- 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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Re: [Ifeffit] file causing trouble creating chis
by Adam Webb 15 Mar '05

15 Mar '05

Hi, I looked at the file. But as with your first file, I have no trouble saving chi files. I used athena 0.8.34 on Windows 2000. You should not have any trouble with XP. BTW the file you sent says it was created with Athena 0.8.30. I think it should still work but it might indicate a problem with your installation. You could try unistalling and re-install and get the updates when the updater runs. I hope this helps, Adam > 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 ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

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blank chi files still
by Daniel Carter 15 Mar '05

15 Mar '05

Bruce, Matt, Adam, others, I'm still having this problem with Athena where I try to save data as a chi file and the file is created, but empty. The chi files should be several killobytes large, but mine are 0 KB. I've just upgraded to the newest version of Athena 8.037. I wonder, is it my data or my operating system? No one else seems to be having these sorts of problems. --Dan

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Athena functionality report
by Raul Barrea 14 Mar '05

14 Mar '05

Hi Bruce, I found a difference in functionality in Athena when I tried to use "open file" or "open many files" in the main menu . When using the many files option I found this message: Athena trapped a warning! The following message was trapped by Athena: Athena0.8.034warnC:\Program Files\Ifeffit\horae\stash\ATHENA.TRAPCODE(0x21a5d800 ) at athena line 1363 main::__ANON__('Tk::Error: Can\'t call method "lower" without a package or objec...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al ) line 402 Tk::Error('MainWindow=HASH(0x21072a84)', 'Can\'t call method "lower" wit hout a package or object reference...', '[\&main::read_file,1]', '(menu invoke)' ) called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at athena line 1419 When I opened the same file alone using the "open file" option , Athena says the file is not monotonically sorted and it cannot be opened. So, that's the problem with the file. Then, Athena offers to sort the data and continue loading the file. Why this message is not shown when I opened multiple files? I tried to open only one file (the one that is not monotonically sorted) using the "open many files" option and the message was the same as the "open file"option. When using the "many files" option with many files, Athena does not show that message window and stays partially inactive (menu options are active but plot options are not active). A few sample file are atached. Thanks, Raul -- Raul Barrea, Ph.D. Assistant Research Professor of Physics, Associate Director Biophysics Collaborative Access Team (BioCAT) CSRRI, Dept. BCPS, Illinois Institute of Technology BioCAT/APS/435B/Sector 18 Argonne National Laboratory 9700 South Cass Avenue, Argonne, IL 60439 Tel.: (630) 252-0541 Fax: (630) 252-0545 Email: barrea(a)bio.aps.anl.gov Email: barrea(a)iit.edu pager: barrea-pager(a)bio.aps.anl.gov # File header: # Date and time: Sun Feb 20 23:25:41 2005 # Original name of the file: whiteCuscan.154 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -74.0000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 431984.40375 132525.96670 241.67263 8779.18220 435848.70000 132897.63333 141.66667 8779.82148 436557.03333 134347.63333 225.00000 8780.77597 435390.36667 132805.96667 150.00000 8781.72001 436465.36667 133330.96667 200.00000 8782.66579 437065.36667 133889.30000 183.33333 8783.61330 438248.70000 134264.30000 241.66667 8784.55950 437082.03333 134222.63333 141.66667 8785.50438 437123.70000 133539.30000 150.00000 8786.44947 437282.03333 134014.30000 150.00000 8787.39629 436107.03333 133122.63333 108.33333 8788.34332 434823.70000 133097.63333 166.66667 8789.29057 434557.03333 132589.30000 191.66667 8790.23802 433707.03333 132772.63333 183.33333 8791.18568 422148.70000 129089.30000 150.00000 8792.13508 429932.03333 131405.96667 158.33333 8793.08316 437498.70000 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Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.7000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 432284.41115 133059.31319 158.33724 8779.18524 434157.03333 132955.96667 241.66667 8779.82756 437123.70000 133730.96667 250.00000 8780.78358 436932.03333 133655.96667 191.66667 8781.72915 436957.03333 133989.30000 183.33333 8782.67341 437665.36667 133889.30000 216.66667 8783.61939 438032.03333 134189.30000 183.33333 8784.56559 436982.03333 134022.63333 150.00000 8785.51047 437232.03333 133439.30000 250.00000 8786.45709 436223.70000 133564.30000 150.00000 8787.40544 437707.03333 133880.96667 175.00000 8788.35095 436365.36667 134472.63333 266.66667 8789.29667 434840.36667 132680.96667 241.66667 8790.24565 431982.03333 132805.96667 275.00000 8791.19331 420565.36667 128739.30000 141.66667 8792.13966 429857.03333 131897.63333 158.33333 8793.08622 438582.03333 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Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.8000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. 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Original name of the file: whiteCuscan.153 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.9000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. 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Original name of the file: whiteCuscan.150 # Beamline: 18ID # User's Comments: User's comments 1 # User's Comments: User's comments 2 # Scan type, mode: EXAFS Continuous Scan, Fixed-Time Mode # Monochromator type: Si_111, mono 1 # Int. Motor 1 name: energy_MO1_1m # Start, end, step: 8.7790 , 9.2790 , 0.0010 # Int. Motor 2 name: theta_MO1 # Start, end, step: 13.0183 , 12.3054 , 0.0014 # Scan time: 60.00 # Number of scans: 1 # Undulator linked, offset: 0.1000 # Ext. Motor 1 name: stepper19 # Start, end, step: -71.0000 , -75.0000 , -0.1000 # Ext. Motor 1 position: -73.6000 # Ext. Motor 2 name: stepper20 # Start, end, step: 5.9000 , 8.5000 , 0.1000 # Ext. Motor 2 position: 6.2000 # Scaler channel_number/column_name/dark_current: # ch#6/I0/1951 ch#7/I1/2611 ch#15/CuKalfa/0 # Dark current last measurement: Sun Feb 20 20:17:51 2005 # # # # # # # # # # Energy I0, I1, CuKalfa # 8779.02544 432592.75209 132475.96547 175.00432 8779.20655 435715.36667 133297.63333 233.33333 8779.86866 436465.36667 133597.63333 183.33333 8780.82316 437198.70000 133547.63333 233.33333 8781.76874 438007.03333 134439.30000 175.00000 8782.71301 437823.70000 133214.30000 66.66667 8783.66053 438132.03333 134872.63333 183.33333 8784.60826 437873.70000 133439.30000 125.00000 8785.55315 437923.70000 134372.63333 141.66667 8786.49825 437890.36667 133622.63333 191.66667 8787.44509 436590.36667 133614.30000 208.33333 8788.39213 435848.70000 133114.30000 166.66667 8789.33938 436748.70000 133489.30000 158.33333 8790.28685 434573.70000 133222.63333 141.66667 8791.23452 420948.70000 128247.63333 183.33333 8792.18240 431765.36667 132214.30000 183.33333 8793.12897 437840.36667 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2 1

Residual
by yetao＠chem.uga.edu 11 Mar '05

11 Mar '05

Hi, Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve. Best, Ye

4 5

back to work....
by Bruce Ravel 10 Mar '05

10 Mar '05

Hi everyone! I am back from vacation and (on March 7th) started my new position here in Argonne's Environmental Research Division. I had a splendid vacation and am very excited about my new position. For those of you who are APS users, I'll be spending a good fraction of my time at sector 10 (MR-CAT). Stop by and say hi -- especially those of you that I have met in person! I have to confess that I have not been following the discussions on the mailing list very closely in the last several weeks, but I see that there have been a number of bug reports and other problems that people have encountered with the software. I am still settling into my new job and my new home, but I hope to get back to work on the codes real soon. And I will certainly resume active participation in the discussions on the list. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Environmental Research Division, Bldg 203, Room E165 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/

3 2

Re: [Ifeffit] Athena Chi file created, but nothing there
by Adam Webb 08 Mar '05

08 Mar '05

Dan, I think the problem was when you first imported the data. When you import the data, Athena tries to figure out what type it is. In your case the first file is very short and Athena probably selected XANES data. This disables the k,q etc since they don't apply. Re-import your data but be sure to select mu(E) as the Data Type in the import window. The rest of your problems should go away. Cheers, Adam > Dear mailing list -- > > I'm having difficulty creating a chi file. First off I cannot > plot my data files in k, q , etc. The files can only be plotted in E > or merged and plotted in k, q, etc. > > Second, when I go to the file menu to create a chi(k) from the > marked original text file, Athena won't let me. That is to say the > only option is create to Save Mu(E) and when I do that a file is > created with nothing in it. > > When I merge 2 data files and create a chi(k) file from that, > again, a file is created and named, but nothing is there. Is there > something wrong with my data files? I don't see any error messages. > Let me know if you need more info. > > I'll also attach my athena file. > > Thanks, Dan ------------------------------------------------------ M. Adam Webb Ph.D., MCIC Alberta Synchrotron Institute (http://www.asi-cls.ca/) 8308 - 114 Street, Suite 2080 Edmonton, Alberta, T6G 2E1, Canada Phone: (780)492-5464 Fax: (780)492-6160 Email: adam.webb(a)asi-cls.ca

2 1

Athena Chi file created, but nothing there
by Daniel Carter 04 Mar '05

04 Mar '05

Dear mailing list -- I'm having difficulty creating a chi file. First off I cannot plot my data files in k, q , etc. The files can only be plotted in E or merged and plotted in k, q, etc. Second, when I go to the file menu to create a chi(k) from the marked original text file, Athena won't let me. That is to say the only option is create to Save Mu(E) and when I do that a file is created with nothing in it. When I merge 2 data files and create a chi(k) file from that, again, a file is created and named, but nothing is there. Is there something wrong with my data files? I don't see any error messages. Let me know if you need more info. I'll also attach my athena file. Thanks, Dan

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Re: uncertainties in "relative" values (Josh Kas)
by joshua jason kas 27 Feb '05

27 Feb '05

Hi Scott, if I understand correctly, the absolute uncertainties in the sizes are still large when you fit sizA and delta_size=(sizeB-sizeA), but I think that the uncertainty in the parameter delta_size showing the difference between the two could be very small, showing that there is a correlation between sizeA and sizeB. In order get this behavior I think you have to leave sizeA unconstrained when you do the multiple-dataset fit. If the uncertainty in delta_size is small, then the absolute uncertainties will be approximately sizeA +- ds_a, sizeB +- ds_a, more or less the same as before, but the uncertainty in sizeB given sizeA is much smaller sizeB = sizeA + delta_size +- dds. -Josh Kas > Hi Matt, > > I tried that, before realizing it didn't really do anything. > Performing a multi-dataset fit with two guessed variables, say size_A > and sizeA_v_sizeB, is of course completely equivalent to just having > the two sizes as guessed variables. And if size_A is set to some > arbitrary (but reasonable) value, sizeA_v_sizeB is equivalent to just > fitting size_B, and produces the "absolute" uncertainty again. This > would be different if the fit were truly multi-dataset in the sense > that we had parameters in common between samples, so that > constraining the size of A had some effect on the fit for B. But the > parameters that are in common, like S02, we constrained to a standard > rather than refining through a multi-dataset fit. > > I like your analogy to airline tickets...that is something like the > situation we seem to have. > > --Scott Calvin > Sarah Lawrence College > >> Hi Scott, >> >> Would it make sense to define a factor between the size of the >> two (or more) particles, say "sizeA_v_sizeB" and vary *that* in >> a fit of the two particles, keeping all the other things >> (k-weight, ranges, etc) the same for the two fits? That is, >> instead of asking "what is the size of particle A and what is >> the size of particle B?", ask "what is the size of particle A >> and how much bigger is particle B?". If you're observations are >> right, sizeA_v_sizeB should be statistically different from 1. >> >> --Matt >> >> PS: The price of airline tickets vary widely with many factors, >> but for any given flight, the price (starting "retail" price) of >> a first class ticket is always higher than a coach ticket. Of >> course, the coach ticket on some flights can easily be twice the >> price of a first class ticket on other flights. But everyone >> knows first class is always more expensive than coach. ;). > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 24, Issue 11 > *************************************** >

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[Fwd: FEFF Q]
by Bruce Ravel 27 Feb '05

27 Feb '05

Ryan, I am on vacation right now, so I have taken the liberty of forwarding your mail to the Ifeffit mailing list. Hopefully someone there will offer up an answer to your questions. Regards, B ---------------------------- Original Message ---------------------------- Subject: FEFF Q From: "R Tappero" <rtappero(a)udel.edu> Date: Fri, February 25, 2005 5:55 pm To: ravel(a)phys.washington.edu -------------------------------------------------------------------------- Hello Dr. Ravel, My name is Ryan Tappero and I am a graduate student in Dr. Sparks Env. Soil Chem research group. I am preparing for an XAFS experiment with M. Newville at APS. I read a recent paper (attached) where the authors used FEFF7 to generate theoretical phase and amplitude functions for cluster models (density functional theory/ DFT optimized structures). I am collaborating with one of my group members on this project, and he has completed the molecular orbital calcs for our proposed clusters. He has provided me with a set of coordinates for the optimized sorption complexes. I can not figure out how to input the x,y,z, coordinates into FEFF in order to generate the dominant scattering paths (for use with theoretical fitting of the XAFS data). Can you point me in the right direction? Sincere Thanks, Ryan Tappero Env. Soil Chem. U of DE, PLSC rtappero(a)udel.edu 410-996-9819 ravel <mailto:ravel@phys.washington.edu> @phys.washington.edu

2 1

Postdoc position at HASYLAB
by Edmund Welter 15 Feb '05

15 Feb '05

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) is a postdoc position in the XAFS business available. For more information please follow: http://www.desy.de/v2/docs/1107528217-e.pdf The main tasks of the succesfull applicant will be the operation of the X1 XAFS-beamline, to take care of the industrial XAFS users (This gives ample opportunities to use all the very nice programs which are topic of this list...) and last but not least HASYLAB strongly encourages postdocs to work in their own field of science. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter -- Dr. Edmund Welter HASYLAB at DESY e-mail : edmund.welter(a)desy.de Notkestr. 85 fon : (+49)-40-8998-4510 D-22603 HAMBURG fax : -2787 GERMANY secretary : -2304

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RE: About Cu2+ xafs
by Anatoly Frenkel 13 Feb '05

13 Feb '05

Dear Igor, Your problem is very interesting: the dependance of EXAFS analysis results on the FEFF model, and I am cc'ing my response to the group. Obviously, there does not exist a unique way to solve it. It is also true that it is important to know which set of results to choose because if you apply s02 to analyze your unknown compounds, whether it is 0.8 or 1.0 matters. There are several approaches that keep you from breaking your head trying to understand the underlying physics between SCF and nSCF and which of the two values of E0 are better . To choose which model is better, you have to approach it systematically by applying these models (SCF, nSCF and SS) to different systems where you know what debye waller factors should be (e.g., by performing temperature-dependent studies and comparing the resuls you obtained for DWF against those predicted by Einstein or Debye models. This has been done by many and it is a foolproof method. However, it is hard to do temperature dependent studies in solutions, and thus your options may be limited. You can also analyze pure Cu foil data measured in the same conditions at the same beamline, and obtian its S02 (it should be about 0.95 as I remember) and then impose it on your Cu2+ complex. However, this procedure does not allow the S02 in aqueous solutions to be slightly different than in the bulk Cu compounds, and we know that they may be different because the chemistry is strongly different, chemical potentials are discontinuous, and the argument of chemical transferrability of amplitudes and phases may not work. Also, it doesn't answer the question which FEFF calculation to prefer for the analysis of the complexes, but it helps a bit because it gives you some ballpark estimate what S02 should be. So, the first approach is to take S02 from Cu foil or Cu oxide data and impose it on the Cu in solution data. It may be a good start. By the way, in your case, both answers deviate by 10% from the average value: S02 = 0.9. That means, if you do not know which model is more reliable, pick 0.9 and your coordination numbers will be defined with 10% accuracy. It is a good accuracy in case of solutions. The second important question is what to do with E0 and distances. They do correlate, as your results show, and they should. However, the first nearest neighbor (equatorial) distances are identical between the two models. The second, axial, distances are different but overlap within the uncertainties. May be that one should be preferred that gives more realistic E0? Unfortunately, E0 is loosely defined in XAFS analysis (FEFF sets it at the muffin tin level) and it can be within 10-20 eV above Fermi energy. Since Fermi energy must be below 1s-3d transition energy, both of your results are, technically, legitimate. Unfortunately, there is no way to tell what should be the r_axial - partly, because it depends on pH and other factors, but it looks like both your models do give good agreement with expectations. What all these models have in common is that they are all based on theoretical calculations which means that they contain a black box and are hard to check experimentally. Some time ago, I adjusted FEFFIT to solve these problems by "bypassing" the black box part of them. I used an old-fashioned way of EXAFS analysis by using experimental standards instead of theoretical standards. For example, if you are certain that Cu2+ in aqueous solution is octahedrally coordinated, you can use this data set as experimental standard. If you extract the scattering amplitude and phase from this data set, the amplitude function will contain f(k) and S02 in it, and thus it spares you from trying obtaining it from the fit unambigously. Moreover, the phase function will have E0 and delta(k) informations in it as well, and if you align your standard and unknown in energy, the best results for delta r will be less model dependent if you relied on E0 obtained by FEFF. Here is a short paper where this method is explained in detail. http://pubweb.bnl.gov/people/frenkel/EXP-FEFF/thiols.pdf Regards, Anatoly Anatoly Frenkel Yeshiva University anatoly.frenkel(a)yu.edu -----Original Message----- From: Igor Frota de Vasconcelos [mailto:idevasco@nd.edu] Sent: Tuesday, February 08, 2005 9:39 AM To: Frenkel, Anatoly Subject: Re: About Cu2+ xafs Dear Dr. Frenkel, Thanks for your message! I will try put the whole story in a nut shell without leaving important details out! I am working with two different models for my hydrated Cu2+. The first one is a simple one with four water molecules on the equatorial plane, and two in the z axis. The four equatorial O's are 2 A away from the central Cu while the two axial O's are 2.29 A. I positioned the hydrogen atoms according to some molecular dynamics simulations of hydrated Cs and Pb (MD simulation of hydrated Cu2+ is harder because of the Jahn-Teller distortion). I also put eight water molecules in a second shell at 3.95 A to try to minimize truncation effects in the self-consistent calculation. I then used feff8.20 to calculate paths self-consistently (I will call this SCF) and not self-consistently (nSCF). The other model is the one you suggested in the mailing list (I'll call this one SS). The results using the latest linux based horae package are (the subscripts e and a denote equatorial and axial O's (I did not include results from multiple-scattering and hydrogen paths): 1) SCF: S02 = 0.9982900 +/- 0.0616710 E0 = -7.5800660 +/- 0.5694190 dr_e = -0.0443480 +/- 0.0034370 => r_e = 1.955652 +/- 0.0034370 ss_e = 0.0069170 +/- 0.0004820 dr_a = -0.0760780 +/- 0.0346330 => r_a = 2.213922 +/- 0.0346330 ss_a = 0.0320830 +/- 0.0076460 Reduced chi-square : 466.198889482 R-factor : 0.000652086 Measurement uncertainty (R) : 0.000306860 2) nSCF: S02 = 0.7977480 +/- 0.0758730 d_E0 = 1.1833490 +/- 0.8799960 dr_e = -0.0448740 +/- 0.0057950 => r_e = 1.955126 +/- 0.0057950 ss_e = 0.0051430 +/- 0.0008710 dr_a = -0.0107380 +/- 0.0451450 => r_a = 2.279262 +/- 0.0451450 ss_a = 0.0338300 +/- 0.0138210 Reduced chi-square : 2078.758619285 R-factor : 0.003396526 Measurement uncertainty (R) : 0.000306860 3) SS: S02 = 0.8082010 +/- 0.0866670 d_E0 = 1.1847890 +/- 1.6045490 dr_e = -0.0329940 +/- 0.0067630 => r_e = 1.957006 +/- 0.0067630 ss_e = 0.0049640 +/- 0.0008280 dr_a = -0.0959300 +/- 0.1364220 => r_a = 2.194070 +/- 0.1364220 ss_a = 0.0460070 +/- 0.0358600 The nSCF and SS results are very similar but some SS errors are significantly larger. Therefore I will base my comments and comparisons on the SCF and nSCF results. As you can see, the structural parameters are pretty much within error! S02 and d_E0 however, differ quite a lot. Although the d_E0 of 1.18 from the nSCF seems more reasonable than the -7.58 value from the SCF, the SCF fit is much better (lower reduced chi-square and R-factor). The S02 values are not within error. My problems are, then, two-folded: The first is a practical one: I don't know which S02 and d_E0 to pick and it is really bad because nailing them down (specially S02) is the whole purpose of the analysis of this standard. The second problem is of philosophical nature and more important than the first one because its clarification will provide the answer for the first problem and also some peace of mind. I do not understand why the E0 corrections (d_E0's) are so different. The fact that the correction obtained from SCF calculation is larger (and apparently worse) than that obtained from the nSCF calculation (absolute values) seems counter intuitive to me. The E0 value I picked for background subtraction is 8989 eV, and applying the corrections, I find an edge energy of 8990.1 eV and 8981.5 eV respectively. This second value falls in the pre-edge region, pretty much on the 1s-3d transition bump. Despite the evidences, I tend to trust the SCF's d_E0 value the most but would like to understand the physics (or lack of) behind the different feff calculations! I apologize if I bored you with unecessary details! Thank you very much for your attention and willingness to help! I really appreciate it! Best regards, Igor Anatoly Frenkel wrote: Dear Igor, I am getting back to your question now. It would help if I knew what E0 value you are getting. What is the value of s02 that you are obtaining? How are you modeling the Cu2+ standard compound? Are you using a bulk reference of a Cu-O bond (e.g., by using CuO oxide, or you are using a method in one of the IFEFFIT posts that I suggested (by using SS and OVERLAP cards)? If you tried one but not another, it is important that you compare them because the small clusters have all sort of truncation effects that cumulatively change photoelectron scattering amplitude and phase from those in the bulk. If both models produce similar FEFF paths for the first nearest Cu-O distance, it does not matter which one to choose in order to fit the standard compound. If they are different, use them separately when you fit the EXAFS data, and see which one gives you a more reasonable values of s02 and E0. I'll wait until I have a feedback from you because without knowing exactly what you are doing it is hard to give advice on what to do. From my experience with different Cu2+ complexes, these systems can be reliably analyzed. Let me know where you are getting stuck. Regards, Anatoly [Anatoly Frenkel] From: Igor Frota de Vasconcelos [mailto:idevasco@nd.edu] Sent: Wednesday, January 26, 2005 12:16 PM To: Frenkel, Anatoly Subject: About Cu2+ xafs Dear Dr. Frenkel, I am Igor Vasconcelos and I work under the supervision of Dr. Bruce Bunker at the University of Notre Dame's Physics department. I am currently working with some XAFS data on Cu(II) adsorbed on bacterial cell walls. I started out with (Cu(H2O)6)+2 standard to have a better feeling about the Cu+2 systems and to obtain a reliable estimate of S02 to use in the samples' fits. I am using SCF FEFF8.20 paths to fit the data and, although structural parameters make sense, I have exhausted my resources and still haven't understood a rather strange Eo value I am getting. I suspect it has to do with the way feff performs the calculations. I understand you have an extensive knowlegde on this system and I am hopeful you will be willing to provide me some help. I have followed recent posts in the ifeffit mailing list from you and I have two of your papers (Env. Science Tech. 1998 and 2000) on the subject as references. I would be very grateful if you would take the time to receive my question and answer it, in case you have the time and the inclination. I am looking forward to hearing from you. Thank you in advance for your attention, Igor -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco

2 1

Debye-Waller factors for metal oxides ?
by TAO,Ye 09 Feb '05

09 Feb '05

Dr.Rehr mentioned the calculation of DWs using spring constants with the equation-of-motion method(EM) and the recursion method(RM). I wonder if these two methods can be incorporated into ifeffit like Debye and Enstein model. I use EM to calculate the DWs for metal complex molecules, and they work pretty well for a preliminary analysis, but I have to input the calculated DW factors into Artemis one by one manually :-( Ye

1 0

DW Factor follow up
by Ian James Drake 07 Feb '05

07 Feb '05

> Hi, > > Thank you for all this valuable information. > > Can I make a general statement in comparing the DW of metal and its crystalline oxide at a given >temperature? For example, I find the DW for Al metal to be 0.015A in the first scattering path >(Al-Al) at 25C (using correlated Debye model). However, the fitted value of the DW for Al oxide >in the first path (Al-O) was 0.001 A. In both fits, the CN was set to a constant since it is >known from other techniques. Can a general statement be made comparing relative magnitudes of >metal-metal DW and metal-oxygen DW-factors? > > Is there a good general resource for the Debye temperatures of metal oxides, like zeolite or >Al2O3? > > Thank you again for all your guidance. > > Ian Drake

1 0

RE: [Ifeffit] Debye-Waller factors for metal oxides ?
by Kelly, Shelly D. 07 Feb '05

07 Feb '05

I agree with John Rehr. With a temperature dependent data set, the best model that I have found is to allow each atom pair to have a thermal and static disorder component. Sigma2 = debye(Temp,Td_O1) + stat_O1 (This example is for the first oxygen (O1) shell of the metal oxide) The static disorder component should be the same for all data sets from the same sample at the different temperatures. The thermal component should increase as the temperature increases. If you are lucky a Debye or Einstein model will work well enough. You will have to test both. In addition, the thermal change in sigma2 should be about the same for different samples that are closely related. (We could argue about this last point. The best thing to do is to test this constraint by first not imposing it and determine within the uncertainties in the measurement, if it is true. I have found that it usually is an okay constraint.) In the end, you simultaneously model the temperature dependence and the sample dependence spectra all together. You constrain the static disorder term to be independent of temperature, and you constrain the debye temperature to be independent of sample change. This should impose enough constraints on sigma2 values to accurately look at changes in coordination number. Of course the coordination numbers do not change as a function of temperature but only as a function of sample changes. HTH Shelly Shelly Kelly ---------------------------- skelly(a)anl.gov Bldg 203, RM E113 phone: (1) 630-252-7376 Argonne National Laboratory fax: (1) 630-252-9793 Argonne, IL 60439 www.mesg.anl.gov > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of John J. Rehr > Sent: Monday, February 07, 2005 10:07 AM > To: XAFS Analysis using Ifeffit > Cc: John J. Rehr > Subject: Re: [Ifeffit] Debye-Waller factors for metal oxides ? > > > > The lack of accurate Debye-Waller factors in complex materials, like > metal oxides, can be a real problem. In my view, simple phenomenological > methods like correlated Debye and Einstein models can't always be trusted. > > There is an alternative approach to fitting DW factors in such systems > which might be useful. The idea is to fit a few spring constants k_ij > between > the atoms, rather than the DW factors themselves, e.g., for the most > important > sites. This is efficient since the spring constants are temperture > independent. This has been tested by Rossner et al. using their Bayesian > approach [Rossner, H. H. and Krappe, H. J., (2004). Phys. Rev. B 70, > 104102] > The fitting is does via an analytical formula for the Debye-Waller factors > based on a fast recursion method [Poiarkova, A. V. & Rehr, J. J. (1998). > Phys. Rev. B 59, 948]. > > Of course, such an approach still misses contributions to the DW factors > due to structural disorder, which are addititive. > > J. Rehr > > > > On Sun, 6 Feb 2005, Ian James Drake wrote: > > > Hi, > > > > There is little discussion over the significance of fitted Debye-Waller > > factors (ss2) found for metal centers in metal oxides of heterogeneous > > catalysts. I am searching for a better way of determining how > reasonable > > these values are in the fits I get. > > > > 1. Are phenomenological models like the correlated Debye model and > Einstein > > model appropriate? It seems that Debye temperatures are hard to find for > > oxides. > > > > 2. Is there an equivalent value for ss2 in x-ray crystallography data > that I > > can refer to for comparison in these materials? What should I look for > in > > reviewing published x-ray crystallographic data? > > > > 3. Is the temperature dependence reported for the ss2 for some metals > (like > > Cu and Al) similar to their respective oxides? For example, in Debye- > Waller > > factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: > > Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three > > between 25C and 300C. Would I expect a factor of three increase in > > crystalline zeolites (AlO4 structural units). > > > > 4. Specific to my work: I have studied Al containing oxides at > temperatures > > between 25 and 300 C. I would like to quantify coordination changes > by > > doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at > temperature > > and I observe no change in the broadening of the data. Likewise, the > fitting > > shows no sensitivity in the Debye-Waller factor. It is nearly constant > at > > 0.001 A over the temperatures of interest. Since ss2 and the > coordination > > number (CN) are correlated, I would like a way to bind the error on the > > fitted CN by modeling real physical changes in the Debye-Waller factors. > Do > > you have any suggestions? > > > > Looking forward to your thoughts. > > > > Ian Drake > > Graduate Student > > UC Berkeley > > _______________________________________________ > > 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

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EXAFS sample prep
by Kelly, Shelly D. 02 Feb '05

02 Feb '05

Hi Ritika, I hope you do not mind, I'm sending this to the Ifeffit mailing list since others might be interested as well. This email message is about how to prepare an EXAFS sample. We are talking about measuring a Ti-edge from some sample in solution. But any edge and any sample in any matrix will also work just file. You want to set-up your sample so that you have a lot of Ti atoms in the path of the x-ray beam. This is because the EXAFS signal comes from the adsorption from the Ti atoms. Hence more Ti atoms give more adsorption events resulting in a smaller statistical error in the EXAFS spectra. BUT..... In transmission mode the EXAFS signal comes measuring the number of x-rays incident on the sample and transmitted through the sample. If all the x-rays are adsorbed by the Ti atoms in the sample then you do not have any transmitted x-ray signal. Hence you get really noise data because you have no statistically significantly transmitted x-ray signal. So you need your sample to be thin so that a lot of the x-rays pass through the sample such that you have something to measure. In fluorescence mode the EXAFS signal comes from the x-rays emitted by the Ti atoms as the core hole is re-filled. These emitted x-rays need to escape the sample without being re-adsorbed by the sample. Hence the sample needs to be dilute for fluorescence mode measurements. When you make a measurement in fluorescence mode it is always best to collect the transmitted x-ray signal as well. Then you can make a comparison to see if "self adsorption effects" are small. Transmission measurements typically have better signal to noise ratio than fluorescence measurements. So if you can, make your measurements in transmission mode. You can use Tkatoms or Artemis to calculate the best sample thickness and the best concentration to use for the measurements and which EXAFS mode will work best for your samples. >From the components of your sample you can calculate the thickness of the sample that will give 2.5 adsorption lengths. The transmitted x-ray intensity is given by the incident x-ray intensity multiplied by the exponential of the absorption coefficient times the sample thickness. I = I0 * exp(-mu(E) * x) Where I is the transmitted x-ray intensity I0 is the initial x-ray intensity Mu(E) is the absorption coefficient = weighted sum of absorption coefficient from each atom in the beam. X is the thickness of the sample. IF mu(E) * x = 2.5 then the percent of transmitted x-rays is about 10% of the incident x-ray intensity. This is just enough at NSLS where the incident x-ray intensity will be about 10^6 x-rays per second. This means that 10^4 x-rays per second will hit your transmitted Ion chamber. You want to make the transmitted ion chamber adsorb all (99%) of theses x-rays. Then your statistical error in the measurement will be 1/sqrt(N) or 1/sqrt(10^4) or 1%. You need to have at least this many x-rays to measure. At the beam line you measure the total absorption edge. The EXAFS signal, if you are lucky, makes up about 10% of the absorption edge. Hence you need to have a statistical error of no more than 1% to make a measurement. If you can make the sample thinner then you do even better. Now for the other problem: You want to get as many Ti atoms into the sample with a total sample thickness of 2.5 absorption lengths. To do this part you need to calculate the absorption of just the Ti atoms in the sample. I call this delta_mu(E). If you can get the delta_mu(E) * x to be between 0.1 and 1.0 with the total absorption of the sample below 2.5 then you can make the measurement in transmission mode. This means that between 10% and 70% of the absorption in the sample will be due to the Ti atoms. This is enough to get a good transmission signal. If you adsorption from the Ti atoms in the sample is between 1% and 10% then you will hope to make the measurement in fluorescence mode. Now for the practical part: Say you have a solution with 1% Ti-stuff in water by NUMBER of atoms. If you usually work by weight then you need to convert to number for this calculation. Take the feff.inp file for Ti-stuff. Look at the top of the file. You should find total_mu(E) (absorption of the entire sample at the Ti edge), and delta_mu(E) (absorption of Ti atoms at the Ti-edge). Then use Hephaestus to calculate the total_mu(E) for water at the Ti edge energy. To get the total absorption you need to calculate the weighted average for water and Ti-stuff. See how thick you can make your sample and satisfy the criteria for less than a total absorption length of 2.5. (99%_by_number_water_atoms * total_mu(E)_for_water + 1%_by_number_Ti-stuff * total_mu(E)_for_Ti-stuff ) * sample_thickness = 2.5 Once you have that thickness then you can see what the absorption for just the Ti atoms is. 1%_by_number_Ti-Stuff*delta_mu(E)_for_Ti * sample_thickness = absorption_length_for_Ti And then you can figure out if you have a fluorescence or transmission experiment. Absorption_length = 0.1 to 1.0 you have transmission. Absorption_length=0.01 to 0.1 you have fluorescence. Usually you have to go around and around with this sort of calculation to optimize the conditions for the measurements. Hope that Helps Shelly

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