Re: [Ifeffit] Re: question on Athena data import
Bruce Ravel schrieb: On Thursday 07 December 2006 08:15, Gerrit Schmithals wrote: Matt Newville schrieb: Very nice! I'd be happy to give you some space on http://cars9.uchicago.edu/~ravel/software/contrib.html, if that would help. You could use the wiki for this. Hello Bruce, Hello Matt, I appended the script file along with a couple of textfiles for testing. There is a description at the top of the file that explains how to use it. I think both the wiki and the Athena homepage are good places to offer it. Can I leave it up to you where you want to have it? I only tested it on Windows so maybe you want to give it a try on Linux/Mac first. Gerrit, Please take a look at the User Contributions part of this wiki page http://cars9.uchicago.edu/iffwiki/HoraeSoftware I'd like to make sure I haven't misrepresented you in any way ;-) B Hello, everything looks fine. I hope it will be useful. Gerrit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] FEFF and XANES
Dear all, I have a FEFF related question (I know that this is an IFEFFIT list, but I guess the subjects are closely related). I try to model some of my Cr XANES data with FEFF (following the procedure outlined in an excellent publication in Chem Phys 300 (2004) 13-22 the authors have shown that it is possible to explain the Cr XANES spectra at least qualitatively by the means of FEFF calculations). I have however still some trouble to understand the difference (or the relation) between the XANES results given in the xmu.dat file and the l-projected density of states results (ldosXX.dat). Due to rho(E)=rho_0(E)[1+chi(E)] I would expect them to conincide (if the rho is calculated for the correct l i.e. if the matrix element is non-zero). However I observed that the ldos and the xmu do not always coincide is this possible? Furthermore at the white line position (from what I know, the white line is commonly interpreted as being due to the transition into unoccupied but bound states)! the xmu shows strong intensity whereas the ldos do not (maybe one comment: I assume that the e-scales in the ldos-file and in the xmu-file are the same). I am using FEFF8.2 with the SCF, DOS, XANES and FMS card. I would be obliged for your help. Thanks Jakob P.s.: for hydroxide structures FEFF is always returning bad counts if I include the protons into the FEFF calculation however this might be also due to bad input structures. ___ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 Email: [EMAIL PROTECTED] http://www.ito.ethz.ch/SoilChem/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] CN and bond distances in Artemis
Hi all, First of all, I would like to thanks Anatoly for his file and everybody for useful comments. I have analysed Anatoly's data and I have obtained a good value for S02 = 0.85 or 0.82 (depending on the number of variables used). So, my data is the problem, and it is not my analysis, but maybe my measurements need a more accurate analysis with Athena as Scott suggested. I was not at synchrotron measuring platinum samples and I only know that are measured in fluorescent mode. As Bruce said, I have no beamtime now for more measurements. I have more questions, related and not related to the last subject, but I am still thinking about them: The first one is easy, it is about the Nyquist theorem. I read in a paper that the formula is 2·deltak·deltaR/pi + 2. The last +2 is new for me and I am afraid that Artemis does not consider it. I am sure that it is a silly thing. I will try to correct again Ptfoil considering self-absorption in order to obtain a spectrum similar to Anatoly's or Bruce's one. And then, I will apply the same correction for supported platinum catalysts, right? I also observed that Anatoly's Pt foil shows good signal even for large k (20 A-1). Nevertheless, obviously platinum catalysts spectra possess lower signal and specially for high values of k where the noise is big. The question is, despite Pt foil has a good signal until 20 A-1, it is usually used a smaller k-range (i.e. 3-12 A-1), right? I normally use a k-range of 3-12. And finally, how to calculate bond distances from Reff and deltaR? Thank you very much Best regards, JA begin:vcard n:Maciá Agulló;Juan Antonio tel;fax:0034-965903454 tel;work:0034-965909350 x-mozilla-html:FALSE org:University of Alicante;Department of Inorganic Chemistry adr:;; version:2.1 email;internet:[EMAIL PROTECTED] title:Ph. D. Student fn:Juan Antonio Maciá Agulló end:vcard ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] CN and bond distances in Artemis
Juan: For S02 from fluorescence measurements or data collected at other times/beamlines, etc, I would ask what purpose this S02 is serving in your analysis. I'd guess that you do the normal thing of fixing this value for several paths and then float the coordination numbers so that amp = S02 * N for some number of paths.As you have experienced, S02 does have some inherent uncertainty in it due to modes of measurement and sample preparation. Be sure to fold that into your analysis! I have more questions, related and not related to the last subject, but I am still thinking about them: The first one is easy, it is about the Nyquist theorem. I read in a paper that the formula is 2·deltak·deltaR/pi + 2. The last +2 is new for me and I am afraid that Artemis does not consider it. I am sure that it is a silly thing. Artemis/Ifeffit use (2 DeltaK DeltaR / pi) as a real number (not rounding) and leaves out the +2. I will describe this as the correct way of doing it. More importantly, if it matters for your results, the uncertainties in the fitted parameters *should* be very high. I will try to correct again Ptfoil considering self-absorption in order to obtain a spectrum similar to Anatoly's or Bruce's one. And then, I will apply the same correction for supported platinum catalysts, right? I'm not sure I understand this. But, you may want to apply absorption corrections to data collected in fluorescence when the Pt concentration is high (say, 1%), especially when comparing data with a range of concentration and where accurate absolute coordination numbers are important. Also, don't spend too much time analyziing the Pt foil just to get S02. I also observed that Anatoly's Pt foil shows good signal even for large k (20 A-1). Nevertheless, obviously platinum catalysts spectra possess lower signal and specially for high values of k where the noise is big. The question is, despite Pt foil has a good signal until 20 A-1, it is usually used a smaller k-range (i.e. 3-12 A-1), right? I normally use a k-range of 3-12. Analyze as far out in k as the data goes. It's usually pretty easy to tell when the noise in the data is larger than the signal.For room temperature data, it's often the case that the data stops around between 10 and 14 A^-1. And finally, how to calculate bond distances from Reff and deltaR? For single scattering paths,R = Reff + deltaR. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] FEFF and XANES
Hi Jakob, As you have noted the fine structure in the projected DOS and the XAS is the same, so the relation between them is: XAS = gamma(E) LDOS, where gamma(E) = mu_0(E)/rho_0(E), where gamma(E) is a smoothly varying atomic-like quantity which is essentially a ratio of embedded atomic matrix elements. In systems with a white line $mu_0$ and hence, gamma(E) will likely be peaked at threshold. As a result the XAS is smoothly related to the LDOS with appropriate selection rules. This discussion assumes core-hole effects are small, and final state broadening is applied both the the LDOS and XAS. J. Rehr On Mon, 11 Dec 2006, Frommer Jakob wrote: Dear all, I have a FEFF related question (I know that this is an IFEFFIT list, but I guess the subjects are closely related). I try to model some of my Cr XANES data with FEFF (following the procedure outlined in an excellent publication in Chem Phys 300 (2004) 13-22 ? the authors have shown that it is possible to explain the Cr XANES spectra at least qualitatively by the means of FEFF calculations). I have however still some trouble to understand the difference (or the relation) between the XANES results given in the xmu.dat file and the l-projected density of states results (ldosXX.dat). Due to rho(E)=rho_0(E)[1+chi(E)] I would expect them to conincide (if the rho is calculated for the correct l ? i.e. if the matrix element is non-zero). However I observed that the ldos and the xmu do not always coincide ? is this possible? Furthermore at the white line position (from what I know, the white line is commonly interpreted as being due to the transition into unoccupied but bound states)! the xmu shows strong intensity whereas the ldos do not (maybe one comment: I assume that the e-scales in the ldos-file and in the xmu-file are the same). I am using FEFF8.2 with the SCF, DOS, XANES and FMS card. I would be obliged for your help. Thanks Jakob P.s.: for hydroxide structures FEFF is always returning ?bad counts? if I include the protons into the FEFF calculation ? however this might be also due to bad input structures. ___ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Z?rich Universit?tstrasse 16, CHN F19 CH - 8092 Z?rich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 Email: [EMAIL PROTECTED] http://www.ito.ethz.ch/SoilChem/ ___ Ifeffit mailing list Ifeffit@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
