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

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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a basic (?) EXAFS question
by Juraj Majzlan 18 Apr '05

18 Apr '05

Hello, I have a question about fitting an EXAFS dataset. The compound is FeAs2, crystalline, and will be used as a model for further study. I was able to fit the first three shells very well. However, when I try to fit the fourth shell, I either get amplitude that is too high (> 2, with large errors), or 0.0. There are several single-scattering and several multiple-scattering paths in that region. Sometimes, only excluding one of the MS paths leads immediately from amplitude of >2 to 0.0. I'd appreciate any advise about what is the meaning of these changes and the inability to fix the spectrum. Attached are few pictures from Artemis. Thank you, Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de

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RE: [Ifeffit] a basic (?) EXAFS question
by Kelly, Shelly D. 18 Apr '05

18 Apr '05

Hi Juro, Another thing to try, is to simply sum up all the paths from the crystal structure. Then compare the chi(k), and real and mag of the FT. Then plot the individual contriubtions from each of the paths to see how many are significant and how the different paths are contibuting to the overall model. If the model with all the paths is way different from the data then there may be a problem with the structure. SK ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Sun 4/17/2005 2:52 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] a basic (?) EXAFS question Hi Juro, I think you'd have to give us more information about how you did the fits. A few obvious questions are: what R range did you use for the fit? what was floated and what was fixed in the fit? how far out does the data go in k-space? I'm afraid that I don't know the crystallographic details of loellingite, but the EXAFS for many crystal structures get very complex by the fourth shell. This is especially true in slightly disordered structures where multiple-scattering and single paths nearly overlap. Part of the reason for this is that multiple-scattering paths can "spread out" in R-space, making it difficult to know where to stop including paths. --Matt On Sun, 17 Apr 2005, Juraj Majzlan wrote: > Hello, > > I have a question about fitting an EXAFS dataset. The > compound is FeAs2, crystalline, and will be used as a model > for further study. I was able to fit the first three shells > very well. However, when I try to fit the fourth shell, I > either get amplitude that is too high (> 2, with large > errors), or 0.0. There are several single-scattering and > several multiple-scattering paths in that region. > Sometimes, only excluding one of the MS paths leads > immediately from amplitude of >2 to 0.0. > > I'd appreciate any advise about what is the meaning of > these changes and the inability to fix the spectrum. > > Attached are few pictures from Artemis. > > Thank you, > > Juro Majzlan > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de > _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Problems running Adobe Illustrator and IFFEFFIT package programs
by Matthew Ginder-Vogel 14 Apr '05

14 Apr '05

Hello, I was running Adobe Illustrator and then started up Hephaestus and Illustrator immediately crashed. For the sake of science I tried a couple other programs (sixpack and Athena) with similar results. Another person in my research group has also experienced these problems. I just wanted to alert other people to the perils of running Illustrator with one of the other programs. thanks, matt -- ******************************************** Matthew Ginder-Vogel Doctoral Student Department of Geological and Environmental Sciences Stanford University Soil and Environmental Biogeochemistry Group gindervm(a)pangea.stanford.edu ********************************************

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Fwd: Re: Wrong window project file
by Scott Calvin 01 Apr '05

01 Apr '05

Thanks, Bruce. I'm moving this thread back to the ifeffit board: > >On Thursday 31 March 2005 18:41, you wrote: >> Incidentally, trying to shrink down the file has made me notice there's a >> lot of leftover stuff in the zip file--it looks like every data file I've >> ever used for chi data is still in there, as well as an old fit for each of >> those. Artemis almost never crashes any more (yay!), so those aren't a >> legacy of crashes--it just appears that every time I change data files it >> leaves the old one (and the associated fit) sitting in the project file. >> Since I sometimes use the same model with lots of different data, that >> starts to add up. > >Before I actually split Artemis into two branches, I was already starting to >think about the concept of maintaining a history of all fits done. The >presence of all that stuff makes no sense in the context of the stable >branch, but it is much more sensible in the development branch. > >The data should all be chi(k) data -- not so big and it compresses well. >Project files are big because the feff calc, not because of the data. The example I sent you had about 300 k of the zipped project file in old chi data, and the total file is 3 M, so yes, most of it in this case is FEFF calculations. I'm concerned, though, that the former number can only go up. Here's what I think is a reasonable hypothetical: someone has a really stable Artemis model that they like for their materials, and they use it over and over again on various samples. Unlike the file I sent you, it might also use a fairly small number of FEFF paths. Combine that with the fact that the time used by Autosaves is of course quite dependent on the size of the project file (and maybe the number of files in it? I'm not sure how the zipping algorithm works in that respect), and it becomes potentially annoying. I don't consider this a high priority issue, but it seems like something worth thinking about. >Another future reason for hanging onto all the data is batch functions. >Suppose you had a temperature series and wanted to fit each of the scans with >the same model. Wouldn't it be cool to tell artemis-of-tomorrow to fit all >the data and then show the temperature dependence of one of the sigma^2s? Yes, it would be very cool. I guess I'm just asking for a "clear history" option or something like that. In the mean time, I'm happy to do this manually if I know it won't confuse Artemis. If I just root around in the zipped project file and remove the old .chi and .fit files, will that confuse Artemis in any way? --Scott Calvin Sarah Lawrence College

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Re: sigma squared
by Bruce Ravel 01 Apr '05

01 Apr '05

Hi Karla, These are excellent questions for the mailing list, so I am taking the liberty of CCing my answers to the list. That way, other people can have a chance to answer your excellent questions. On Thursday 31 March 2005 14:10, you wrote: > Hello, > I am fairly new to EXAFS data analysis. I am currently working on > data that I collected from 10-ID at the APS. Aha! My new home! I just collected my first spectra from that beamline a couple of weeks ago. ;-) > I have a couple of questions. First, in Artemis, when I click on > the "x" buttons to select my k- and r-ranges, the window never seems > to correspond to where I clicked. Is this a bug? Probably not. The default in Artemis is use a Kaiser-Bessel window. The various strange words to describe FT windows ("Kaiser-Bessel", "Hanning", "Welch", and so on) refer to different functional forms for the window. None of the functional forms will be 0 at the specified boundary -- instead they all have window sills that extend a bit below the boundary. Thus, if you use the Kaiser-Bessel window, set kmin=2, and dk=1, the window will become non-zero at about 1.5. In short, it's not a bug. It's an unexpected (for you, at least ;-) feature of the functional form of the window. Try setting dk or dr to 0 then replotting. The FT may not look good, but the window plotted by Artemis will be what I think you were expecting. > Second, why does Artemis allow a physical parameter like sigma > squared to be negative? There are a few ways I could answer this question. I could talk about how Artemis allows arbitrarily sophisticated fitting models where the sophisticated user needs complete freedom to specify the fitting model. But that's a little abstract, so let's consider a slightly more concrete example. Suppose that your sample has some kind of oxygen-coordinated iron atom and you have reason to believe that there is a high level of disorder in the first coordination shell. So you choose to run Feff using some model compound that itself has much disorder in the first shell. You then use the first shell paths that came from the Feff calculation to model your unknown data. In this case a negative sigma^2 might be telling you that your unknown has *less* disorder than you model compound. In more general terms, the negative sigma^2 is probably trying to tell you something. You should remember that sigma^2 is correlated to other terms in the fit, most importantly to the various amplitude terms, such as coordination number and S02. If sigma^2 is negative, then the fitten value for amplitude is probably to small. A negative sigma^2 will puff up the signal to compensate for the amplitude term being rather too small. If Artemis did not allow sigma^2 to go negative, you might never know about this kind of problem. So I would say that this too is a feature of the program and not a bug. > Lastly, I have had a hard time figuring out these math expressions > despite reading over the mailing lists. Can you use the ">" sign so > that sigma squared is always greater than 0? How else can I write a > math expression so that the fitting never gives me a sigma squared > that is less than 0? Any help would be greatly appreciated! Using ">" won't work. ">" is not a symbol in Ifeffit's math parser. This is a topic that has come up many times over the past few years on the mailing list. In fact, I think that someone should write a FAQ entry on this topic. Here are a few suggestions: 1. Guess a parameter like this: "guess ss 0.003", then use it on the sigma^2 line of the path page like this: "abs(ss)". 2. A very similar approach is to use the max function. In the sigma^2 line of the path page, say this: "min(ss, 0)". This can be improved slightly. Doing this: "min(ss, 0.001)" constrains the sigma^2 for the path to be no smaller than 0.001. 3. If you start reading the mailing list archives here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-February/001650.html you will find a conversation between Matt and Scott about a way to impose a penalty for a sigma^2 being too small rather than forcing to be above a hard boundary. Matt's scheme is kind of involved... If you use any of these approaches, I would encourage you to do so with hesitation. As I mentioned above, the negative sigma^2 is not a short coming of Ifeffit or Artemis. Much more likely, it is useful information that you should heed and use to figure out what shortcoming in your fitting model is leading that to happen. HTH, 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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installation of horae in fedora2
by ynliu＠eps.mcgill.ca 22 Mar '05

22 Mar '05

Hello,all We finally succeeded in installing horae-048 in Fedora 2! It took us a long time to figure out why Tk could not be detected, but it turned out that the right version of Tk is the key. We found Tk-804.027 working in our Fedora2 system. The right order of installation is also important. We had to restart everything in installing horae after we set up Tk.If you are using this Tk-804.027, you don't need to look for unix folder as said on some web,just simply gunzip tar -xvf finename.tar (enter the new folder Tk-804.027) make make install(after this,you can make test if you want) And then the installation of horae will jsut go fluently following the instructions! To use athena or artemis, you need to enter the fold where athena.pl and artemis.pl are,and then "perl athena.pl". cheers Yanan ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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file causing trouble creating chis
by Daniel Carter 15 Mar '05

15 Mar '05

Ok Matt, I thought you might have a general idea for how I could gather more info for you about the problem. I did mention previously this weekend to you that I am using windows XP. I also had thought I'd posted a file, but I'd just sent it to Adam. From now on I will send a file every time I have a problem. This is with athena version 8.034. Matts theory that there is not enough of a Mu(E) range sounds good to me so far. --Dan

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