[Ifeffit] EXAFS simulations - peak too high
Hello. I am running some EXAFS simulations Au L3 on Au clusters with SR coating. In the outer shell Au sits between 2 S atoms. 4 Au atoms are in the neighborhood up to 3.5 Angström. Expecting two peaks in the chi(R) - one for Au-S and one for Au-Au (here it can be several little ones) I find that for 1 out of 5 sites the Au-Au peak is way too high. Is something in the FEFF code weighing an Au-Au path for this site too much? Does anyone have some ideas on that? Thanks, Lisa ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] EXAFS simulations - peak too high
You are probably trying to investigate the staple motif? People from Dalhouse University, Peng Zhang and others used FEFFIT for this purpose and analyzed Au-S and Au-Au contributions in such situations. Their papers explain the way FEFF modeling was done. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Lisa Bovenkamp [lbovenk...@lsu.edu] Sent: Monday, February 03, 2014 1:27 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] EXAFS simulations - peak too high Hello. I am running some EXAFS simulations Au L3 on Au clusters with SR coating. In the outer shell Au sits between 2 S atoms. 4 Au atoms are in the neighborhood up to 3.5 Angström. Expecting two peaks in the chi(R) - one for Au-S and one for Au-Au (here it can be several little ones) I find that for 1 out of 5 sites the Au-Au peak is way too high. Is something in the FEFF code weighing an Au-Au path for this site too much? Does anyone have some ideas on that? Thanks, Lisa ___ 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
Re: [Ifeffit] EXAFS simulations - peak too high
Dear Anatoly. Yes, I know that paper. In order to expand that study from pure gold to bimetallic clusters I want to be sure and repeat the results that this group found. Thanks for mentioning it. Dear Scott, That was the answer I was looking for. I believe the paths are reinforcing each other. This is now obvious from the Im chi(R). Thanks for the presentation of yours. Now one question remains: Do I discard/disregard this site from my calculations (in the averaging process) or not? Thanks. Lisa ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] EXAFS simulations - peak too high
Hi Lisa, On Feb 3, 2014, at 4:24 PM, Lisa Bovenkamp lbovenk...@lsu.edu wrote: Dear Scott, That was the answer I was looking for. I believe the paths are reinforcing each other. This is now obvious from the Im chi(R). Thanks for the presentation of yours. Now one question remains: Do I discard/disregard this site from my calculations (in the averaging process) or not? No; the calculation is telling you must include it, because it is particularly important! Presumably your averaging process involves a weighted average of chi(k), or maybe chi(R) (it doesn't matter which). It is invalid to average the magnitudes of chi(R). --Scott Calvin Sarah Lawrence College ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] EXAFS simulations - peak too high
Lisa, On Mon, Feb 3, 2014 at 12:27 PM, Lisa Bovenkamp lbovenk...@lsu.edu wrote: Hello. I am running some EXAFS simulations Au L3 on Au clusters with SR coating. In the outer shell Au sits between 2 S atoms. 4 Au atoms are in the neighborhood up to 3.5 Angström. Expecting two peaks in the chi(R) - one for Au-S and one for Au-Au (here it can be several little ones) I find that for 1 out of 5 sites the Au-Au peak is way too high. Is something in the FEFF code weighing an Au-Au path for this site too much? Does anyone have some ideas on that? Thanks, Lisa I'm a little confused by what you're asking. Is SR scratch resistant? As Scott points out, you should not expect one peak for Au-S and one peak for Au-Au in chi(R). Au-Au will almost certainly give a double peak in chi(R) due to the resonance in the scattering for heavy scatterers. When you say for 1 out of 5 sites the Au-Au peak is way too high, what are you comparing it too? Are the path degeneracies the same, is there any disorder term included in the simulation, etc. But if you're running a simulation, wouldn't you know what scattering paths contributed to the different peaks, and especially if the paths include multiple scattering? --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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
[Ifeffit] EXAFS simulations
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 first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1 Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 18). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is reasonably expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli athena_Cu.prj Description: athena_Cu.prj ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
