[Ifeffit] Problem writing Feff 9 input
I have a CIF file that I checked using Mercury to insure that the structure was correct. When I run ATOMS and then use the FEFF.INP file it produces, there seems to be a mistake made. When I view the structure using the JMOL application in FEFF, there are atoms in the wrong locations. FEFF will not run, as atoms are too close together. I tried to remove the atoms, from the list of atoms too close together generated by the executing list, but it does not solve my problem, and the atoms are still in the wrong place. I then tried to cut and paste the coordinates in to a FEFF input file, as was shown how to do when working with non-crystalline materials. This doesn’t work. I also tried to redo the example that Bruce showed, which also won’t open in FEFF, a problem with line 25, though I have been unable to figure out what that problem is. Is there a difference in writing input files for FEFF9? I am at a loss as to why simply cutting and pasting the example doesn’t work. Also, when I try to add coordinates to the FEFF.INP file, I get what looks like a ball in JMOL, and the feff program runs continuously in a loop, with no real calculations being performed. Any help would be greatly appreciated! Thanks, Ted Shaner Department of Chemistry Tulane University Office: Percival-Stern 5016 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] asking questions effectively (yes, *you* need to read this email)
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Athena: problems with LCF
Nina, I see that no one has responded to this email, which arrived while I was on travel. As I alluded to in my email from earlier today, yours was the sort of question that is very hard to answer. While I am sure that your explanation was clear to *you*, it is less so for the rest of us. If you can document your problem -- preferably in a way that one can reproduce on their own computer -- you will be much more likely to get a useful answer. As for the algorithm, it is as simple as the name implies. The standards are added up according to their weights and compared to the unknown. The weights are the variables in the fit. If you open the Ifeffit buffer from the Edit menu, you can watch the ifeffit commands as they are being sent to the Ifeffit library. This will show you (albeit in a rather verbose manner) how the data are being prapred for the fit. The call to the minimize() function then sends the fit off to a standard Levenberg-Marquardt non-linear, least-squares minimizer. You can also examine the Athena source code at http://cars9.uchicago.edu/svn/horae/trunk/athena_parts/lcf.pl but you will find that the encoding of the fit is interspersed in a rather confusing way with the graphical layout. B On Wednesday, August 03, 2011 08:53:19 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. 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, results were disappointing despite all spectra were carefully energy calibrated and normalized, so I decided to create simple mathematical ternary mixtures by summing up the spectra of the individual reference spectra (edge step normalized) and tried the fitting again to exclude mixing-failures and check sensitivity of LCF with the idealized spectra. Unfortunately, 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. Thanks a lot! Wishes, Nina ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
