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

Reporting math expressions in scientific papers
by MauRo 02 May '05

02 May '05

Hi folks, I would like to ask you if it exist one common convention, apart the XAFS society one, to report IFEFFIT results when you have unusual math expressions. In particular, I have used a two-phase model (two FEFF calculations) to fit my sample and for the amplitude variable I have these math expressions: amp_feff1 = amp * x amp_feff2 = amp * y = amp * (1-x) In this way I can estimate the global amplitude variable and introduce a "percentage" of the two chemical compounds (correlation is kept under control). How to explain what I have done to a non-ifeffiter? Mauro --- Mauro Rovezzi <laluvedda(a)gmail.com> Physics student @ GILDA BM08 c/o ESRF (Grenoble, France)

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???
by Elena Ion 02 May '05

02 May '05

Hello, Questions from a beginner in EXAFS...using Athena and Arthemis >From where to get the error bars for number of neighbours, distance and sigsqr (ss)? What are Chi-square,Reduced Chi-square and R-factor and how should be their values in a fit? Sometimes it happen that "R-factor for this data set" does not have the same value as the first R-factor from results. Why? many thanks, Elena

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Fwd: help about Arthemis
by Bruce Ravel 30 Apr '05

30 Apr '05

Mahendra, I am forwarding your question and my answer to the Ifeffit mailing list. I recommend that you make use of that resource for your EXAFS and analysis software questions. Once you make the sum of paths, you should find that, in the File menu, the menu item for "Save fit as" is enabled. I acknowledge that is somewhat confusing -- you made a summation, not a fit. But as far as Artemis is concerned, summations and fits are very similar. In any case, you can use that item in the File menu to save your summation in k, R, or q space. There is a small bug in there. If you have not imported data yet, you can still save the summation in the manner I described, but the information written to the header will be incorrect. That will not preclude using the file, however. Hope that helps, B ---------- Forwarded Message ---------- Subject: help about Arthemis Date: Friday 29 April 2005 15:19 From: koppolu uma mahendra kumar <mahixs(a)gmail.com> To: ravel(a)phys.washington.edu Dear Dr.Bruce Ravel, i am a new user of Arthemis. i calculated an exafs signal using phase and amplitudes calculated from Feff. i used the option "sum of paths(no fit)" in Arthemis. i am not able to save this as an ascii file. Please help me to go ahead. thanking you mahendra kumar ------------------------------------------------------- -- 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/

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horae-051 debian packages
by Carlo Segre 28 Apr '05

28 Apr '05

I have built and uploaded the 051 version for Debian. I will convert to rpms as soon as I have time. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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new tarbell, again
by Bruce Ravel 28 Apr '05

28 Apr '05

The 051 release is up on my website and on SourceForge. Carlo, Paul, Stefano, and Matt helped iron out all the problems in Athena and horae_update. Thanks guys! 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 and voice mail: (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/

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new release of Athena, Artemis, and Hephaestus
by Bruce Ravel 27 Apr '05

27 Apr '05

Hi folks! After a rather long hiatus, I have finally released a new source code tarball for my codes. You can grab it from SourceForge or from my web site. The linux, unix, and Max OSX users can run the horae_update script at any time. If history is any guide, Carlo will have new debian packages on SourceForge lickedysplit ;-) I plan to build new Windows executables on Monday morning. Hopefully there will be a Windows updater package soon after that. The list of new features, improvements, and bug fixes is quite long. Here is a summary of the most important new developments: Athena: ** You can now rebin your data using Ifeffit's rebin() function. Rebinning can be done on the fly in the column selection dialog as the data is imported or you can use the rebinning dialog which is found under the Data menu to rebin data already imported into Athena. ** After editing a parameter in one of the little text entry boxes, you can hit "enter" or "return" and the data will be replotted. This is a keyboard shortcut for the red plot buttons. ** There are several cosmetic changes on the main page intended to convey more information about the state of a data group. The large blue text in each section on the main page changes its shade of blue depending on whether the group is "up to date" with respect to that group of parameters. This will make sense when you see it! Artemis: ** This is almost certainly the last release for which there will be distinct stable and development versions of Artemis. Very soon I will be retiring the 0.7 branch of Artemis and renumbering the development branch as Artemis 0.8. For now the "artemis" program still refers to Artemis 0.7 and the "diana" program still refers to the development version. Soon, there will be no "diana" and "artemis" will refer to version 0.8. Here is a short PDF document with lots of pictures describing the major changes between 0.7 and 0.8: http://leonardo.phys.washington.edu/~ravel/misc/artemis0.8.pdf Hephaestus: ** I added a fluorescence line finder which works almost exactly like the current edge finder. I hope everyone enjoys the latest versions. I encourage everyone to try out the development version of Artemis. Have fun! Bruce -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (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/

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this time for sure!
by Bruce Ravel 25 Apr '05

25 Apr '05

Hi! I just uploaded release 050 of the source code tarball for Athena, Artemis, and Hephaestus to SourceForge and my web site. This version fixes some problems related to perl/Tk 804 that surfaced after the previous release two days ago. I think that this version should work well. I'm keeping my fingers crossed! Unfortunately, the horae_updater script that you linux and Mac users have on your computers will not work due to some changes at SourceForge. Grrrr! You can grab an updated version of the updater here: http://leonardo.phys.washington.edu/~ravel/software/packages/horae_update That version should work around the new changes at SF. I built and tested the codes on Windows today. I am using a new system for building Windows executables. Athena and Artemis worked fine, but there was a problem with Hephaestus. Hopefully I'll get that problem solved and a new Windows updater will become available soon. I'm really excited about this release -- Athena has seen lots of improvements and the development version of Artemis is almost ready for widespread use -- so I am eager to get over these hurdles. Regards, 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 and voice mail: (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/

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an interesting Atoms problem
by Bruce Ravel 22 Apr '05

22 Apr '05

Hi! This week I received an interesting question about Atoms whose answer will, I think, be of wide interest to the denizens of this list. The fellow who started the discussion had an atoms.inp file for ammonium tetraoxorhenate, (NH4)ReO4. Here is the input data: space = I 41/a a = 5.995 c = 12.440 rmax=10 core = Re1 atoms # elem. x y z tag Re 0.00000 0.00000 0.00000 Re1 O 0.20450 0.37860 0.17020 O1 N 0.00000 0.00000 0.50000 N1 These data ran atoms to completion, but then Feff stopped after issuing the statement about computing the "muffin tin radii and interstitial parameters" with this error message: WARNING: NO ATOMS CLOSE ENOUGH TO OVERLAP ATOM 10, UNIQUE POT 3!! My correspondant found this message a little cryptic and asked for advice. You will notice that the input data for atoms did not specify the hydrogen positions. Often it is fine with both Atoms and Feff to neglect the positions of the hydrogen atoms. For example, in a mineral phase with water molecules in the crystal structure, one can often just specify the positions of the water oxygens and neglect the water hydrogens. Doing so will still let both Atoms and Feff run to completion and leave you with a Feff calculation that is quite useful in analysis. So what happened here? Apparently my correspondent presumed that ammonium is like water in that specifying the locations of the hydrogens is not essential to the Feff calculation. Like in water, the hydrogens are fairly tightly bound to the nitrogen -- less than an Angstrom away -- so it might be ok. In this case, however, the hydrogens are essential. Adding the hydrogen position H 0.37200 0.45600 0.03300 H1 avoids the problem during the Feff run. Feff finishes and the analysis can proceed. It turns out that, while the N and the H are, indeed, quite close together, the N is quite a long way away from its next nearest neighbor, which is oxygen. The oxygen shell is split into two subshells, the closer of which is at about 2.85 Angstroms from the N. When Feff goes to compute the muffin tin potential, a near neighbor separation of 2.85 Angstroms is too large and it is unable to determine the radii of the atoms. That is the meaning of Feff's slightly cryptic error message. With the intervening hydrogen atoms, Feff's algorithm for constructing the muffin tins is no longer ill-defined -- the separation between atoms is no longer too large. To conclude, while it is probably unlikely that the hydrogen locations can be well measured by the EXAFS experiment, it is quite important to include the hydrogens in the theory. The rule of thumb that says that hydrogens in hydrated crystal structures can be neglected is not a very good general rule. This is certainly a case where the hydrogens cannot be ignored. Well, *I* thought it was interesting. Hopefully you did too! 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/

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RE: [Ifeffit] Estimation of Pt and Au particle size
by Barton, David (DG) 19 Apr '05

19 Apr '05

Scott: Thank you for your detailed and prompt response. I look forward to testing out your example file of fitting Pt particle size, it should be a good starting point to begin this type of "rough" analysis. After working though this "rough" analysis we will then consider if our data quality will allow for a more detailed analysis of particle shape or distribution. Where we want to eventually take this analysis is to determine if we can measure differences in the particle size distribution in a series of samples. Ifeffit Community: I am still open to additional example Artemis files, especially if someone has a file that they would want to share related to fitting Gold particle sizes. Regards, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Scott Calvin > Sent: Tuesday, April 19, 2005 9:29 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Estimation of Pt and Au particle size > > > Hi David, > > Sure thing. I'll send you a Pt file as a separate email; I'll also > send you a copy of the paper we're currently preparing for > publication. The final versions we used we're big Ifeffit scripts > rather than Artemis files, but I'm sure I can scare up a > representative Artemis file from earlier in the process. > > Just a brief comparison of the two methods I've seen out there: > > 1) Fit the coordination number of each shell. Anatoly Frenkel has > several publication related to this. > > 2) Assume the crystallites are "roughly" spherical and constrain the > coordination numbers in a fit to reflect this. The only size-related > fitting parameter is then R, the radius of the crystallite. I have > written a few papers related to this method. > > Method 1 has the advantage that it can in principle handle any > morphology; Anatoly has used it with supported catalysts (they may > even have been Pt, but I don't recall offhand) and distinguished > between shapes like rafts, hemispheres, etc.. > > Method 2 has the advantage that is uses only 1 size-related > parameter. For a complicated fit or one with limited data quality, > that's nice. On the other hand, if the morphology is far from > spherical (e.g. needles), then it doesn't work very well. This method > can even be used with an empirical standard (as opposed to a > theoretical standard like FEFF) to give a (rough) model-independent > estimate of size. > > So I tend to think method 1 is better when you have a very uniform > sample, as can happen with supported catalysts, while method 2 is > often appropriate when you have a "messier" sample with roughly > spherical particles, as is often the case when wet chemical methods > are used. > > It should also be noted thatusing both techniques there have been > many reports that for polydispersed samples EXAFS yields a mean > smaller than that found by other methods (e.g. Scherrer analysis). > Part of that can be explained by the different weightings inherent in > the different techniques (EXAFS reads a 10 nm and 10 micron > crystallite as essentially identical, but "notices" a 1 nm > crystallite, while XRD would find the 10 micron signal dominant), but > I am not yet convinced that there isn't something else at work as > well. My group is currently planning a follow-up study of Pt to > resolve this question. > > --Scott Calvin > Sarah Lawrence College > > >Ifeffit Community: > > > >Over the past year or so I have seen several discussions of > >estimation of metal cluster size (collections of several to hundreds > >of metal atoms) using coordination numbers derived from EXAFS > >fitting. I was wondering if anyone on the list would be willing to > >share an example of their Artemis project file where this analysis > >was done successfully for Pt and/or Au particle sizes. As a first > >pass I am just interested in roughly estimating an average particle > >size with future considerations for estimations of particle size > >distributions if data quality and theory allows. > > > >Thanks in advance to anyone willing to share their project files. > >Given the number of experts in the field reading this list it just > >seemed to make sense to build upon the back giants. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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Estimation of Pt and Au particle size
by Barton, David (DG) 19 Apr '05

19 Apr '05

Ifeffit Community: Over the past year or so I have seen several discussions of estimation of metal cluster size (collections of several to hundreds of metal atoms) using coordination numbers derived from EXAFS fitting. I was wondering if anyone on the list would be willing to share an example of their Artemis project file where this analysis was done successfully for Pt and/or Au particle sizes. As a first pass I am just interested in roughly estimating an average particle size with future considerations for estimations of particle size distributions if data quality and theory allows. Thanks in advance to anyone willing to share their project files. Given the number of experts in the field reading this list it just seemed to make sense to build upon the back giants. Regards, Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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