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

How to keep enot,delr, and ss within acceptable limits
by Hashem Stietiya 14 Jan '09

14 Jan '09

Dear All, I am currently using ARTEMIS to fit Zn-O, Zn-Zn paths to first and second shells, respectively. Many times I would get unacceptable values for enot, ss, and delr. My question is: is there a way to tell ARTEMIS that I want these parameters to be within acceptable limits? For example, you cannot have negative ss, so how can I avoid any fit result that produces negative values for ss? Or high extremely high values for enot and delr? I appreciate your assistance and guidance. Regards, Hashem Stietiya School of plant, Environmental and Soil Sciences Louisiana State University

5 7

Trouble with fitting with Arthemis
by Kleper Oliveira Rocha 13 Jan '09

13 Jan '09

Hi all, Please, help me. When I try to do any fit in Arthemis, setting all parameters unless one, been this one any of the parameters, the fit gives for the answer -1.0000 +/- 0.000000 like example down. What is happening? ============================================================ Independent points = 8.239257812 Number of variables = 1.000000000 Chi-square = 0.120000000E+37 Reduced Chi-square = 0.165762849E+36 R-factor = NaN Measurement uncertainty (k) = 0.000437667 Measurement uncertainty (R) = 0.000724906 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): * amp = -1.0000000 +/- 0.0000000 (1.0000)* Set parameters: enot = 0 delr = 0 ss = 0.003 c3 = 0.0001 c4 = 0.00001 -- Kleper de Oliveira Rocha Chemical Engenieer Doctorated Tels. 55 016 3351-8694

4 11

Re: [Ifeffit] SCF and FMS radius
by joshua jason kas 13 Jan '09

13 Jan '09

Hi Eugenio, I would call all of the spectra that you sent converged. It is true that they are not the same to all digits of output, but you really don't need things to be that accurate. Theoretical and experimental errors are much larger, especially in the near edge. When converging w.r.t. the SCF and FMS radius, you really only need to be sure that changes in the spectrum due to finite cluster size are small compared to the differences between theory and experiment. You can probably get by with a much smaller cluster even. Cheers, Josh Kas On Mon, 12 Jan 2009, 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. SCF and FMS radius (Bruce Ravel, Feng Wang & Josh Kas) > (Eugenio Otal) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Jan 2009 23:40:07 -0200 > From: "Eugenio Otal" <eugenioh(a)gmail.com> > Subject: [Ifeffit] SCF and FMS radius (Bruce Ravel, Feng Wang & Josh > Kas) > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <da22ad30901121740x764c0babjf20f055285a4d9b2(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Bruce, Feng and Josh, > I am simulating erbium hydroxide from its crystal structure information, > what does really mean well ordered? > Of course I can?t answer you that, I hope someday would know the answer, and > for the dummies question... I see the changes only close to the edge. > I?ll read the paper deeply , and what I see in the abstract, the SCF and FMS > should converge faster. > I attach 3 packages with 3 results and its .inp files, I hope you can help > me. > Thanks in advance, euG >

1 0

looking for Zn(OH)2 EXAFS spectrum
by Samuel Legros 13 Jan '09

13 Jan '09

Hi everybody, I am loking for the Zn(OH)2 EXAFS spectrum. If someone have it, i would be very grateful if he (or she) would like to send it to me. Thank you in advance -- Samuel LEGROS Doctorant CIRAD basé au CEREGE Directeur : Emmanuel DOELSCH Europole de l'arbois BP 80 13545 Aix-en -provence FRANCE Tel : 04 42 97 17 76 Fax : 04 42 97 15 59

1 0

SCF and FMS radius (Bruce Ravel, Feng Wang & Josh Kas)
by Eugenio Otal 12 Jan '09

12 Jan '09

Hi Bruce, Feng and Josh, I am simulating erbium hydroxide from its crystal structure information, what does really mean well ordered? Of course I can´t answer you that, I hope someday would know the answer, and for the dummies question... I see the changes only close to the edge. I´ll read the paper deeply , and what I see in the abstract, the SCF and FMS should converge faster. I attach 3 packages with 3 results and its .inp files, I hope you can help me. Thanks in advance, euG

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 71, Issue 8
by joshua jason kas 12 Jan '09

12 Jan '09

Hi Eugenio, I am not familiar whith the system, but it seems a bit strange to me. What edge are you running? Can you send some of your calculations and a feff input file? I've seen cases where the FMS is still not converged at 1000 atoms, but the SCF radius usually converges much faster. Cheers, Josh Kas > > Hello, > I am simulating the XANES spectra of a erbium atom in an interstitial site > of ZnO. I needed a SCF radius of 9.75 (316 atoms) and FMS radius of 11.90 > (599 atoms) to obtain no change in the simulated spectra (differences of > 0.01% or less) > Now I am trying to simulate Er(OH)3 and it is using SCF 10.90 (622 atoms) > and I still haven found convergence, I will need more even larger radius for > FMS. > Does the XAS phenomena have this distances? Has this distances physical > meaning? > Thanks, euG > > > > > > > > > 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - > > Lic. Eugenio H. Otal > E-mail: eotal(a)citefa.gov.ar > eugenioh(a)gmail.com > > 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - >

1 0

Re: [Ifeffit] SCF and FMS radius
by Feng Wang 12 Jan '09

12 Jan '09

Bruce and Eugenio, It is generally believed that the cluster size (or called spatial resolution) is mainly limited by MFP, to around 1 nm (in the near-edge region), but further spatial limitation may come from elastic scattering (i.e. through phase cancellation). This is what we tried to understand through FEFF calculations in one paper. I put the abstract here in case you want to check: We have investigated the factors that determine the degree of localization of the information obtainable from electron energy loss or x-ray absorption fine structure. Inelastic scattering of the excited core electron limits the volume of specimen contributing to the backscattered intensity to a diameter in the range of 12 nm, dependent on the excited-electron energy and the composition and crystal structure of the sample. Phase cancellation between the backscattered waves further reduces the effective diameter that determines the observed fine structure to below 1 nm. Since the spatial resolution attainable by transmission electron microscopy can approach 0.2 nm or can even be below 0.1 nm (with aberration correction), we predict that delocalization arising from the excited-electron range may limit the resolution of images based on changes in core-loss fine structure. (J. Appl. Phys. 104, 034906 (2008)). Feng > On Sunday 11 January 2009 12:23:26 pm Eugenio Otal wrote: > > I am simulating the XANES spectra of a erbium atom in an interstitial site > > of ZnO. I needed a SCF radius of 9.75 (316 atoms) and FMS radius of 11.90 > > (599 atoms) to obtain no change in the simulated spectra (differences of > > 0.01% or less) > > Now I am trying to simulate Er(OH)3 and it is using SCF 10.90 (622 atoms) > > and I still haven found convergence, I will need more even larger radius > > for FMS. > > Does the XAS phenomena have this distances? Has this distances physical > > meaning? > > Eugenio, > > The mean free path is quite long just above the Fermi energy. It is > conceivable that, in a well ordered material, the cluster size required for > convergence can be quite large. I believe that a very large cluster -- > something like 13 A -- is needed for pure silicon. Of course, I doubt that > erbium hydroxide is that well-ordered! > > So, are you are seeing physics associated with the mean free path or a problem > in Feff's construction of the potentials? I'm afraid I don't know how to > answer that, but hopefully John or one of his gang will weigh in. Do you see > the changes larger than your threshold over the entire data range or only > very close to the edge? > > Good luck, > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ==================================== National Institute for Nanotechnology 11421 Saskatachewan Drive Edmonton, Canada T6G 2M9

1 0

How to get the accurate fittting results from the fit in Artemis
by abhijeet gaur 12 Jan '09

12 Jan '09

Hi Actually I trying to learn the fitting procedure in Artemis but I am not getting the actual bond length in the fit results of artemis . So I want to know that that how to get actual parameter from Artemis.And how to exploit the result of Artemis.

2 1

Query regarding error bars
by Bindu R. 09 Jan '09

09 Jan '09

Hi all, Could any tell me in a simple language about the error bars returned by the EXAFS fitting program? what do they exactly represent?How is it determined?How is the number of iterations decided.In addition to R-factor what are the other parameters which determines a good fit.For a R-factor ~0.001, if the value of chi2~10,000 and reduced chi2 ~ 500, can one consider the fit to be good even if one gets a good match to the experimental spectra. Bindu Dr.Bindu R. Visiting Fellow BG-37 DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Contact Number Lab- 022-2278 2256, 022-2278 2671 Mobile-919892536830 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

3 2

Re: [Ifeffit] posting to the ifeffit mailing list
by JeongEunSuk 07 Jan '09

07 Jan '09

Hello Bruce Ravel I have another questions. I got the charge transfer of TiO2 from FEFF8 as following;Ti: (not absorber) Charge transfer : 0.556 Electron counts for each orbital momentum: 0 0.408 1 6.678 2 2.350 3 0.000O: Charge transfer : -0.280 Electron counts for each orbital momentum: 0 1.843 1 4.354 2 0.087 3 0.000It is known that the electron number of Ti atom ( the atomic number 22) is 1s^2 2s^2 2p^6 3s^2 3p^6 4s^2 3d^2. In the results of FEFF, 0 is s orbital, 1 is p orbital so on.. right? as you know, there is each s-orbital or p-orbital in principal quantum number.which orbital momentum of principle quantum number does 0, 1, 2 and 3 mean? second I cant understand electron counts. I thought that Charge transfer was calculated by electron counts for each orbital momentum, comparing the electron counts of free atom.So I tried to calculate like this: In free oxygen atom case, 2^s has 2 electron, 2^p! has 4 electron. The electron counts calculated by FEFF8 is 1.843 + 4.354 + 0.087 =6.284So charge transfer is 6 - 6.284 = 0.284 The charge thransfer, 0.284, obtained from my calculation is different from the value of FEFF8. How can I get charge transfer form electron counts? > From: bravel(a)bnl.gov> To: eunsuk1986(a)hotmail.com> Subject: posting to the ifeffit mailing list> Date: Mon, 5 Jan 2009 17:10:31 -0500> > > Hi Jeong,> > I think I know what went wrong with your post to the mailing list from last > Friday. I think that you (for some reason) sent the mail to> ifeffit-bounces(a)millenia.cars.aps.anl.gov> rather than to> ifeffit(a)millenia.cars.aps.anl.gov> > The second address is the normal point of entry to the mailing list. The > other address is part of the mailing list administration. I am not sure how > you ended up sending email there. Weird. If you make sure to send your mail > to the second address, it should get posted without any problems.> > If you do have any problems posting to the mailing list, I will probably be > notified automatically. But if you attempt to send mail to the mailing list > and have any problems, please let me know as soon as possible so I can try to > correct the problem.> > Regards,> B> > -- > > Bruce Ravel -------! ----------------------------- bravel(a)bnl.gov> > National Institute of Standards and Technology> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2> Building 535A> Upton NY, 11973> > My homepage: http://xafs.org/BruceRavel> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ _________________________________________________________________ 블로그에 윈도우 라이브 메신저(베타)를 홍보하면 선물을 드립니다! http://windowslive.msn.co.kr/wlm/customer/view.asp?sectionDiv=2&seq=272

2 1