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
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-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Lisa Bovenkamp [lbovenkamp@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
Hi Lisa,
Without thinking too much about your particular structure (I wouldn't be surprised if someone on the list chimes in with that kind of info by the time I finish composing this!), I am very confident it is not a fault in the FEFF code.
Ad you probably know, chi(R) is NOT a radial distribution function, although they are related. For one thing, multiple-scattering can play a role, and it may be that in one of the sites multiple scattering may be enhancing the peak--perhaps there are more sulfur atoms collinear with the gold-gold paths, for instance. In addition, chi(R) is complex valued, meaning that different paths can reinforce or cancel in a non-linear way if you just look at the magnitude. In other words, the chi(R) magnitude of the combination of Au1 - Au2 and Au1 - Au3 might be larger than the sum of the individual magnitudes of the individual magnitudes or smaller.
About a decade ago, I analyzed the structure of elemental manganese using EXAFS. Elemental manganese has one of the nuttier crystal structures you'll find in a pure element, with four crystallographically distinct absorbing sites. Because of interference between scattering paths, the "importance" of each site to the fit varied by up to 400% from what would be expected due to abundance.
I never published that result, but I do have the pdf of my presentation to the APS on it, so I'm attaching that.
I'd guess your effect is either something like that or an effect of multiple-scattering.
--Scott Calvin
Sarah Lawrence College
On Feb 3, 2014, at 1:27 PM, Lisa Bovenkamp
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
Lisa,
On Mon, Feb 3, 2014 at 12:27 PM, Lisa Bovenkamp
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
participants (4)
-
Anatoly I Frenkel -
Lisa Bovenkamp -
Matt Newville -
Scott Calvin