Breaking down correlationships between parameters (Chris Patridge) -- Message: 1 Date: Mon, 23 Mar 2015 11:00:19 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: DA4C7D90F90BC249A03505C87F2EB8AB230EE777@didag1 Content-Type: text/plain; charset=utf-8 Hi Scott, Thank you for your comments. Can you please elaborate a little bit more on this In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 23 March, 2015 10:16 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 41 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Breaking down correlationships between parameters (Scott Calvin) 2. Re: Breaking down correlationships between parameters (Matt Newville) 3. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) -- Message: 1 Date: Sun, 22 Mar 2015 13:44:28 -0400 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: e0c66911-7ad2-448c-9f64-f03e262d0...@slc.edu Content-Type: text/plain; charset=utf-8 One side-comment from me: On Mar 22, 2015, at 12:52 PM, Matt Newville newvi...@cars.uchicago.edumailto:newvi...@cars.uchicago.edu wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range). Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation. In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically. ?Scott Calvin Sarah Lawrence College -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150322/f4e7b7e4/attachment-0001.htm -- Message: 2 Date: Sun, 22 Mar 2015 15:56:20 -0500 From: Matt Newville newvi...@cars.uchicago.edu To: XAFS Analysis using
Re: [Ifeffit] Breaking down correlationships between parameters
Hi Bruce, Thanks for your comments and links of your lectures. I forgot to mention that I use Artemis for fitting my data. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 23 March, 2015 15:37 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 45 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Breaking down correlationships between parameters (Bruce Ravel) 2. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) -- Message: 1 Date: Mon, 23 Mar 2015 09:27:05 -0400 From: Bruce Ravel bra...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: 551014a9.4090...@bnl.gov Content-Type: text/plain; charset=utf-8; format=flowed On 03/23/2015 08:54 AM, Rana, Jatinkumar Kantilal wrote: The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ? At no point in your emails did you say that you are using Artemis to do your fitting. The comment I am about to make may not, therefore, be relevant to you. In Ifeffit and Larch -- and therefore in Artemis -- we DO NOT fit N*SO2. Fits in Ifeffit, Larch, and Artemis use a set of user-defined parameters as the variables of the fit. As part of the fitting model, the user relates the variables of the fit to the parameters of the EXAFS equation using math expression. This benefit of the generality of the fitting model allows the user to easily encode prior knowledge into a fit. The cost is that the parameters have to be interpreted in some kind of physical context. To answer you question specifically, Artemis allows you to set or float parameters for N and S02 and to define the amplitude term of the EXAFS equation for each path in any way that you see fit. In that way, you can implement all the suggestions that Matt, Scott, and Chris have made. I discuss this in some detail starting at page 35 of this presentation. https://speakerdeck.com/bruceravel/advanced-topics-in-exafs-analysis Among the lectures at http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html, this is the one called Fit Evaluation and Fitting multiple structures. HTH, B -- Bruce Ravel bra...@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/ -- Message: 2 Date: Mon, 23 Mar 2015 14:36:31 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: DA4C7D90F90BC249A03505C87F2EB8AB230EE7F0@didag1 Content-Type: text/plain; charset=utf-8 Hi Scott, Thanks for your explanation. It means the reverse can also be true, i.e., I can guess N1 (nearest-neighbors in the first shell) and S02 by setting N2, N3 and N4 to values known from other analysis. I did a quick check by fitting the data. I conducted two fits: 1) setting S02 and guessing only N1 2) guessing both N1 and S02. To my surprise, both the fits gave very similar results, except that the fit#1 refined value of N1 to a higher side, while fit#2 estimated N1 closer to a physically reasonable value (as expected). I always constrained S02 when refining N for any path, due to 100% correlation between them. However, I am surprised to know that they can be refined independently. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 23 March, 2015 14:19 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 44 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov
Re: [Ifeffit] Breaking down correlationships between parameters
Hi Scott, Thanks for your explanation. It means the reverse can also be true, i.e., I can guess N1 (nearest-neighbors in the first shell) and S02 by setting N2, N3 and N4 to values known from other analysis. I did a quick check by fitting the data. I conducted two fits: 1) setting S02 and guessing only N1 2) guessing both N1 and S02. To my surprise, both the fits gave very similar results, except that the fit#1 refined value of N1 to a higher side, while fit#2 estimated N1 closer to a physically reasonable value (as expected). I always constrained S02 when refining N for any path, due to 100% correlation between them. However, I am surprised to know that they can be refined independently. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 23 March, 2015 14:19 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 44 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Breaking down correlationships between parameters (Scott Calvin) -- Message: 1 Date: Mon, 23 Mar 2015 09:18:21 -0400 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: 78c1636c-91cf-4c8c-9d48-3ec361bb7...@slc.edu Content-Type: text/plain; charset=utf-8 Hi Jatin, The key is that S02 should be the same for all paths. For example: Suppose you are very confident path 1 has a coordination number of 6, because of prior knowledge you have about the system. Paths 2, 3, and 4 have unknown coordination numbers, however. N1 (i.e. the degeneracy of path 1) you set to 6. You guess S02, N2, N3, and N4. Of course, the way Artemis and Ifeffit implement that, you're writing N1*S02 for the S02 field of Path 1, N2*S02 for the S02 field of Path 2, etc., and then setting N1 = 6 and guessing S02, N2, N3, and N4. There is now enough information for S02, N2, N3, and N4 to each be fitted without 100% correlation. ?Scott Calvin Sarah Lawrence College On Mar 23, 2015, at 8:54 AM, Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de wrote: Hi Chris, The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ? Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 23 March, 2015 12:16 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 42 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) 2. Re: Breaking down correlationships between parameters (Chris Patridge) -- Message: 1 Date: Mon, 23 Mar 2015 11:00:19 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: DA4C7D90F90BC249A03505C87F2EB8AB230EE777@didag1 Content-Type: text/plain; charset=utf-8 Hi Scott, Thank you for your comments. Can you please elaborate a little bit more on this In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ
[Ifeffit] crystallite size determination by EXAFS
Dear all, I have some questions regarding crystallite size determination by EXAFS. I am investigating a system where there is a formation of metallic Cu in the system. I could see the presence of metallic Cu in the sample by XRD and EXAFS. However, high resolution TEM does not show any evidence of metallic Cu, perhaps the crystallite size is much smaller than the resolving power of the microscope and/or these crystallites are highly disordered. Nevertheless, I thought of estimating the size of Cu crystallites by EXAFS. I know at least two approaches described by two prominent members of the mailing list, Scott Calvin and Anatoly Frenkel. The approach by Scott Calvin (http://link.aip.org/link/JAPIAU/v94/i1/p778/s1Agg=doi) estimates crystallite size based on an assumption that they are spherical in shape. On the other hand, Anatoly Frenkel’s approach estimates both size and shape of crystallites based on the number of neighbors in each coordination shell obtained from EXAFS fit http://pubs.acs.org/doi/abs/10.1021/jp012769j I have questions about the second approach. I would like to know how to calculate the number of neighbors in various coordination shells as a function of cluster size for different shapes ? Conversely, if one knows the number of neighbors in various shells from EXAFS fits, then how to correlate those numbers to clusters of different sizes and shapes as discussed by Anatoly Frenkel. I know my questions are very specific, but I am sure many in the list would have already tried both these approaches and may provide some valuable insights. Many thanks in advance ! With best regards, Jatin 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 Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] correlating number of nearest neighborst to the particle
Dear Scott and Anatoly, Thanks a lot for your valuable suggestions. I may get back to you for any questions, once I go through both the approaches in literature and implement them in the form of a fit. Best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 09 January, 2014 19:18 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 10 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: correlating number of nearest neighborst to the particle size (Scott Calvin) 2. Re: correlating number of nearest neighborst to the particle size (Anatoly I Frenkel) -- Message: 1 Date: Thu, 9 Jan 2014 13:11:41 -0500 From: Scott Calvin scal...@sarahlawrence.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] correlating number of nearest neighborst to the particlesize Message-ID: e6fe5676-5821-46a2-abad-b383ae402...@slc.edu Content-Type: text/plain; charset=utf-8 Hi Jatin, There are two strategies that have been used to do this that you can find in the literature, both of which are by members who frequent this list (myself and Anatoly Frenkel). I have published articles outlining a strategy where you assume the shape of the particles. Most often in my case that has been spheres, but it could be plates or hemispheres or whatever. Then you derive how the coordination number depends on dimensions for that shape (as I said, I an others have done that for spheres), and make those dimensions free parameters in an Ifeffit (e.g. Artemis) fit. Anatoly has published articles outlining a strategy where you treat the coordination numbers themselves as free parameters, and then check for consistency with various shapes. I think Anatoly's method is better when the nanoparticles are very consistent; i.e. they have a narrow size distribution and consistent shapes, and when data quality is good. I think my method may work better when the nanoparticles are messier or when the data is more limited, if only because it requires fewer free parameters. A typical reference for Anatoly's method is A View from the Inside:? Complexity in the Atomic Scale Ordering of Supported Metal Nanoparticles Anatoly I. Frenkel,*,?,?, Charles W. Hills,? and, and Ralph G. Nuzzo*,?,? The Journal of Physical Chemistry B 2001 105 (51), 12689-12703 A typical reference for my method is ?Estimating crystallite size in polydispersed samples using EXAFS,? S. Calvin, C. J. Riedel,* E. E. Carpenter, S. A. Morrison, R. M. Stroud, and V. G. Harris, Physica Scripta T115, 744 (2005). although that can be a little hard to find. Another reference which is more widely available is ?Comparison of extended X-ray absorption fine structure and Scherrer analysis of x-ray diffraction as methods for determining mean sizes of polydisperse nanoparticles,? S. Calvin, S. X. Luo, C. C. Broadbridge, J. K. McGuinness, E. Anderson, A. Lehman, K. H. Wee, S. A. Morrison, and L. K. Kurihara, Appl. Phys. Lett. 87, 233102 (2005). --Scott Calvin Sarah Lawrence College On Jan 9, 2014, at 12:55 PM, Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de wrote: Hi All, I would like to estimate the size of Cu nanoparticles grown in my sample by EXAFS fitting. I can refine the number of nearest neighbors in these Cu nanoparticles up to 4 shells (say NN1, NN2, NN3 and NN4), by constraining S02 to the value obtained by fitting the data of Cu reference foil. But, how do I correlate the refined values of nearest neighbors to the actual size of Cu nanoparticles ? Any help in this regard would be much appreciated. Regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You
[Ifeffit] correlating number of nearest neighborst to the particle size
Hi All, I would like to estimate the size of Cu nanoparticles grown in my sample by EXAFS fitting. I can refine the number of nearest neighbors in these Cu nanoparticles up to 4 shells (say NN1, NN2, NN3 and NN4), by constraining S02 to the value obtained by fitting the data of Cu reference foil. But, how do I correlate the refined values of nearest neighbors to the actual size of Cu nanoparticles ? Any help in this regard would be much appreciated. Regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: 09 January, 2014 17:51 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 131, Issue 8 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. Query re: Athena and Artemis user guides (Leon Clarke) 2. Re: Query re: Athena and Artemis user guides (Bruce Ravel) 3. Re: Query re: Athena and Artemis user guides (Kathy Dardenne) 4. Re: Demeter 0.9.19 (Schima, Frank) -- Message: 1 Date: Thu, 9 Jan 2014 15:56:29 + From: Leon Clarke l.cla...@mmu.ac.uk To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Query re: Athena and Artemis user guides Message-ID: 83CF3E8AA2102C4598B316168B472EFE98BEEECD@drmb1 Content-Type: text/plain; charset=us-ascii Dear Dr Ravel and Demeter users, I recollect that the Athena and Artemis user guides used to be available as PDF files (which I found useful). Am I correct that the latest guides are now only accessible as internet pages, as I can't seem to find a download link? Best regards, Leon - Dr Leon J. Clarke Lecturer in Environmental Analytical Chemistry Division of Chemistry and Environmental Sciences School of Science and the Environment Faculty of Science and Engineering Manchester Metropolitan University John Dalton East Oxford Road Manchester M1 5GD E-mail: l.cla...@mmu.ac.ukmailto:l.cla...@mmu.ac.uk WWW: http://www.sste.mmu.ac.uk/ Tel: +44 (0)161 247 1412 Before acting on this email or opening any attachments you should read the Manchester Metropolitan University email disclaimer available on its website http://www.mmu.ac.uk/emaildisclaimer -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140109/4361200f/attachment-0001.htm -- Message: 2 Date: Thu, 09 Jan 2014 11:23:13 -0500 From: Bruce Ravel bra...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides Message-ID: 52ceccf1.3050...@bnl.gov Content-Type: text/plain; charset=windows-1252; format=flowed On 01/09/2014 10:56 AM, Leon Clarke wrote: I recollect that the Athena and Artemis user guides used to be available as PDF files (which I found useful). Am I correct that the latest guides are now only accessible as internet pages, as I can?t seem to find a download link? I just put links to PDF copies of the two Users' Guides on the Demeter home page: http://bruceravel.github.io/demeter/ A couple things to note: 1. When you install either from source or from the Windows installer, full HTML copies of the users' guides get installed as well. 2. The PDF files are generated from the same source as the html. I have spent a lot of time making the html look reasonable. (Not great, but reasonable!) The PDF are pretty rough and have some obvious layout problems. But I just skimmed through both of them. They are usable, though certainly not beautiful. Thanks for asking. I had stopped updating the PDF versions because I didn't know that anyone was using them. How 'bout that! B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://xafs.org/BruceRavel Software:https://github.com/bruceravel -- Message: 3 Date: Thu, 9 Jan 2014 17:34:13 +0100 From: Kathy Dardenne kathy.darde...@kit.edu To: 'XAFS Analysis using Ifeffit' ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Query re: Athena and Artemis user guides Message-ID:
Re: [Ifeffit] Determining errors in R_fit
Dear Anatoly and Jason, Thank you so much for your feedback !! With best regards, Jatin From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of ifeffit-requ...@millenia.cars.aps.anl.gov [ifeffit-requ...@millenia.cars.aps.anl.gov] Sent: Saturday, November 17, 2012 7:00 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 117, Issue 15 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. Determining errors in R_fit (Rana, Jatinkumar Kantilal) 2. Re: Determining errors in R_fit (Anatoly I Frenkel) 3. Re: Determining errors in R_fit (Jason Gaudet) -- Message: 1 Date: Fri, 16 Nov 2012 18:33:05 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Determining errors in R_fit Message-ID: F11168F9CA572049ADA84F3072DE5DB16D329DB2@didag1 Content-Type: text/plain; charset=us-ascii Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20121116/4b054964/attachment.html -- Message: 2 Date: Fri, 16 Nov 2012 18:47:48 + From: Anatoly I Frenkel afren...@yu.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Determining errors in R_fit Message-ID: 545f89325f51764c902d37b42c9f4d531361d...@yuwexcpm12.yuad.uds.yu.edu Content-Type: text/plain; charset=iso-8859-1 If Y = A + A*X, where A is a constant, X is an independent variable, and you know that X has uncertainty Delta X, then uncertainty in Y is: Delta Y = A * Delta X. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Rana, Jatinkumar Kantilal [jatinkumar.r...@helmholtz-berlin.de] Sent: Friday, November 16, 2012 1:33 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Determining errors in R_fit Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20121116/b71385c5/attachment-0001.htm -- Message: 3 Date: Fri, 16 Nov 2012 13:49:03 -0500 From: Jason Gaudet jason.r.gau...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject
[Ifeffit] Determining errors in R_fit
Dear Ifeffit users, I have a very simple doubt about reporting the uncertainties in R_fit. In the fit, I have assumed that a bond length changes by a constant fraction, *alpha* such that Delta R = R_effective * alpha and, R_fit = R_effective +/- Delta R I can get uncertainties in the fitted value of *alpha* from artemis. But the question is how to work out the uncertainties in the R_fit. Will it be same as that of *alpha* ?? Thanks in advance !!! With best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Ratio of peak amplitudes in R-space
Dear Ifeffit community, I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ? For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process. I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone. As we know that amplitude of peak decreases with increase in distance from central absorber. Can I compare the amplitude ratio of first two peaks for various states of same sample ?? Many thanks in advance !!! With best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ratio of peak amplitudes in R-space
Dear Christopher, Dear Scott, Thank you so much for your valuable feedback. I will now attempt to quantify the observed change in amplitude ratios by fitting data with theoretical standards. With best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: Mittwoch, 5. September 2012 15:26 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 115, Issue 2 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. Ratio of peak amplitudes in R-space (Rana, Jatinkumar Kantilal) 2. Re: Ratio of peak amplitudes in R-space (Christopher Patridge) 3. Re: Ratio of peak amplitudes in R-space (Scott Calvin) 4. How to write feff.inp file for CO adsorbed Cu? (Zhaomo Tian) 5. Re: How to write feff.inp file for CO adsorbed Cu? (Jason Gaudet) -- Message: 1 Date: Wed, 5 Sep 2012 12:01:01 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Ratio of peak amplitudes in R-space Message-ID: F11168F9CA572049ADA84F3072DE5DB135C7180D@didag2 Content-Type: text/plain; charset=us-ascii Dear Ifeffit community, I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ? For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process. I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone. As we know that amplitude of peak decreases with increase in distance from central absorber. Can I compare the amplitude ratio of first two peaks for various states of same sample ?? Many thanks in advance !!! With best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120905/724b5c4d/attachment-0001.htm -- Message: 2 Date: Wed, 5 Sep 2012 08:28:27 -0400 From: Christopher Patridge patri...@buffalo.edu To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ratio of peak amplitudes in R-space Message-ID: cafay88eqj_rjlkeynbdhn-yqc55ualhxfype396oerm3f7k...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Jatin, If these changes are systematic and you somewhat understand the physical or chemical process associated with the sample, then why not just build a model and do a structural fitting?A simple peak ratio comparison maybe helpful but a much stronger argument and interpretation can be made if you use a structural model to extract these comparisons several methods for building a model are available. buena salud, Chris Patridge On Wed, Sep 5, 2012 at 8:01 AM, Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de wrote: Dear Ifeffit community, I was wondering If I can make a qualitative comparison about the amplitude ratio of first two shells for various states of same sample ? For example, I have a sample which is measured at various states, say A, B, C, D and E during any physical or chemical process. I get systematic change in the ratio of first two peaks at each state. This could be interpreted either as change in disorder or as change in number of atoms associated with first two shells as a result of any physical or chemical change material has undergone. As we know that amplitude of peak decreases with increase in distance from central absorber. Can I compare the amplitude ratio of first two peaks for various
Re: [Ifeffit] Theoretical value of S02 for different absorber
Dear Dr. Ravel, Thank you very much for your prompt reply. I followed the instruction on (http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calculation) and activated S02 card by making S02 0.0 in feff.inp file. As a result, FEFF calculated S02. However, I get confused when I compare FEFF calculated S02 with reported value in literature and the one obtained from my own fit. For example, S02 for Mn absorber FEFF calculated 0.94 Fitted value for my sample ~0.75 Fitted value for various Mn-oxides ~0.75 Other reported value from Mn fit ~0.70-0.80 (http://www.sciencedirect.com/science/article/pii/S0020169397057496) S02 for Fe absorber FEFF calculated ~0.94 Fitted value for Fe-foil ~0.70 Fitted value for various Fe-oxides ~0.70 Reported value by calculation 0.69 (http://prola.aps.org/abstract/PR/v169/i1/p27_1) It is well known that S02 is a property of central absorbing atom and is considered to be constant between 0.7 - 1.0. However, in real world, S02 is affected by various systematic errors like thicker samples (in transmission), absorption by other elements in sample at given energy range and many more. These factors can suppress the amplitudes of EXAFS oscillations resulting in lower value of fitted S02 than it should be for a given absorber. The reason I am so much curious about S02 is, if I know what should be (or should be considered) the value of S02 for a given absorber than I can possibly understand the reasons of fitted S02 being too low or too high. For instance, S02 and Sigma2 are highly correlated for first shell. So from fitted value of S02 and Sigma2 of first shell, I could possibly understand changes in local structure. So I would like to put forward very simple but still confusing question that which value of S02 should be considered, FEFF calculated or the one obtained by fitting standards (either reference foils or reference compounds measured on same beamline) and why. Many thanks in advance !!! With best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: Mittwoch, 4. April 2012 19:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 5 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. Theoretical value of S02 for different absorber (Jatin Rana) 2. Re: Theoretical value of S02 for different absorber (Bruce Ravel) -- Message: 1 Date: Wed, 4 Apr 2012 17:45:13 +0800 (SGT) From: Jatin Rana jatin_rana2...@yahoo.com To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Theoretical value of S02 for different absorber Message-ID: 1333532713.14873.yahoomail...@web193501.mail.sg3.yahoo.com Content-Type: text/plain; charset=utf-8 Dear Ifeffit users, Can anyone recommend a reference where I can get calculated value of S02 for various elements ? I would like to compare them with my fitted values. Many thanks in advance !! With best regards, Jatin Rana -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20120404/f4bc6ef3/attachment.html -- Message: 2 Date: Wed, 4 Apr 2012 08:19:34 -0400 From: Bruce Ravel bra...@bnl.gov To: Jatin Rana jatin_rana2...@yahoo.com, XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Theoretical value of S02 for different absorber Message-ID: 201204040819.35087.bra...@bnl.gov Content-Type: Text/Plain; charset=iso-8859-15 On Wednesday, April 04, 2012 05:45:13 am Jatin Rana wrote: Dear Ifeffit users, Can anyone recommend a reference where I can get calculated value of S02 for various elements ? I would like to compare them with my fitted values. http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calculation -- 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 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter
Re: [Ifeffit] Theoretical value of S02 for different absorber
Dear Dr. Newville, Thank you so much for your reply. Things are very much clear now. With best regards, Jatin From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of ifeffit-requ...@millenia.cars.aps.anl.gov [ifeffit-requ...@millenia.cars.aps.anl.gov] Sent: Thursday, April 05, 2012 7:00 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 6 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Theoretical value of S02 for different absorber (Rana, Jatinkumar Kantilal) 2. Results Reporting (John Farell) 3. Re: Results Reporting (Bruce Ravel) 4. Re: Theoretical value of S02 for different absorber (Matt Newville) -- Message: 1 Date: Thu, 5 Apr 2012 10:44:05 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Theoretical value of S02 for different absorber Message-ID: 6FCB59A6A97E13429B863B7014B57E4B10E2E8@didag1 Content-Type: text/plain; charset=utf-8 Dear Dr. Ravel, Thank you very much for your prompt reply. I followed the instruction on (http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calculation) and activated S02 card by making S02 0.0 in feff.inp file. As a result, FEFF calculated S02. However, I get confused when I compare FEFF calculated S02 with reported value in literature and the one obtained from my own fit. For example, S02 for Mn absorber FEFF calculated 0.94 Fitted value for my sample ~0.75 Fitted value for various Mn-oxides ~0.75 Other reported value from Mn fit ~0.70-0.80 (http://www.sciencedirect.com/science/article/pii/S0020169397057496) S02 for Fe absorber FEFF calculated ~0.94 Fitted value for Fe-foil ~0.70 Fitted value for various Fe-oxides ~0.70 Reported value by calculation 0.69 (http://prola.aps.org/abstract/PR/v169/i1/p27_1) It is well known that S02 is a property of central absorbing atom and is considered to be constant between 0.7 - 1.0. However, in real world, S02 is affected by various systematic errors like thicker samples (in transmission), absorption by other elements in sample at given energy range and many more. These factors can suppress the amplitudes of EXAFS oscillations resulting in lower value of fitted S02 than it should be for a given absorber. The reason I am so much curious about S02 is, if I know what should be (or should be considered) the value of S02 for a given absorber than I can possibly understand the reasons of fitted S02 being too low or too high. For instance, S02 and Sigma2 are highly correlated for first shell. So from fitted value of S02 and Sigma2 of first shell, I could possibly understand changes in local structure. So I would like to put forward very simple but still confusing question that which value of S02 should be considered, FEFF calculated or the one obtained by fitting standards (either reference foils or reference compounds measured on same beamline) and why. Many thanks in advance !!! With best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: Mittwoch, 4. April 2012 19:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 5 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. Theoretical value of S02 for different absorber (Jatin Rana) 2. Re: Theoretical value of S02 for different absorber (Bruce Ravel) -- Message: 1 Date: Wed, 4 Apr 2012 17:45:13 +0800 (SGT) From: Jatin Rana jatin_rana2...@yahoo.com
[Ifeffit] Problem with handling doped material
Dear Ifeffit users, I apologize for my previous post with subject Difficulty in running feff8.2 being ill-defined and lacking adequate supporting informations, I try to redefine the problem again. I want to perform EXAFS fit on data for Li2Mn1.5Ni0.5O4 material measured on Mn K-edge. (i.e. case of handling dopant by modifying feff.inp files) I used Li2Mn2O4 structure (attached as Li2Mn2O4.inp file) to generate feff.inp file With Mn core atom (attached as Li2Mn2O4_feff.inp) and run through Feff8.2. It worked well. Now, when I modified Li2Mn2O4_feff.inp file such that Mn is core atom but all back scatterers are now Ni instead of Mn (attached as Li2Ni2O4_feff.inp), feff8.2 terminates after 17 SCF iterations. I have no idea why, since it never happened before. Looking at both feff.inp files they are identical except with the fact that in case of Li2Ni2O4_feff.inp, I replaced all Mn back scatterers with Ni. Am I doing something wrong (unknowingly) ?? I am using Windows 7 machine but I tried it on another windows xp machine also and the result is same. Can anyone on mailing list help me getting out of these problem ?? Any help would be much appreciated. With best regards, Jatin -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-requ...@millenia.cars.aps.anl.gov Sent: Dienstag, 18. Oktober 2011 19:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 104, Issue 24 Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. Difficulty in running feff8.2 (Rana, Jatinkumar Kantilal) -- Message: 1 Date: Tue, 18 Oct 2011 15:10:31 + From: Rana, Jatinkumar Kantilal jatinkumar.r...@helmholtz-berlin.de To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Difficulty in running feff8.2 Message-ID: 6CA1A94BC28ABA4F9E1D360B3E249AEC0E3BC4A8@didag1 Content-Type: text/plain; charset=us-ascii Dear ifeffit users, Recently, I am facing difficulty in running feff8.2 on one particular feff.inp file. I have measured Mn K-edge data for Li2Mn1.5Ni0.5O4. I want to perform feff calculation of Li2Mn1.5Ni0.5O4 in order to fit the data. I have structural data for Li2Mn2O4. To have an overall feff calculation of Li2Mn1.5Ni0.5O4, I need to perform feff calculation two times, i.e., one with Li2Mn2O4 (with Mn as core) and second with Li2Ni2O4 (i.e. with Mn as core and rest of Mn atoms replaced by Ni). Then I can add both feff calculations appropriately to generate resultant theoretical chi(k) and go ahead with fitting. The problem is, I could successfully run feff8.2 on Li2Mn2O4, but when I run it on Li2Ni2O4 it stops after performing few iterations without any notifications. I am not able to understand why feff terminates half way. I have never faced such problem before. Can anyone help me ? Please see the attached feff.inp file which I am trying to run. I have activated SCF card in that. Many thanks in advance !! With Best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20111018/4a5c6e1f/attachment.html -- next part -- A non-text attachment was scrubbed... Name: feff.inp Type: application/octet-stream Size: 9986 bytes Desc: feff.inp URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20111018/4a5c6e1f/attachment-0001.obj -- ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 104, Issue 24 Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
[Ifeffit] Difficulty in running feff8.2
Dear ifeffit users, Recently, I am facing difficulty in running feff8.2 on one particular feff.inp file. I have measured Mn K-edge data for Li2Mn1.5Ni0.5O4. I want to perform feff calculation of Li2Mn1.5Ni0.5O4 in order to fit the data. I have structural data for Li2Mn2O4. To have an overall feff calculation of Li2Mn1.5Ni0.5O4, I need to perform feff calculation two times, i.e., one with Li2Mn2O4 (with Mn as core) and second with Li2Ni2O4 (i.e. with Mn as core and rest of Mn atoms replaced by Ni). Then I can add both feff calculations appropriately to generate resultant theoretical chi(k) and go ahead with fitting. The problem is, I could successfully run feff8.2 on Li2Mn2O4, but when I run it on Li2Ni2O4 it stops after performing few iterations without any notifications. I am not able to understand why feff terminates half way. I have never faced such problem before. Can anyone help me ? Please see the attached feff.inp file which I am trying to run. I have activated SCF card in that. Many thanks in advance !! With Best regards, Jatin Helmholtz-Zentrum Berlin f?r 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 Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de feff.inp Description: feff.inp ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
