Re: [Ifeffit] EXAFS simulations
Ciao Sebastiano, did you use the mu-column of the xmu.dat? If so, the main difference between the chi.dat and the xmu.dat is that the mue_0 (as calculated by FEFF) is already subtracted in the former while it needs to be subtracted by Athena in the latter. Some of the difficulties you mentioned are thus due to problems of Athena to do a decent background (i.e. mue_0 and normalization) processing if there is no pre-edge region. Thus the effect of changing the absorption energy in Cu Bulk 4 from 8988.430eV to 8988.431eV is not caused by a *wrong* Enot but by a change in the edge-jump of almost 50% (due to a different *pre-edge*). Thus using the chi.dat seems to be the better (i.e. more reproducible) choice in this case (a precautionary note though: the mue_0 as calculated by FEFF will most likely differ between the central and the peripheral atoms; this may be part of the cluster-effect or an artifact (I assume that this is only a problem in the XANES region but I don't know, so you should check this by plotting the single mue_0). HTH Jakob ___ 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 web: http://www.ibp.ethz.ch/research/soilchemistry From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Fri 10/24/2008 09:57 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 68, Issue 21 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 [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. Re: Fit XANES spectra using Athena (Adam Webb) 2. EXAFS simulations (Cammelli Sebastiano) -- Message: 1 Date: Fri, 24 Oct 2008 07:39:55 +0200 From: Adam Webb [EMAIL PROTECTED] Subject: Re: [Ifeffit] Fit XANES spectra using Athena To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi Jenny, I don't know what exactly you are trying to do so I can't say which method is better but I can make a comment. It all comes down to the number of independent variables. The Gaussian and step functions are independent of each other. The heights, widths and positions can all be adjusted. In the linear combination you change everything together so for example, the ratio of the peak height and the step height doesn't change. The result is that you need more spectra to get the same number of degrees of freedom as in the least-squares peak fit. Cheers, Adam Jenny Cai wrote: Hello everyone, Sorry for bothering you again. I am using least-squares peak fit and linear combination fit to analyze my samples. I have spent tons of time on it, and it really makes me crazy. Why can't I get consistent results from these two methods? Please see the attached file. Both of these methods work well individually, but linear combination fit always need more peaks than peak fit to get an 'ok' fitting. Should I stick on one method for all my samples, no matter what results the other one gives? It is confusing me so much. Could anyone help me out? Thank you in advance for your help! Jenny -- Message: 2 Date: Fri, 24 Oct 2008 09:57:35 +0200 From: Cammelli Sebastiano [EMAIL PROTECTED] Subject: [Ifeffit] EXAFS simulations To: ifeffit@millenia.cars.aps.anl.gov Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the
Re: [Ifeffit] Energy shift (???)
Hi eunsuk1986 (unfortunately you did not share your full name with us...) I had some trouble with reading your feff.inp. Nevertheless the problem of the absolute alignment of FEFF xmu and experimental data has been the subject of earlier questions. I' am citing form a list contribution of J. Rehr (Aug 3rd 2003): The FEFF calculation of the absolute energy is not meant to be highly accurate, and errors of several eV for K-shells of large Z atoms are not unusal. Thus you did nothing wrong in the input file. To match FEFF and experiment you *always* have to shift the FEFF absolute threshold to match experiment.. There is no way (I am aware of) to tell FEFF do this absolute shift (you can and you often need to shift the position of the Fermi level though) but you can do this with every plot program. Thus you should not worry too much about the absolute energies in your xmu but a lot about relative energies (i.e. the positions of the single resonances). HTH Jakob ___ 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 web: http://www.ibp.ethz.ch/research/soilchemistry From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Mon 8/18/2008 09:46 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 66, Issue 9 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 [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of Ifeffit digest... Today's Topics: 1. Energy shift (???) -- Message: 1 Date: Mon, 18 Aug 2008 16:46:26 +0900 From: ??? [EMAIL PROTECTED] Subject: [Ifeffit] Energy shift To: ifeffit@millenia.cars.aps.anl.gov Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ks_c_5601-1987 Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites:Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * potxsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.1 * emin emax resolution LDOS -2020 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 18O -1 -1 1 2 30Zn -1 -1 1 ATOMS 0.0 0.0 0.00 Zn1 0.0 0.0 0.0 2.063021 O1 2.06302 -1.95951 0.0-0.651481 O1 2.06497 0.97978-1.69700-0.651481 O1 2.06500 0.97978 1.69700-0.651481 O1 2.06500 0.97978-1.69700 -2.714502 Zn1 3.34788 0.97978 1.69700 2.714502 Zn1 3.34788 0.97978 1.69700-2.714502 Zn1 3.34788 0.97978-1.69700 2.714502 Zn1 3.34788 _ ???, ?? ??? Windows Live Hotmail! ?? ???! http://www.hotmail.com http://www.hotmail.com/ -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20080818/aac9c4ad/attachment.html -- next part -- A non-text attachment was scrubbed... Name: data and FEFF_model.jpg Type: image/jpeg Size: 24357 bytes Desc: not available Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20080818/aac9c4ad/attachment.jpg -- ___ Ifeffit mailing list
[Ifeffit] FEFF-SCF and Enot in Artemis
Dear all! Recently I read the two inspiring XAFS13-contributions of Shelly and Bruce dealing with the energy-shift (p.132) and the use of SCF-calculations (p. 137). In this respect I have a question regarding the Enot parameter in Artemis: Plotting the mue (4th column in xmu.dat) of a FEFF8.4 SCF calculation (of a transition metal oxide; here: Fe or Cr) against the second column (e) of xmu.dat, I end up with a fairly decent reconstruction of my experimental XANES: the onset of the pre-edge resonances is located at negative energies (if I am right this is referred to as E_0 (bottom of the conduction band)) and the energy zero (i.e. Fermi energy) is located somewhere in the rising part of the absorption edge. If I then use the same (SCF) potentials and let FEFF do a path-expansion run, the header of the feff.dat contains a (negative) quantity called edge, which gives exactly the difference between E_0 and E_fermi (as also explained in Matt's article: J. Sync. Rad., 2001, pp. 96-100). In the xmu.dat, k seems to be calculated relative to E_0 (i.e. to a negative energy in the 2nd (e) column). Plotting a path in Artemis (or the xmu calculated for a single path) I had the impression that again k is referenced to E_0 (onset of the pre-edge feature) rather than to E_fermi (somewhere in the rising part of the edge). Is this true? Assuming that I set the E0-parameter in Athena to the first inflection point of the main edge (so in the upper nomenclature to something like E_Fermi) and assuming further that I do a shell-fit in Artemis, wouldn't I expect to end up (in an ideal case) with an Enot similar to the quantity edge given in the feff.dat rather than a Enot of (close to) 0? I also found a mailing-list contribution (dating back to 2004) of Wojciech and Matt addressing a similar topic - still it is not clear to me what the effect on Artemis' Enot will be. I hope I did not confuse too many things. I will greatly appreciate any hint clarifying this situation. With many thanks and best regards Jakob ___ 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 web: http://www.ibp.ethz.ch/research/soilchemistry ___ 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
