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

Re: [Ifeffit] R-factor
by vikrai＠comcast.net 06 Jul '05

06 Jul '05

Alison, I don't think that the difference of R-factors you mention is a big deal. You did not mention in your message more important thing. Did you get the same values of parameters? Besides, it is hardly to expect to find a signal caused by photoelectron backscattering at R<1 A. So the lower limit in R-space fitting equal to 0.1 A is too small probably. As well as the lower limit in q-space fitting because in proteins in this momentum region only full multiple scattering approach should work correct. Victor Krayzman -------------- Original message -------------- > Bruce, > > I've looked, and my R-factors for the back-transformed > space are not necessarily twice the value of the R-factors > for the k-space fits. In fact, they are often quite > close. For example, just recently I had a k-space > R-factor of 0.102 and a q-space R-factor of 0.113. Now, I > realize those numbers are very close, but I'm afraid if I > try to publish this, then I will get criticism for the > q-space R-factors being larger. If I can explain it, then > maybe it won't be a problem. > > I do see what you're saying about the complex vs. real > function, and that definately makes sense, but they don't > differ by a factor of 2. Hmmm. > > alison > > On Wed, 6 Jul 2005 09:43:03 -0500 > Bruce Ravel wrote: > > On Tuesday 05 July 2005 18:39, Alison Costello wrote: > >> I have a question regarding the calculation of the > >>R-factor. I am > >> currently using SIXPACK to process my protein EXAFS > >>data, and I fit the > >> data in both k-space and in q-space (back-transformed > >>k-space). I > >> typically will use k-ranges = [1-13.6] and for > >>multiple-scattering fits, > >> will use an R-range of 0.1 - 4.5. Sometimes, the > >>R-factor for the q-space > >> fit is greater than the R-factor for the k-space fit, > >>which should not be > >> true, as the back-transformed space filters out noise. > >> I am confused as to > >> why this occurs, and am wondering if the R-factor for > >>the back-transformed > >> space is calculated differently than for k-space fits. > > > > Alison, > > > > I would expect the R factor to be bigger in k space due > >to the high frequency > > portions of the data that get filtered out of the q > >space data. That is what > > happened in the one example I just tried. > > > > What are some example values of the R-factors? Do they > >differ by about a > > factor of 2? > > > > One thing that occurs to me is that chi(q) is a complex > >function while chi(k) > > is a real function. In Ifeffit those two functions > >should have the same > > number of points, but the R factor in q is computed > >using both parts of the > > complex function. Thus it would seem reasonable if they > >differed by about 2 > > and there were no significant Fourier components in the > >data beyond your rmax. > > > > B > > > > -- > > Bruce Ravel ----------------------------------- > >bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room > >E-165 > > Argonne National Laboratory > > phone: (1) 630 252 5033 > > Argonne IL 60439, USA > > fax: (1) 630 252 9793 > > > > My homepage: http://feff.phys.washington.edu/~ravel > > EXAFS software: > >http://feff.phys.washington.edu/~ravel/software/exafs/ > > > > _______________________________________________ > > 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

1 0

R-factor
by Alison Costello 06 Jul '05

06 Jul '05

I have a question regarding the calculation of the R-factor. I am currently using SIXPACK to process my protein EXAFS data, and I fit the data in both k-space and in q-space (back-transformed k-space). I typically will use k-ranges = [1-13.6] and for multiple-scattering fits, will use an R-range of 0.1 - 4.5. Sometimes, the R-factor for the q-space fit is greater than the R-factor for the k-space fit, which should not be true, as the back-transformed space filters out noise. I am confused as to why this occurs, and am wondering if the R-factor for the back-transformed space is calculated differently than for k-space fits. Thank you. alison

3 2

Too Many Atoms
by rvv052＠mail.usask.ca 01 Jul '05

01 Jul '05

The problem that I have is that with 141 crystallographic sites for a DNA molecule and a space group p 4 2 2, I end up with 611 atoms after running ATOMS. This gives me the error: Feff 6L.02 Fatal Error: Too many atoms in ATOMS list. Maximum is 500. I tries decreasing the number of crystalographic sites by removing hydrogen atoms, but then I got another error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP. I tried increasing the Rmax as indicated, but this only served to increase the number of atomes, leading me to the error given above. I was hoping that someone could help me with this problem. Remko van den Hurk

2 1

RE: [Ifeffit] feff data
by Barton, David (DG) 23 Jun '05

23 Jun '05

Steven, Sorry for the duplicate....I sent the previous message as HTML (shame on me) beta-Ga2O3 files are attached. I attached the CIF (crystallographic information file) and an Artemis project that has the FEFF.inp inside it. CIF files can be opened directly in Artemis by choosing the File option, Import ATOMS files, and then select *.CIF in drop down box. If you need just the FEFF.inp for another purpose you can just cut it out of Artemis project and paste it to a text file. Dave Barton -------------------------- Dear all, Does anyone out there, by any chance, have feff data or .inp file of Gallium oxide (any of GaO, Ga2O, and Ga2O3)? I tried to create an .inp file but it was out of my ability. If somebody has one or can give me an information where or how to get, I will do appreciate it. Thank you. Steven Steven Sangyun Lim Associate Research Scientist Dept. of Chem. Eng., Yale University Tel : 203-432-4365

4 3

RE: [Ifeffit] feff data
by Barton, David (DG) 22 Jun '05

22 Jun '05

Steven, beta-Ga2O3 files are attached. I attached the CIF (crystallographic information file) and an Artemis project that has the FEFF.inp inside it. CIF files can be opened directly in Artemis by choosing the File option, Import ATOMS files, and then select *.CIF in drop down box. If you need just the FEFF.inp for another purpose you can just cut it out of Artemis project and paste it to a text file. Dave Barton _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Steven S. Lim Sent: Wednesday, June 22, 2005 10:14 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] feff data Dear all, Does anyone out there, by any chance, have feff data or .inp file of Gallium oxide (any of GaO, Ga2O, and Ga2O3)? I tried to create an .inp file but it was out of my ability. If somebody has one or can give me an information where or how to get, I will do appreciate it. Thank you. Steven Steven Sangyun Lim Associate Research Scientist Dept. of Chem. Eng., Yale University Tel : 203-432-4365

1 0

feff data
by Steven S. Lim 22 Jun '05

22 Jun '05

Dear all, Does anyone out there, by any chance, have feff data or .inp file of Gallium oxide (any of GaO, Ga2O, and Ga2O3)? I tried to create an .inp file but it was out of my ability. If somebody has one or can give me an information where or how to get, I will do appreciate it. Thank you. Steven Steven Sangyun Lim Associate Research Scientist Dept. of Chem. Eng., Yale University Tel : 203-432-4365

1 0

IFEFFIT for OS X 10.4
by Ann Liang 21 Jun '05

21 Jun '05

Hi all, I just recently upgraded my computer from Mac OS X 10.3 to 10.4 (Tiger). I was not able to open programs in the IFEFFIT package. Please help. Thanks, Ann -- ANN LIANG Bruce. C. Gates Catalysis Research Group Chemical Engineering & Materials Science University of California at Davis One Shields Ave. Davis, CA 95616 530-752-3544 (office) 530-752-1031 (fax)

5 6

EXAFS mean free path in small particles
by Laurent Menard 21 Jun '05

21 Jun '05

Disclaimer: I'm an experimentalist and not a theorist. I'm not sure that Zhao and Montano's calculations are correct. I think their calculation for the transition probability assumes that the electron density is constant when, in actuality, there is a spatial dependence resulting from quantum confinement effects. As a result, the energy of the surface plasmon peak as calculated by Zhao and Montano is constant for all cluster sizes at approximately the classical value of omega(bulk plasmon)/3^0.5 and shows an increase with decreasing particle size. Including quantum confinement results in a blue shift of the surface plasmon resonance with decreasing particle size and a decrease in transition probability for decreasing particle sizes (as suggested by Anatoly). This change in the calculation will also impact the bulk plasmon and I don't know what that trend will be. As far as their experimental demonstration with Fe nanoparticles is concerned, I really can't make an assessment about the experiment since they don't indicate how the nanoparticle size was determined and I'm not familiar with their preparation of the nanoparticles. I'm not sure from this paper what the impact on the MFP will be although there very well could be some effect on the EXAFS. Personally, when I began working on EXAFS of nanoparticles and small clusters (Au13), I was leery of using the bulk phase and amplitudes to fit the data. My experience to this point has been that there have not been observable deviations of coordination numbers for nanoparticle systems using these FEFF inputs. That being said, I tend to agree with Matt that this is something that people working in this area need to think about a bit more than it seems they have judging by the literature. I would like to see some (correct) theoretical assessments that support the assertion that bulk phases and amplitudes are ok for nanoparticles that I think has been demonstrated by validating EXAFS results with other techniques (mostly electron microscopy). -Laurent

1 0

EXAFS mean free path in small particles
by matthew marcus 20 Jun '05

20 Jun '05

I'm working on a couple of projects involving nanoparticles, and a collaborator pointed out an old paper by Zhao and Montano (PRB 40,3401(1989)) which claimed theoretical reasons why the electron mean free path in nanos should be smaller than in bulk. This would cause coordination numbers to be underestimated. The effect is supposedly due to a surface plasmon which grows in importance as particle size shrinks. I have reasons why I think this paper exaggerates the possible effects, but I'm posting this to see what other people think about this effect. The paper seems to have gone down into obscurity, but that doesn't mean it isn't right. Thanks. Matthew Marcus

4 6

EXAFS mean free path in small particles
by Matthew 17 Jun '05

17 Jun '05

A couple of notes on this group treat the Zhao&Montano Al-plasmon results as if they were experimental truth. They are in fact theoretical, based on what I think is a jellium model, though that word isn't used. Their only experimental data is on matrix-isolated Fe particles. mam

1 0