December 2007 - Ifeffit - millenia.cars.aps.anl.gov

(no subject)
by Luanga Nchari 27 Dec '07

27 Dec '07

Merry Christmas to all. I am a research student with the following questions: · Does Artemis have a cumulant expansion feature? How can it be used to correct anharmonicity?I suspect this might answer why my fit in K-space is not quite in phase eventhough the fit in R-space is good. Other suggestions would be welcome. Thanks, Luanga Nchari · ___________________________________________________________ Support the World Aids Awareness campaign this month with Yahoo! For Good http://uk.promotions.yahoo.com/forgood/

2 1

error while running FEFF6l through SixPack
by Susan Amrose 19 Dec '07

19 Dec '07

I'm a new user trying to use FEFF6l through the "Make FEFF SS Paths" module in SixPack. I downloaded iffefit-1.2.10.exe and installed everything to default locations (which puts a copy of feff6l.exe inside the fefftemp folder of Sixpack, where I am told it needs to be). I open the "Make FEFF SS Paths" module, enter scattering information and go to run FEFF. I select FEFF6/7 and enter "feff6l" next to FEFF Command (without quotes). I hit Run FEFF - then I get an error: ----- Error: 3 IOError Exception in Tk callback Function: <method PT.runfeff of PT instance at 00A2503C> (type: <type 'instance method'>) Args: () Traceback (innermost last): File " Pmw.pyc", line 1772, in __call__ None File "<string>", line 308, in runfeff None IOError: [Errno 2] No such file or directory: 'feff0001.dat' <http://cars9.uchicago.edu/%7Eifeffit/src/ifeffit-1.2.10.exe> ----- I'm running Windows XP through Parallels on an Intel Mac (running Leopard). Other modules of SixPack are running fine. I tried updating SixPack from the SixPack website (as was suggested in the ifeffit install documentation). Does anyone have any ideas? Thank you!! Susan

1 1

Re: [Ifeffit] Overlapping scattering paths
by van der Veen Renske 19 Dec '07

19 Dec '07

Dear Bruce Thanks a lot for your reply! I admit that I was a bit naive in expecting EXAFS to give me the full molecular structure with 0.01 A resolution... I learn now that there is "no free lunch"! Nevertheless, doing EXAFS is fun :-) As a reply to my mail to the mailing list, somebody from the same institution where I work contacted me and offered to help a bit out. Your answer and his help made me to fit a very reasonable model to the data. In case somebody is interested what exactly led to my success, below I describe what I did. Please correct me if you think I did something stupid. First a short introduction to what I'm actually fitting: I measured 2 transmission spectra of a molecule of 38 atoms, containing a weak Pt-Pt bond and 4 rigid P-O-P bridges, dissolved in ethanol. Each of the Pt atoms is surrounded by 4 P-atoms in a square-planar way. Beside the bridging O's, each P atom also binds to 2 terminal oxygens, one singly-bonded and one doubly bonded. This makes the total molecular composition: Pt2 P8 O20 H8. The ultimate goal of the project is to measure the excited state structure of this molecule in a time-resolved fashion. This is what I did: (1) I realized that the molecule in the crystal structure (used as an input for ATOMS/FEFF) had reduced symmetry. The salt I used was a K-salt and coulombic forces between K+ ions and the O atoms in the molecule distort the structure. Because charges are more homogeneously distributed in solution, I thought that a more symmetric starting structure would be better. Therefore, I "built" my own molecule in which especially the symmetrically equivalent P=O and P-O distances are the same. (of course one should be very careful in building own molecules; not every structure is thermodynamically stable. In my case the bond distances and angles are very similar to ones in the crystal structure, so I assume the structure is physically "possible") (2) Because I wanted to increase the information content extrinsically, I determined sigma_sq for the Pt-Pt distance by making use of optical Raman measurements in solution. Assuming a harmonic oscillator, I calculated sigma_sq from the wavenumber of the Pt-Pt vibration. In consequent fits I fixed the value of sigma_sq_Pt to this value (if let free one of the other sigma_sq values gets negative; this is probably due to the correlations) (3) I fitted from "shell-to-shell" (although in a molecule one cannot speak of "shells", I mean distinct separated regions in the FT spectrum). An iterative procedure of fit-grab-fix, while looking at the statistical variables and the values of the fitting parameters, led to the final good fit. The present model is extremely simple: 4 SS paths (Pt-P(near),Pt-P(far), Pt-O(bridge), Pt-Pt) and one important (nearly) colinear MS path (4-legged P-Pt-P scattering, this path was expressed in terms of SS paths: delr_MS=2*delr_SS and ss_MS=2*ss_MS). All the SS paths to the terminal O atoms could be left out due to the large Debye-Waller factors, i.e. on the order of 0.02-0.06 A^2. Including them and/or the Pt-O-P MS paths lead to a small decrease of the R-factor, but an increase or no change in the reduced chi-square! (HOW CAN THIS BE?) Leaving them out has the advantage that the other fitting parameters have smaller error bars. I am actually not sure whether I should include them or not...they do "clean-up" the fit...but including them also changes the values of the other parameters... As a final result I got an R-factor of 0.01. The error bars on the fitted values are still pretty large (up to 50%) and the correlations between variables are still present, but at least I am confident now that the model makes sense. From Bruce's email I understand that large error bars and correlations are unavoidable for overlapping scattering contributions without further (extrinsic) information. For the future I consider measuring at different temperature in order to break the correlations between the DW factors, although I am not sure whether this makes sense in solution (do the DW factors change enough in solution?). This was my fitting story. Comments/suggestions are welcome! Regards, Renske > Message: 2 > Date: Tue, 18 Dec 2007 08:56:22 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Overlapping scattering paths > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200712180856.22803.bravel(a)bnl.gov> > Content-Type: text/plain; charset="utf-8" > > On Sunday 16 December 2007 04:08:00 van der Veen Renske wrote: > > Hello EXAFS experts, > > > > I started using Athena and Artemis two weeks ago by > applying it to the > > EXAFS analysis of a moderately complicated molecule in > solution. The > > final fit is very good (R=0.006) but the errors on the fitting > > parameters are very large and there are many high > correlations between > > parameters that shouldn't be correlated (even though I do multiple > > k-weighted fitting). I think the problem is that there are > at least 4 > > scattering pathways that overlap in the FT (spread in path > lengths of > > +-0.4 Angstrom). In addition, these scattering paths > involve different > > atoms and bonds, so that I have to define different delta_r and > > sigma_sq parameters for all of them. > > > > My question is now: how could I reduce the error bars of > the fitting > > parameters that belong to these overlapping scattering > paths? Or is it > > hopeless without further information of the system? > > Hi Renske, > > You question is at the very heart of the problem of EXAFS > analysis. I hope you won't be disappointed that I do not > have an easy answer for you. > > With Feff and Ifeffit, we treat EXAFS as a signal processing > problem in the sense that we consider a band width defined > buy the Foruier transform range in k and the fitting range in > R. That band width sets some kind of upper limit on the > amount of information we can ever hope to extract from the > signal. Typically, that is not a very large number. Also > typically, we have complicated structural problems about > which we are trying to gain insight with that limited > information content. > > The whole trick in using the Fourier transform to help us > interpret our data is to rely on different paths contributing > different Fourier components to the measured signal. In the > case of, say, the first and second coordination shells of > copper metal, that works extremely well. In most cases -- > not so much because, as you have observed, paths contributing > significant spectral weight may have overlapping Fourier components. > > If all we have is the EXAFS signal itself, we would be stuck > where you are right now -- reasonable fits but huge > correlations. The only way out of this problem is to rely on > other information. Sometimes that other information might be > intrinisc to the problem, other times extrinsic. Let me give > a couple of examples. These examples may be pretty far away > from what you are working on. Since you gave us a very scant > description of your problem, I cannot speak directly to it. > > An example of intrinsic knowledge would be the handling of > the short oxygen bond in a uranyl or plutanyl compound. In > those cases, there is a dioxo-actinide chain consisting of > two double bonded oxygen atoms on either side of the actinide > atom forming a linear chain. These bonds are very stiff and > contribute a strong multiple scattering signal that often > overlaps with single scattering signals around 3 angstroms. > Those MS paths do not, however, require the use of new > parameters. The bond length and sigma^2 parameters for the > MS paths can be easily written in terms of the parameters for > the SS paths to those oxygen atoms. In that way, the > contribution of those MS paths is added correctly to the fit > without having to introduce any new parameters. That is a good thing. > > Examples of extrinsic knowledge are easy to come across. One > example might be the temperature dependence of a sigma^2 > parameter in a temperature series measurement, which should > behave like a single frequency (or Einstein) oscillator. > Another example might be knowledge that you bring to the > problem from, say, vibrational spectroscopy emasurements on > the same compound. In that case, you would expect EXAFS and > the other measurement to be consistent, within the caveat > that the time and length scales of the XAS measurement are very short. > > So, I don't think I have answered your specific question, but > hopefully, I have written something useful to you. If you > would like to ask a more specific question about your > problem, feel free to ask on the list. As you have no doubt > seen even in the last two weeks since you started using our > codes, folks on the list are very welcoming to newcomers and > very generous with useful information. > > 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/ > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 58, Issue 15 > *************************************** >

1 0

Re: [Ifeffit] Give me some advices
by wang.kefan＠gmail.com 18 Dec '07

18 Dec '07

Hi Leandro Thank you for your helpful advices. The title should be change to "Please give me some advices" , and I am sorry for this error. *The attached .prj file can be opened by Athena rightly by changing the download file's extend name .bin to .prj, if someone else want to join our discuss.* Then go to our topics: The QDs samples were prepared by MBE and XAFS measurements, as you guessed, were performed at a synchrotron facility in fluorescence mode. Since the Si/Ge intermixing happened frequently during growth, there is certainly Si in so-called Ge quantum dots(QDs, or nanocrystal). However, now I am very caring for if the GeOx in the QDs. The XAFS spectra show that there may be GeOx in the Ge QDs, but since the QDs were covered *in situ* by a 15nm Si cap layer the oxidizing process of QDs by air should not happen. This inconsistency between XAFS and experiments is the real reason for that I want to extract the truth from strict softwae analysis. 1, I have the bulk Ge and diluted SiGe standard spectra, but they do not resemble with these spectra as you mentioned. I am sure that the QDs is a combination of Ge and Si elements, and am not clear if the O exists. The growth temperature is beyond 500oC, and annealing was performed from 550-800oC(all temperature uncalibrated with +/- 50oC ). The amorphous Ge seems to be impossible, but can not exclude it. *In situ* RHEED also can not tell me if the deposited Ge is crystallizing. 2, If I truncate the k to 10 A-1, the fit result is accepted or not? Kefan

2 1

different edge step by linux and window vista
by Shanshan Liu 18 Dec '07

18 Dec '07

Dear all, It seems there is a problem when I use athena to open the file under the windows vista environment. According to the specific scan channel, the data gave the big different edge step by linux and windows.(Other parameters are similar), and the figures seem strange(I do not know what caused it). Now I am sending the screen-shot that I see. Please help me about that. Thank a lot. Shanshan Liu BCPS Dept. Illinois Institute of Technology

3 4

Overlapping scattering paths
by van der Veen Renske 18 Dec '07

18 Dec '07

Hello EXAFS experts, I started using Athena and Artemis two weeks ago by applying it to the EXAFS analysis of a moderately complicated molecule in solution. The final fit is very good (R=0.006) but the errors on the fitting parameters are very large and there are many high correlations between parameters that shouldn't be correlated (even though I do multiple k-weighted fitting). I think the problem is that there are at least 4 scattering pathways that overlap in the FT (spread in path lengths of +-0.4 Angstrom). In addition, these scattering paths involve different atoms and bonds, so that I have to define different delta_r and sigma_sq parameters for all of them. My question is now: how could I reduce the error bars of the fitting parameters that belong to these overlapping scattering paths? Or is it hopeless without further information of the system? Best regards, Renske Renske M. van der Veen PhD student Chergui Group EPFL Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3171 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

2 1

Give me some advices
by wang.kefan＠gmail.com 17 Dec '07

17 Dec '07

Hi I have used the Athena 0.8.054 to processing the EXAFS data of Ge quantum dots. You can find the .prj file in the attachment. In fact, they are a seriers of samples with or without annealing at high temperature. Surely, the data after annealing is difficult to deal with. Please do not hesitate to give me some advices! Such as the issues on normalization, deglitching, truncating, etc. Thanks a lot. PS, I think this is a good way to exchange experiences and learn knowledges. Kefan -- Kefan Wang School of Physics and Electronics Henan University, 475004 E-mail: kfwang(a)henu.edu.cn; wang.kefan(a)gmail.com

2 1

Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?
by wang.kefan＠gmail.com 16 Dec '07

16 Dec '07

Hi everyone Thanks to Matt, Bruce, Richard, Anatoly! Kefan -- Kefan Wang School of Physics and Electronics Henan University, 475004 E-mail: kfwang(a)henu.edu.cn; wang.kefan(a)gmail.com

1 0

Re: [Ifeffit] Is there a Artemis User's Guide like the Athena?
by Ravel, Bruce 14 Dec '07

14 Dec '07

> Hi Bruce > I have spent 1 month to learn the Athena by using your "ATHENA User's Guide" > updated at Aug. 31,2007. I am very satisfied with it and thank you very > much. Now I am learning the ARTEMIS. However, till now I can not find a > suitable guide for a beginner. The PPT wrote by Shelly is not suitable for > me. And the "artemisdoc.pod" is also puzzled me. Is there a Artemis User's > Guide like the Athena? > Thanks > Kefan > -- > Kefan Wang > School of Physics and Electronics > Henan University, 475004 > E-mail: kfwang(a)henu.edu.cn; wang.kefan(a)gmail.com Hi Kefan, I suspect that my answer to this question will be of broad interest, so I am taking the liberty of CCing the Ifeffit mailing list. Thank you for the very kind words regaridng Athena. I am pleased that you found the Athena User's Guide so helpful. Sadly, I have not yet written a document of comparable extent for Artemis. I certainly understand that there is a need for comparable user guide, but finding the time and energy to write one has not yet happened. Writing the Athena User's Guide was fairly exhausting and I need to take a break before embarking on a similarly large document for Artemis. I have to defend Shelly's various presentations. I think they have a lot of good information in them. I think that using them along with other resources can give you enough of an overview of Artemis to get started. I strongly recommend that you work through Scott Calvin's ZnO example, which can be foun at http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib ZnO is somewhat of an idealized example -- many of us work on problems that are pretty far removed from a simple crystal like ZnO. However, Scott's example is quite thorough. Working through it while carefully following his comments in the project journals will introduce many of Artemis' features. As for the pod file -- those are the files that get displayed when you click on one of the documentation buttons from within Artemis. I acknowledge that they are thin on details and somewhat out of date. The last bit of advice I can give you is to read the papers written by the names you see on the Ifeffit mailing list. The folks who offer answers to question on the list are also some of the best practitioners of EXAFS analysis using Feff. Although it might seem funny to read papers by Anatoly Frenkel or Paul Fons if you are studying environmental science (or Shelly Kelly's if you are a materials scientist), I strongly recommend doing so anyway. Their science might be pretty far away from what you do, but the EXAFS analysis strategies are quite instructive and are certainly transferable. I know that is not the answer you were hoping for, but it may be helpful nonetheless. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

4 4

two issues with Athena on Windows and one with Artemis
by Ravel, Bruce 14 Dec '07

14 Dec '07

Hi, For the last few weeks, I have been doing experiments at beamlines with Windows machines. This has afforded me more time than normal using my programs under Windows. I am appreciating my linux machines more than normal, but that is not the point of this email ;-) I have found a few issues that I wanted to address even though no one has yet mentioned them on this list. 1. Combo-box menus: In Athena, combo boxes are used for a variety of purposes. For instance, in the alignment dialog, a combo box is used to select the data group for use as the alignment standard. It seems that selecting items from the drop-down list does not work as expected. Clicking to post the drop down menu then clicking on your choice does not cause your choice to be inserted into the combo-box text area. The work-around that I have found is to first *right* click on your selection, then *left* click on it. I cannot explain why this works and I wish the whole thing just worked correctly. At least there is a work-around! (Another work-around is to move the appropriate group to the top of the list, but I dislike the right-click/left-click solution less ;-/ .) 2. Several people have mentioned privately that the most recent version of Athena seems very sluggish on Windows. I agree and so, I think, does Matt. We changed how the compiled parts get compiled for the most recent release and perhaps some bed seeting were used. We'll look into for the next release. While doing some profiling on my new coding project, Demeter, I figured out a reasonably simple and very fruitful optimization for the interaction between my perl code and the Ifeffit library. I will implement that for the next release of Athena. Hopefully the next version will be snappier. For now, I apologize that the performance of Athena is less than it should be. 3. In Artemis, there are two or three menu items which involve importing something from a file. One example is "Import variables from text file" under the GDS menu. On Windows, this fails to post the file selection dialog and spews error messages to the console. This bug will be fixed in the next release. Sadly, there is no work-around that I know of. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at Brookhaven National Laboratory Building 535A Upton NY, 11973 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0