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

Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

2 8

Purple & Red E Derivatives
by Andrew Korinda 25 Feb '11

25 Feb '11

While working in Athena today I noticed something peculiar while looking at the derivative plots of mu(E) data. When I plot the current group (red button) the plot can be spiky. However, when I plot as marked group (purple button) everything is much smoother and more rounded. Smoothed data will do the same thing. It always happens whether I have mu(E) or norm(E) selected. I have never noticed a difference in how any of the other plots current when switching between marked and active plotting. I didn't see anything in the documentation about how the derivatives are calculated so I'm turning to all of you. Have any of you noticed this? Does anyone know if there is a difference in how the derivatives are calculated in each plotting function? Andy Korinda Notestein Lab Northwestern University

4 6

parseval's theorem and athena
by kirshstein＠googlemail.com 17 Feb '11

17 Feb '11

Hello, I would like to use parseval's theorem (as described in a document called: Error Reporting Recommendations: A Report of the Standards and Criteria Committee, Adopted by the IXS Standards and Criteria Committee July 26, 2000 ) to quantify the statistical noise in my spectra. In section 3 (as shown in the attachment), it says that for the formula to work, the forward FT has to be normalized by sqrt(deltak/Pi). (delta k is the spacing of points in k space) What is the normalization used for FFT in athena? if it is not sqrt(deltak/Pi), what is it? how does the parseval theorem formula need to be modified as a function of FT normalization? Many thanks for answers! Regina

2 3

FEFF question Te K edge
by Andrea L Foster 16 Feb '11

16 Feb '11

Hello All, sorry if this is not the correct venue...I tried to join a feffusers list I saw at http://leonardo.phys.washington.edu/feff/html/mailing_list.html but I got bounces when I subscribed and tried to post. my problem is below, and I'm sure one of the many knowledgeable folks on this group can help: I am starting to run FEFF6L calculations for Tellurium phases. I used published structure report of calaverite (AuTe2) and Na2TeO3_5H2O to generate ATOMS.INP files which I then used to generate FEFF.inp files. These two very different Te minerals gave me the following error when running FEFF6L (following is a copy of a little of the FEFF output): Running "C:\Program Files\Ifeffit\bin\feff6l.exe" feff.inp Feff 6L.02 Disodium Tellurite 5-hydrate Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... ...I have stopped copying the FEFF output there. I do not think that the problem is with the crystal structures as they are pretty simple (though human error is never to be minimized, especially mine ;). ATOMS returned no errors when it ran. The interatomic distances generated in feff match those reported in the crystal structure report...and the coordination numbers appear to be correct (for example the sodium tellurite structure should have 3 closest oxygen neighbors, and does, at the correct distances)... so I don' t know how to troubleshoot this error when nothing appears wrong geometrically. I have attached the 2 feff.inp files (which list the xtal structure info) in case that helps. They are slightly renamed. thanks for any help, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

1 0

Re: [Ifeffit] Fe in glassy ceramics
by Scott Calvin 16 Feb '11

16 Feb '11

Hi Andrei, It's not unreasonable to model such a thing. Use a highly constrained model for the spinel, not allowing coordination numbers to float and using very few sigma2 parameters. I've published a model like that for fitting spinels here: http://prb.aps.org/abstract/PRB/v66/i22/e224405 My model is more complicated than yours needs to be, because you don't really have site disorder; all the sites are Fe. Then multiply the amplitudes by a guessed parameter representing the fraction of the iron that is in the spinel phase. The remaining amplitude gets used for the glassy phase, which can possibly be fit by a single iron-oxygen path, which can be cloned from one of the spinel near neighbor paths, but now with most parameters floated. You may very well need to fix S02 based on the value from a standard. Fit over a wide range in the Fourier transform, so that you take advantage of high R peaks to pin down the spinel part. Worth a shot, anyway. The key is being aggressive with assumptions and constraints, and then being honest about how that affects your uncertainties in the end. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Feb 16, 2011, at 4:53 AM, Andrei Shiryaev wrote: > Dear colleagues, > > Probably similar questions were already asked, but nevertheless I > would appreciate some advice how to solve the problem. > > We are looking at Fe environment in complex glasses, which underwent > partial crystallization. A fraction of Fe has precipitated as spinel- > like nanocrystals, another fraction remains in glass. Spinel itself > is already challenging for XAFS, but our task is to understand the > Fe fraction in glass (e.g., Fe-O bond length). > > We do not know the exact composition of the crystalline phases, thus > we can not record a suitable standard. Does anybody have an idea how > could we try to separate the Fe in glass from Fe(cryst) contributions? > > I fully realize that the problem is ill-posed, perhaps, some people > had somehow solved this problem. > > Thanks a lot, > Andrei Shiryaev > > Instituteof Physical Chemistry > Moscow > Russia

1 0

Fe in glassy ceramics
by Andrei Shiryaev 16 Feb '11

16 Feb '11

Dear colleagues, Probably similar questions were already asked, but nevertheless I would appreciate some advice how to solve the problem. We are looking at Fe environment in complex glasses, which underwent partial crystallization. A fraction of Fe has precipitated as spinel-like nanocrystals, another fraction remains in glass. Spinel itself is already challenging for XAFS, but our task is to understand the Fe fraction in glass (e.g., Fe-O bond length). We do not know the exact composition of the crystalline phases, thus we can not record a suitable standard. Does anybody have an idea how could we try to separate the Fe in glass from Fe(cryst) contributions? I fully realize that the problem is ill-posed, perhaps, some people had somehow solved this problem. Thanks a lot, Andrei Shiryaev Instituteof Physical Chemistry Moscow Russia

2 1

compiling feff 9
by Eugenio Otal 11 Feb '11

11 Feb '11

Hello, I am trying to compile the feff9 with ifort linux compiler but I find that the code is split in more than one file unlike feff84 that is only one file, feff84.f. I read the manual and I cannot find any help in feff9 manual, in feff84 manual there are more information but it is also not so useful. Would you help me to know how to compile the code with all this files. Kind Regards, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Dr. Eugenio H. Otal Solid State Chemistry and Catalysis Laboratory, Empa - Swiss Federal Laboratories for Materials Science and Technology, Ueberlandstrasse 129, CH-8600 Duebendorf, Switzerland, Tel +41 44 823 41 31, Fax +41 44 823 40 19, eugenio.otal(a)empa.ch, www.empa.ch/abt131,

1 0

Reminder: NASCCSC Abstracts Deadline
by Carlo Segre 08 Feb '11

08 Feb '11

Hello All: In case you had not seen this notice, the Second Annual North american Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs this on August 1-5. This years conference will have special sessions on catalysis and 5f electron systems. Abstract sumissions will be open probably until March 1, 2011. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

1 0

R dependence of S02
by Scott Calvin 05 Feb '11

05 Feb '11

Hi all, I've been pondering how much R dependence we should expect to see in S02; that is, how much R dependence is shown by intrinsic losses. I've looked at quite a bit of the literature, not to mention old threads from this mailing list. One recent (2002) reference is this one by Campbell et al.: http://prb.aps.org/pdf/PRB/v65/i6/e064107 My understanding is that S02 is intended to account for intrinsic losses; that is, those that are determined when the core hole forms. Extrinsic losses, such as inelastic scattering of the photoelectron and the effect of the core-hole lifetime, are accounted for by a mean free path term. The mathematics of how ifeffit implements this are here: http://cars9.uchicago.edu/~newville/feffit/feffit.ps Intrinsic losses are dependent on k for at least two reasons. One is that the cross-section of the intrinsic effects themselves depends on the energy of the incident x-ray. This is evident if one thinks in terms of shake-up and shake-off events. But another reason is that shake-up and shake-off events rob some energy from the primary photoelectron. At low k, ten or twenty electron volts can alter the phase of the primary photoelectron significantly, and thus shake-up and shake-off events will tend to cancel each other out. But at high k, the energy robbed from the photoelectron is less significant, because the EXAFS oscillations are more spread out in energy. Thus, shake-up and shake-off events, while still occurring, will not suppress the EXAFS amplitude as much at high k. S02 therefore gradually rises through most of the EXAFS region to reach a limiting value of 1 well above the top of the EXAFS region. The latter effect--the fact that removing a specified amount of energy from the primary photoelectron has less of an effect at high k than at low--also implies an R dependence. Low R oscillations are further apart in energy than high R oscillations, and thus over a specified k range low R oscillations should be less affected. In other words, S02 should show a modest decrease with increasing R over typical EXAFS ranges. Some papers, in particular those with John Rehr as an author, confirm that S02 should have an R dependence, but don't discuss the implications much. While ifeffit allows for floating ei, a parameter related to the mean free path, as I understand it that will still give a damping of the amplitude that is exponential in R. It seems to me that the S02 dependence on R, in contrast, is likely to be more gentle. Why is this important? Several authors, including myself, have analyzed crystallite size and/ or morphology by comparing the coordination number of successive scattering shells. This is potentially much more accurate than just finding the first-shell coordination number, because it is independent of any amplitude effects that are independent of R, such as normalization errors and many experimental effects. Errors in the mean free path are a bit more significant, but the exponential dependence of the mean free path gives it a very different shape than effects from size and morphology. But an R-dependence of S02 would be troubling, as the functional form might look a bit more like a size effect. So one question is this: does anyone have an order-of-magnitude estimate of how much R dependence to expect in S02 over the EXAFS range? If over a range of 2 to 6 angstroms S02 changed by even a few percent, that could have a significant effect on the kind of size analyses I mentioned in the preceding paragraph. Of course, another question is if I've completely blown it anywhere in my discussion above; I've just been puzzling this out over the last few days! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

1 0