October 2011 - Ifeffit - millenia.cars.aps.anl.gov

Soham Mukherjee has invited you to open a Google mail account
by Soham Mukherjee 10 Oct '11

10 Oct '11

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Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 9
by Soham Mukherjee 10 Oct '11

10 Oct '11

For the first shell, I used cubic phase as my starting model and that gave a pretty good fit. However, when I take wurtzite phase as my starting model and vary two bond lengths (both Zn-S, with the axial bond longer by only 0.004 Ang) independently, my delr and ss go crazy. I think that as the first two S subshells are so close to each other, my data can't identify them (delr and ss) independently. So I defined their delr and ss to be same and the results match pretty well with the cubic phase. The r-factor and reduced-chi square with the two models are very similar.Thanks a lot ! On Sun, Oct 9, 2011 at 10:30 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. lifetime broadening of pre-edge peaks? (Matthew Marcus) > 2. Re: Zinc Sulfide fitting (JeongEunSuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 08 Oct 2011 14:36:56 -0700 > From: Matthew Marcus <mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] lifetime broadening of pre-edge peaks? > Message-ID: <4E90C278.3060602(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Is the core-hole lifetime broadening of pre-edge XANES peaks the same as at > the main edge? I'm looking into issues of de-noising of XANES epsctra, so > need to figure out how narrow real features can be. > mam > > > ------------------------------ > > Message: 2 > Date: Sun, 9 Oct 2011 07:06:52 +0900 > From: JeongEunSuk <eunsuk1986(a)hotmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Zinc Sulfide fitting > Message-ID: <BLU151-W2672826EC60532B7643F18DAFF0(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > hello > > Two phase can be mixed in ZnS. You need to check r-factor and reduced-chi > squrare with two model. > If you want to fit only first shell, > I suggest. > first use cubic zinc-blende model in FEFF, and check goodness of fit. > second, fix the bond length of 3 bonding length and change the bond length > of a rest. > when you use my suggestion, the variables in Artemis is delrS1(changable), > sigmaS1(changable), others(fix) > > > > > Date: Thu, 6 Oct 2011 13:32:24 +0530 > From: soham.chem(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Zinc Sulfide fitting > > Dear Ifeffit Community, > > Zinc Sulfide exists largely in two phases, either the cubic zinc-blende > (F-43m) phase, or the hexagonal wurtzite (P63cm) phase. > > The details of the NN distances are as follows :- > 1. For cubic phase, the NN distances (Zinc to Sulfur bond lengths) are > 2.3028 Angstroms each, 4 such bonds exist in a tetrahedral arrangement; > 2. For hexagonal phase, there are 2 different NN distances (Zinc to Sulfur > bond lengths) 3 bonds having the length 2.3421 Angstroms each, and 1 > axially > elongated bond of length 2.3465 Angstroms. So they differ only by 0.0044 > Angstroms ! > > I am performing a first shell fit to Zinc Sulfide which exists in the > wurtzite phase (hexagonal_P63cm). However, I could fit it quite well taking > the cubic phase (Zinc blende_F-43m) as my starting model. The only thing is > that since bond distances are higher in a hexagonal phase than the cubic > phase, I end up with a considerable delr as I underestimated my starting > bond length value. Taking a wurtzite model involves defining two different > bond lengths (which differ only by 0.0044 Angstroms !), paths 1 and 2 in > the > FEFF, whose sigma^2 values are quite similar. This gives unusually large > delr values and high sigma^2 for the longer axial bond, which looks > suspicious ! > > Do I really need to define the two bond distances separately of so close > values? Or taking a cubic phase will be sufficient? Please find the > attached > project file (artemis.apj) where I have tried out some simulations with > both > cubic and hexagonal models. > > Here are a few details you asked for :- > > The sample is a thin layer, it's pretty homogeneous and had no pinholes > during measurements. The fit details are :- > k_min = 2, k_max = 14 > R_min = 1, R_max = 3 > The potential is self consistent in these calculations > Fitting was performed in the R-space > > Best regards, > Soham. > > _______________________________________________ Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Zinc Sulfide fitting
by grant bunker 09 Oct '11

09 Oct '11

Soham - I don't think you will be able to resolve the small (.0044) distance difference between one S and 3 others. That corresponds to a sigma squared of only 3.6*10^(-6). If you wanted to resolve them by going to higher k you would have to go out to k=pi/(.0088 A) ~ 357 inverse angstroms, which might be a bit of a challenge. More fundamentally the delr parameter that you float would be nearly 100% correlated with the sigma squared, if you are also floating that. The numerical instability associated with parameter correlation can be expected to give you crazy values for both delr and ss (and correspondingly large error bars), which I think you are getting. So the 4 S atoms are effectively at the same distance. It's to just treat them as a single shell of 4 S atoms and describe the mean and SS of that distribution. It's really all the data can tell you without bringing some other information into the fitting process. hope that helps Grant Bunker

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Zinc Sulfide fitting
by Soham Mukherjee 08 Oct '11

08 Oct '11

Dear Ifeffit Community, Zinc Sulfide exists largely in two phases, either the cubic zinc-blende (F-43m) phase, or the hexagonal wurtzite (P63cm) phase. The details of the NN distances are as follows :- 1. For cubic phase, the NN distances (Zinc to Sulfur bond lengths) are 2.3028 Angstroms each, 4 such bonds exist in a tetrahedral arrangement; 2. For hexagonal phase, there are 2 different NN distances (Zinc to Sulfur bond lengths) 3 bonds having the length 2.3421 Angstroms each, and 1 axially elongated bond of length 2.3465 Angstroms. So they differ only by 0.0044 Angstroms ! I am performing a first shell fit to Zinc Sulfide which exists in the wurtzite phase (hexagonal_P63cm). However, I could fit it quite well taking the cubic phase (Zinc blende_F-43m) as my starting model. The only thing is that since bond distances are higher in a hexagonal phase than the cubic phase, I end up with a considerable delr as I underestimated my starting bond length value. Taking a wurtzite model involves defining two different bond lengths (which differ only by 0.0044 Angstroms !), paths 1 and 2 in the FEFF, whose sigma^2 values are quite similar. This gives unusually large delr values and high sigma^2 for the longer axial bond, which looks suspicious ! Do I really need to define the two bond distances separately of so close values? Or taking a cubic phase will be sufficient? Please find the attached project file (artemis.apj) where I have tried out some simulations with both cubic and hexagonal models. Here are a few details you asked for :- The sample is a thin layer, it's pretty homogeneous and had no pinholes during measurements. The fit details are :- k_min = 2, k_max = 14 R_min = 1, R_max = 3 The potential is self consistent in these calculations Fitting was performed in the R-space Best regards, Soham.

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controlling valence state in FEFF9 XANES sims
by Matthew Marcus 07 Oct '11

07 Oct '11

I'm involved in a project involving mixed Fe-Cr oxides. There's some evidence that the presence of Fe2+ in these oxides causes distinctive features to appear in the XANES at the Cr K-edge. I would like to simulate this situation to see if a valence effect could really explain it. However, FEFF9 doesn't seem to have an obvious mechanism for controlling the valence of the atoms or even assuring charge neutrality of the cluster. For instance, as a test, I simulated goethite (FeO(OH)) with and without the H atoms and got almost the same result, even though charge balance works for FeO(OH) and not for FeO(O<nothing>). I know that there is the ION card, but it's not clear how to choose the value so as to get a given formal oxidation state or how to determine what charges are present on any atoms in the cluster. Any ideas out there? Also, I find that the XANES is best simulated if I make S02=0.7 or so. If S02=1, the features are too intense. mam

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d-band vacancies vs d-band center
by Qingying Jia 06 Oct '11

06 Oct '11

Hi All: I am wondering whether there is a specific correlation between d-band vacancies vs d-band center of Pt. We can acquire experimental d-band vacancies of Pt by XAFS from Pt LIII & LII XANES. I assume the downshift of d-band relative to Fermi level (lower d-band center) caused by for example alloying with the second metal will reduce the d-band vacancies since the part above Fermi level gets reduced. But it seems like it is not always true. I appreciate if someone can explain the correlation between these two or give relevant references. Regards, Jias

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Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 4
by Soham Mukherjee 06 Oct '11

06 Oct '11

Dear Ifeffit Community, The attachment didn't open ?! I am resending the same. In any case, I will give all the details :- The sample is a thin layer, it's pretty homogeneous and had no pinholes during measurements. The fit details are :- k_min = 2, k_max = 14 R_min = 1, R_max = 3 The potential is self consistent in these calculations Fitting was performed in the R-space Best regards, Soham. On Thu, Oct 6, 2011 at 12:50 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: Energy shift (Dr. Dariusz A. Zaj?c) > 2. Zinc Sulfide fitting (Soham Mukherjee) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Oct 2011 08:45:05 +0200 > From: "Dr. Dariusz A. Zaj?c" <kicaj(a)ifj.edu.pl> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Energy shift > Message-ID: <4E8D4E71.2000309(a)ifj.edu.pl> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Your attachment do not help in this case... > Do you know something more about sample? I suppose it is a thin layer. > Have you checked if you have no defects, vacancies, etc? > I suppose that you can follow instructions given in this post > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-January/008522.html > but you can be also interested in this topic: > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-June/004293.html > and especially in last posts. > you can also try this suggestion > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-June/009471.html > > In general - could you precise, what is k_{min} for your fit, and did > you use self consistent potential in calculations? > > > > > > W dniu 11-10-06 02:28, JeongEunSuk pisze: > > Thank Dariuz and Bruce. > > TiO is deposited on Si substrate and PtO is fabricated on TiO2. > > I measered EXAFS with Pt L3 edge(11563eV) and The model is decided > > from FEFF8.0. > > PtO has only fist shell like attached files So I chose the simple > > model with octahedral structure (probe atom Pt, others O) > > When the EXAFS was fitted by feffit, the variables were three eo(Enot > > in Artemis, energy shift), do1(distance factor), sigo1(debye-waller > > factor). > > the results of fit is as following > > variable best fit value uncertainty initial guess > > eo = 19.283398 1.726426 0.000000 > > do1 = -0.023227 0.009557 0.096000 > > sigo1 = 0.003790 0.000583 0.003047 > > r-factor: 11 > > reduced-chi square: 95 > > > > Energy shift by fit shows an amount of difference from Pt L3 edge. It > > is my problem. > > To reduce the energy shift, I tried to remove background carefully > > again and to change distance Pt-O. > > However the result was failed. > > > > > > > > ------------------------------------------------------------------------ > > Date: Wed, 5 Oct 2011 08:24:16 +0200 > > From: kicaj(a)ifj.edu.pl > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] Energy shift > > > > Hi, > > could say more precise what kind of energy shift you are talking > > about? the position of the white line or the Enot in Artemis. How big > > it is? Which version of Feff do you use? What do you mean writing > > "removing background carefully"? Background in the EXAFS fit? Any > > pictures to illustrate problem are welcome > > > > W dniu 11-10-05 03:25, JeongEunSuk pisze: > > > > Hell all > > I have the study for PtO nanoparticles with EXAFS. > > When I fitted the data to model, I had a problem for energy shift. > > I thought that the energy shift obtained from fitting must be > > below White line. However it was over white line. > > Although I removed background carefully and changed bond length in > > model, the energy shift was still big. > > I want to know other factors which affect energy shift. > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov <mailto: > Ifeffit(a)millenia.cars.aps.anl.gov> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > _______________________________________________ Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Zinc Sulfide fitting
by Soham Mukherjee 06 Oct '11

06 Oct '11

Zinc Sulfide exists largely in two phases, either the cubic zinc-blende (F-43m) phase, or the hexagonal wurtzite (P63cm) phase. The details of the NN distances are as follows :- 1. For cubic phase, the NN distances (Zinc to Sulfur bond lengths) are 2.3028 Angstroms each, 4 such bonds exist in a tetrahedral arrangement; 2. For hexagonal phase, there are 2 different NN distances (Zinc to Sulfur bond lengths) 3 bonds having the length 2.3421 Angstroms each, and 1 axially elongated bond of length 2.3465 Angstroms. So they differ only by 0.0044 Angstroms ! I am performing a first shell fit to Zinc Sulfide which exists in the wurtzite phase (hexagonal_P63cm). However, I could fit it quite well taking the cubic phase (Zinc blende_F-43m) as my starting model. The only thing is that since bond distances are higher in a hexagonal phase than the cubic phase, I end up with a considerable delr as I underestimated my starting bond length value. Taking a wurtzite model involves defining two different bond lengths (which differ only by 0.0044 Angstroms !), paths 1 and 2 in the FEFF, whose sigma^2 values are quite similar. This gives unusually large delr values and high sigma^2 for the longer axial bond, which looks suspicious ! Do I really need to define the two bond distances separately of so close values? Or taking a cubic phase will be sufficient? Please find the attached project file (artemis.apj) where I have tried out some simulations with both cubic and hexagonal models. With best regards, Soham.

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Energy shift
by JeongEunSuk 06 Oct '11

06 Oct '11

Hell all I have the study for PtO nanoparticles with EXAFS. When I fitted the data to model, I had a problem for energy shift. I thought that the energy shift obtained from fitting must be below White line. However it was over white line. Although I removed background carefully and changed bond length in model, the energy shift was still big. I want to know other factors which affect energy shift.

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Fit in TiO2
by Kleper Rocha 05 Oct '11

05 Oct '11

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