Hello Bruce, Thank you for sharing your software. I found IFEFFIT in google and installed it recently in my MAC OSX computer. Trying to learn how to use it, I took a sample chi_k data (Al, k-edge) and played with the fitting in Artemis. One problem I can't solve by myself is that no matter how I chose the k range, r range, dr, dk, the fitting always stops at k~ 3 even though the data covers k= 1-8. So in the plot, the fit curve is much shorter than the data. Is this a plotting problem or a fitting problem? I've saved and attached the project to this email. Thank you very much for your attention. Yuan
On Friday 20 July 2007, Yuan Ping wrote:
Hello Bruce,
Thank you for sharing your software. I found IFEFFIT in google and installed it recently in my MAC OSX computer. Trying to learn how to use it, I took a sample chi_k data (Al, k-edge) and played with the fitting in Artemis. One problem I can't solve by myself is that no matter how I chose the k range, r range, dr, dk, the fitting always stops at k~ 3 even though the data covers k= 1-8. So in the plot, the fit curve is much shorter than the data. Is this a plotting problem or a fitting problem? I've saved and attached the project to this email.
Thank you very much for your attention. Yuan
Hi Yuan, First off, I want to apologize for the tardy response. Your message to the mailing list arrived at a time when I was very busy. Fortunately, I noticed the email this afternoon while reading other email. The problem you are seeing is due to the unfortunate confluence of two things: (1) the chi(k) data that you imported into Artemis does not start at k=0, and (2) you are using a very old -- version 0.8.002 -- version of Artemis. Versions of Artemis from 0.8.007 on will recognize when the chi(k) data you import is not on Ifeffit's standard k grid and interpolate. So, if you were using a more up-to-date version of Artemis, you would not have seen this problem. You have two choices to fix this problem: 1. Update the Ifeffit package on your machine and rebuild your project file. http://cars9.uchicago.edu/iffwiki/Downloads 2. If you must, for some reason, continue using the old version of Artemis, you will have to do the interpolation yourself. Artemis expects the data to be on a k-grid that starts at 0 and goes in steps of 0.05 invAng until the end of the data. The most direct method of putting chi(k) data into Artemis is to read it directly from the Athena project file. That is, using the Open file dialog in Artemis, select the Athena project file and use the Athena project dialog in Artemis to select your chi(k) data. Regards, B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Bruce (and others, if the spam filter lets this through), At 10:36 AM 8/1/2007, you wrote: 1. The most serious bug is a scenario where Artemis simply hangs when you start it. In the current version, there is bug in the place where Artemis checks for abandoned projects, resulting in the behavior described above. For now, the work-around is to close the Artemis console window then, using your file manager, look at this folder: C:\Program Files\Ifeffit\horae\stash\ In that folder you should find several folders with names like artemis.project.0 artemis.project.1 and so on. Toss each of those folders into the recycling bin and try starting Artemis. It should work now. I've found that I also have to remove the artemis.autosave file or it still won't work. Rather than putting it in the recycle bin, I put it in another folder, and then have Artemis open it as if it were a regular project. Voila! I can still recover the project... --Scott Calvin Sarah Lawrence College
Hi all, I thought you might want to know about the first results from the "EXAFS Divination Set" project I've been plugging. I don't think the results will be any surprised to the veterans on this list, but might give novices an idea of what's possible. To briefly recap, my students made up mixtures of various iron compounds in various proportions, and then I analyzed them "blind." The idea was to see how well XAFS analysis as practiced by an "expert'" can do in that kind of case. Unfortunately, unbeknownst to me, the standards were poorly prepped (i.e. they were very uneven). So these results show what can be done with poor samples. I'm planning a follow-up for this fall using an entirely new set of samples and standards prepped as carefully as we can. Presumably better samples will generate more accurate results. Nonetheless, it's nice to know what can be done under conditions that are far from ideal. The first two samples I analyzed were mixtures of known compounds in unknown amounts (iron and hematite in one case; iron, goethite, and humboltine in the other). My analysis gave the correct percent composition to within 15 percentage points in all cases. The next four samples were mixtures of two or three compounds from a list (iron, hematite, goethite, humboltine, FeO, lepidocrocite, and magnetite). I didn't know which compounds were chosen, whether there were two or three, and how much of each. In two of the four cases I correctly identified the compounds present. In one case I identified two of the three compounds, and noted that there might be a third present in a small concentration but that I couldn't confirm that; the three compounds proved to be present. In the last case I correctly identified the majority compound but misidentified the minor contributor. In three cases I found the correct percent compositions to within 10 percentage points; the last was off badly. The next three samples involved a compound completely unknown to me mixed with one or two compounds known to me. I correctly identified the class of the completely unknown compound. In two cases the percent compositions I found were correct within 10 percentage points; the other within 16. The last sample was a mixture of the complete unknown with one or two compounds chosen from the list, but without me knowing which ones. As already indicated, I correctly identified the class of the complete unknown. I also identified one of the two other compounds as definitely present and the other as most likely if there were a third compound involved. Percent compositions for this sample were not accurate. You could therefore argue that this shows that bad data yields bad results. But I'd tend to look at it another way--even questionable data can yield pretty good results. In all cases but one the substances were correctly identified (twice provisionally as a possible minor contributor), despite the fact that many of the candidate substances are structurally similar in that they involve octahedrally coordinated iron. Percent compositions were usually good rough guides, although on occasion they went astray. I'll leave these data up at http://xafs.org/EXAFS_Divination_Set and let you know when I get the high-quality follow-up project posted... --Scott Calvin Sarah Lawrence College
participants (3)
-
Bruce Ravel -
scalvin＠slc.edu -
Yuan Ping