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

dementer Artemis crashing on XP
by Christopher Patridge 22 Aug '11

22 Aug '11

Hello all, I recently (yesterday) installed the new Dementer package with Strawberry perl on a freshly installed XP Pro SP3. I have tried to open a couple different old Artemis projects (.apj) and once chosen, (D) Artemis shuts down immediately with no warnings messages. The message line reads something like - "converting data to Dementer fit serialization" and then everything disappears. I have attached one of the projects I attempted to open. I can open data from previous Athena projects with no problem. Any help would be appreciated. buena salud, Chris Patridge

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New software being developed
by Bruce Ravel 18 Aug '11

18 Aug '11

Hi everyone, I suppose I should say a few words about this Demeter thing that got mentioned a couple of times today. As some of you may know, I have been working on replacements for Athena, Artemis, and Hephaestus for a while now. The new programs involve better and prettier GUIs, improved plotting capabilities, 100% re-written source code, and lots of new fitting capabilities. I expect that the new codes will be better in almost every way than what we are all currently using. I am getting very close to releasing the new codes for everybody to use. A couple months ago, I asked a small group of people to try out the new programs and to help me find bugs and other problems. This small-scale beta-testing period has been very productive and I have made good progress towards the day when I can begin transitioning everyone from the musty old software to the shiny new software. If beta-testing buggy software sounds like something you might want to try, you can find information about Demeter -- including installation instructions, documentation, source code, and other goodies -- at http://cars9.uchicago.edu/ifeffit/Demeter Be mindful that this is new software. It continues to need testing and it remains likely to crash. If that sounds like fun to you, great! But you then need to be responsible about sending me prompt and useful bug reports. If that sounds like hell to you, you should probably wait for the first stable release. Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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LCF E0
by Pieter-Jan Sabbe 18 Aug '11

18 Aug '11

Dear All I am trying to do a linear combination fit with Athena. To do that i want to first prepare my standard spectra. My unknown sample is (I presume) a combination of Cu and Cu(I)O (cuprite) and Cu(II)O (tenorite). I started with calibrating the Cu to 8979 eV as how the Athena manual say how to do it (I use the zero crossing point at the second derivative). This provided me an E0 and Eshift. I am doubting now for what I should do next: Cuprite and Tenorite have different oxidation states, meanin that the binding energies of the inner electrons will shift and in that way shifting the absorption edge of the compound. Should I look somewhere in a database (does that exist, or articles) for the absorption edge of cuprite and tenorite and set it like that or should I use the same E0 as i did for Cu? Another important thing for me, I have found some old data with some standard reference (powder spectra) measured in fluorescence mode, but my guess they are from different beamtimes, can I use data from different beamtimes/beamlines as standards in a linear combination fit? thank you in advance Pieter-Jan

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Athena: problems with LCF
by Nina Siebers 15 Aug '11

15 Aug '11

Dear All, I acquired Cd L3-edge spectra of some binary and ternary mixtures in varying proportions and for the individual components. The mixtures were created on Cd-mass basis. Then, I tried to fit the reference spectra to the spectra of the mixtures using linear combination fitting of Athena to get their abundance. However, the results were disappointing despite all spectra were carefully energy calibrated and normalized, so I decided to create simple mathematical binary and ternary mixtures by summing up the spectra of the individual reference spectra. After that I did an edge-step normalization in excel and imported the normalized calculated mixtures into Athena. Then, I tried the fitting again to exclude mixing-failures and check sensitivity of LCF with the idealized spectra. Even though the results of the LCF of the mathematical mixtures were better compared to the real mixtures, LCF was also not able to reliable deconvolute these spectra into the individual reference spectra. Does anybody have an explanation for that? It would be nice if somebody could give me information about the mathematical fitting algorithm implemented in Athena. Attached is a data file of three mixtures (two ternary and one binary mixture) including the mathematical mixture created in excel (named calculated at the end). Mixing ratios are named 1to1to1 (meaning 1:1:1 of the components in the same order). For the 1:1:1 ternary mathematical mixture the deconvolution was very good, but the others need improvement. I hope I made my problem clear this time. Thanks a lot! Wishes, Nina

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Re: [Ifeffit] Athena: problems with LCF
by Scott Calvin 15 Aug '11

15 Aug '11

Hi Nina, Thank you for bringing your question to the list. As others have said, the problem lies with not having enough data to normalize effectively, and is compounded by not taking control of the normalization process to make sure its relatively consistent. Standard A, for instance, has a post-edge line that cuts very low through the data, as does D. The 1:1 A to D calculated mixture, though, comes across more evenly. This is a problem even with calculated mixtures, as you chose to import the calculated mixture as a mu(E) file, and not as a norm(E) file. In theory, this should be fixable by fixing the edge step of the calculated spectrum to 1, so that it doesn't try to normalize it again. Something's not quite right when I do that, because the calculated average of A and D sometimes slips below both of the other graphs, and an average shouldn't do that. Nevertheless, it gets us close: an LCF fit now gives us 54.5% A and the rest D. Another approach is to remove the "force weights to 1" checkbox. This is often necessary if normalizations are in doubt. That works quite well here, delivering an A to B ratio of 49 to 53. Summary: --It's best to collect data far enough above the edge so that you establish an unambiguous post-edge trendline, if possible. --Post-edge lines should be examined, and changed if they are inconsistent between spectra being used for LCF. It's better to just eyeball normalization than to use radically different trendlines, for instance. I sometimes play around by eye with trendlines to see what range of normalizations they give, and incorporate that in to my final reported uncertainties. --If normalizations are difficult for a particular set of spectra, it is often better to remove the requirement that weights sum to 1. To the degree that normalizations are off, there will be some error in the values that are found, but at least the fitting routine is able to try to compensate for normalization differences by adjusting the weights. In other words, forcing the sum to be 1 when the normalizations are different forces a bad fit. Allowing them to total to anything allows the algorithm to transfer errors in normalization to errors in weighting. Hope that helps! --Scott Calvin Sarah Lawrence College On Aug 15, 2011, at 5:40 AM, Nina Siebers wrote: > Dear All, > > I acquired Cd L3-edge spectra of some binary and ternary mixtures in > varying proportions and for the individual components. The mixtures > were created on Cd-mass basis. Then, I tried to fit the reference > spectra to the spectra of the mixtures using linear combination > fitting of Athena to get their abundance. However, the results were > disappointing despite all spectra were carefully energy calibrated and > normalized, so I decided to create simple mathematical binary and > ternary mixtures by summing up the spectra of the individual reference > spectra. After that I did an edge-step normalization in excel and > imported the normalized calculated mixtures into Athena. Then, I tried > the fitting again to exclude mixing-failures and check sensitivity of > LCF with the idealized spectra. Even though the results of the LCF of > the mathematical mixtures were better compared to the real mixtures, > LCF was also not able to reliable deconvolute these spectra into the > individual reference spectra. > > Does anybody have an explanation for that? It would be nice if > somebody could give me information about the mathematical fitting > algorithm implemented in Athena. > > Attached is a data file of three mixtures (two ternary and one binary > mixture) including the mathematical mixture created in excel (named > calculated at the end). Mixing ratios are named 1to1to1 (meaning 1:1:1 > of the components in the same order). For the 1:1:1 ternary > mathematical mixture the deconvolution was very good, but the others > need improvement. > > I hope I made my problem clear this time. > > Thanks a lot! > Wishes, > Nina > > > <Mixtures.prj><ATT00001..txt>

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Re: [Ifeffit] how to consider Jahn-Teller distortion?
by Enyuan Hu 09 Aug '11

09 Aug '11

Dear all, Thank you so much for all the suggestions. Dear Matt, thank you for pointing out my rookie mistake and suggested correction. I didn't consider J-T distortion in my new try but the fitting was improved nonetheless. You suggested changing dk from 1 to 4 or 5 for the Kaiser-Bessel window and this has been proved helpful. I guess some appreciation of how the windows function works is needed to really gain insight into why the change of dk is beneficial to the fitting. Also, I was wondering if you can suggest dk values for other windows? Dear Matthew, thank you for your suggestion about using the two shell model. Just like you and Matt pointed out, limited k range poses a great challenge in analyzing J-T distortion. At this point, I do not have enough confidence to implement two shell model. Dear Dominik, thank you for your recommendation of the paper. I looked through it and found that a combination of diagnostic tools was used in that paper. The J-T distortion analysis was based on the results of both XAS and vibrational spectroscopy. Dear Ditty, thank you for your suggestion also. I attached the new fitting file along with the LiCoO3 inp file that you may need. In the new fitting, I actually input the LiMnO2 file (with the same structure as previous LiCoO3) as the sample is more like Fe-doped LiMnO3 (though there're actually substantial doped Ni present and I don't know how to consider that yet). -- Enyuan

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how to consider Jahn-Teller distortion?
by Enyuan Hu 09 Aug '11

09 Aug '11

Dear all, I'm trying to fit the Fe K-edge EXAFS data and I appreciate that Fe in my sample mainly exists as Fe4+, which is associated with Jahn-Teller distortion. The one shell model that considers Fe residing in the standard octahedral apparently didn't give satisfactory result. I'm sorry that even though I found people do fitting considering Jahn-Teller distortion, I am still not aware of how to carry that out in Artemis. Can someone helps me to look at my fitting and give me some guidance on how to implement fitting that considers Jahn-Teller distortion in Artemis? Thank you. -- Enyuan

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Has anyone got this technical problem during the fit?
by NIRAWAT THAMMAJAK 09 Aug '11

09 Aug '11

Dear All, I was just wondering if some of you may have experienced a problem like this in the fit; I was trying to improve the precision of some fit parameters by doing guess, def, and set. In the 61st fit, I tried to split parameters from constraints that i have made. Then, the program didn't show me the results of the fit. I knew that something might have gone wrong, the program forced me to close. Fortunately, there was a window asking me to save it before closing the project. I opened again the project file after it was safely saved. This time, I could not perform any fitting - the green 'Fit' button was frozen and it's not possible to click it. The red message below showed "Artemis trapped one or more errors! Error message dumped to the screen", but I couldn't see such error message on the screen. I closed the project and opened the file again, the 'Fit' button seemed to work this time. Anyway, I still had that red message below said "Artemis trapped one or more errors!...". After clicking at the data file, the red message was gone and replaced by the number of data points, "22 independent points data points (Nyquist): ...". The numbers of the fit and FT parameters were then shown in the boxes on the left as usual, but the title of data was replaced by "o"! I thought it was okay, then I performed other fits. It worked fine. Until the recent fit that I have it blown up, so I saved and closed the project. Now when I try to open the file, I have got the earlier problem, frozen 'Fit' button. Clicking at data file doesn't help as it used to be. I have tried another saved file in this series of .apj files (same data), they have got the same problem. I have tried open another data file like eto.apj in the demo, it's also got that problem with the red message "Artemis trapped one or more errors!.." too. I don't understand what should have gone wrong with the program. Your help will be very much appreciated. Thank you, Nirawat. -- Nirawat Thammajak DPhil Candidate in Inorganic Chemistry Balliol College Oxford OX1 3BJ United Kingdom

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Re: [Ifeffit] how to consider Jahn-Teller distortion? (Enyuan Hu)
by Ditty Dixon 09 Aug '11

09 Aug '11

Hello Enyuan, I am afraid that you are using LiCoO2, structure data base to fit your Fe structure (look like spinal). The feff calculation you did was completely at the Co edge. If you could re post your questions with modified feff calculation somebody could really help, I also need some input in this regards, as I myself might work in some batteries materials. Best wishes, Ditty On Tue, Aug 9, 2011 at 2:47 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. how to consider Jahn-Teller distortion? (Enyuan Hu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 8 Aug 2011 20:47:52 -0400 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] how to consider Jahn-Teller distortion? > Message-ID: > <CAJud35NE3wkcw4MgrYM+cPzDGjO3gAOp3uRzp9t1uzrypHk1=g(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I'm trying to fit the Fe K-edge EXAFS data and I appreciate that Fe in my > sample mainly exists as Fe4+, which is associated with Jahn-Teller > distortion. The one shell model that considers Fe residing in the standard > octahedral apparently didn't give satisfactory result. I'm sorry that even > though I found people do fitting considering Jahn-Teller distortion, I am > still not aware of how to carry that out in Artemis. Can someone helps me > to > look at my fitting and give me some guidance on how to implement fitting > that considers Jahn-Teller distortion in Artemis? Thank you. > > -- > Enyuan >

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Re: [Ifeffit] asking questions effectively (yes, *you* need to read this email)
by Scott Calvin 08 Aug '11

08 Aug '11

One addition to Bruce's appeal: for some subscribers to the list, large attachments are a problem. For instance, some people are still working at dial-up speeds (due to the US' rural digital divide, I was one of those recently), or even have limits on the amount of data they can download in a month. The question, then, is what is a "large" attachment? We've had some discussion of that on the list previously, and never arrived at a hard- and-fast rule. Nonetheless, let me suggest that anything below 1 megabyte is fine--in fact, it should be encouraged so that we can help with the kind of questions Bruce just enumerated. Paul's files, for instance, were 214 KB, or 0.24 MB. I suggest, therefore, that if you have a project file that is large because, for instance, it has many, many fits in its history, please re-save it in a smaller version, and attach that. You should also be careful with screenshots that they are not needlessly large--e.g. saved in a resolution far beyond what is necessary. In the occasional case that the problem or question requires a large file to manifest, such as that described by Nirawat yesterday, some other arrangement needs to be worked out. It's possible, for instance, to use a service such as Dropbox to make the file available without actually attaching it to an email. --Scott Calvin Sarah Lawrence College On Aug 5, 2011, at 3:25 PM, Bruce Ravel wrote: > > Hi everyone, > > This has been a particularly troubling week for me here on the Ifeffit > mailing list. This week we have seen an unusually large number of > poorly asked questions. Not bad questions, mind you, just questions > that have been asked in a manner that makes it hard to provide a > useful response. > > On Tuesday, someone had a question about a fit in Artemis, but only > posted the project file which demonstrated the problem after being > prompted to do so. > > On Wednesday, someone had an issue about LCF fitting in Athena that is > contrary to most people's experience with the program. That person > did not bother to provide an example project file or any other > supporting information to clarify what happened. > > On Thursday, another person had an Artemis problem which was described > in a short and cryptic email. Only after being prompted 3 times to > post an example was someone able to be of help. > > Also on Thursday, we saw the third example in one week of a problem > with Artemis, but no example project file to demonstrate the problem. > > Today, we see someone with a crystallography problem, but we do not > see the actual data that would allow someone to reproduce the problem > on their own computer. > > > > Happily, on Wednesday Paul Bingham posted a clear question and > attached Athena and Artemis project files. He very quickly got two > useful answers. > > > > You do see the lesson here, don't you? If your problem cannot be > reproduced on someone else's computer, it is unlikely that you will > get a satisfying answer. > > Don't wait to be prodded. Supply the project file or crystal data > that demonstrates the problem *in your first email*. > > The so-called experts on this list, including me, really do want to > help you with your problems. But we are not mind readers. You have > to meet us half way. > > B >

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