April 2004 - Ifeffit - millenia.cars.aps.anl.gov

RE: [Ifeffit] Minor bugs in the new versions
by Jensen, Mark P. 28 Apr '04

28 Apr '04

Ifeffit friends, I have done several test with Athena and Artemis this afternoon, and the problem of running Athena and Artemis at the same time does not seem to be solely memory related. On two similar Win2000 machines, my old one with 128 Mb behaved as usual, only Artemis or Athena would run at one time. The first "program box" for Aretmis representing the text window would appear in the task bar, the updater program box would appear and then both would disappear instantly. I do not observe the Aretmis splash screen and she never really starts. It happens so fast that I can't read anything in the text window. This was it's "usual" behavior on the 3 computers I mentioned in the previous e-mail. This happens right from the get-go. Nothing else, other than the manditory windows services and the lab mandated anti-virus software was running. On the other machine, with 256 Mb, I could run both simultaneously. Aha! I'm on to something! When I took 128 Mb out of this 2nd computer, though, I could still start Athena and Artemis simultaneously! Rats, foiled again! Unfortunatley, I couldn't bump up that 1st computer to 256 Mb to see if that would enable both to run simultaneously on that computer. In the past, on the first computer, I have had to shut down other programs to get enough memory to run either Athena or Artemis. Maybe, people with this problem will just have to adopt my old approach and put up with this glitch. Mark ------------------------------ Mark P. Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 USA 630-252-3670 630-252-7501 FAX mjensen(a)anl.gov

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RE: [Ifeffit] Minor bugs in the new versions
by Scott Calvin 28 Apr '04

28 Apr '04

At 02:57 PM 4/28/2004 -0500, you wrote: >1. Lack of complaints doesn't mean that he problem is rare. > Mark brings up an interesting issue. I'd kind of like to get the sense of the community on this. Given that, unlike Ifeffit itself, Artemis and Athena are beta versions (a "0" starts the version number), all of us who use that software are beta testers. Thus part of our responsibilities, in exchange for getting to use really nifty and cutting-edge software, is to report bugs to Bruce. Unfortunately, reporting bugs in a responsible way is somewhat time-consuming (not nearly as time-consuming as writing the software in the first place, of course!). For example, a really minor bug which has already been discussed is the one that occasionally makes the right panel of Athena get wide. It's not something that bothers me, but it's clearly a bug. I don't feel like I'm being helpful, though, if I report to Bruce that something like this "occasionally" happens without being able to make it happen reproducibly. So I never reported it. If, on the other hand, some bug is either making it harder for me to do what I want to do, or it seems likely to cause some other unsuspecting user grief, or I can see exactly under what circumstances it occurs, I generally investigate and make a bug report. So my question is what perspective everyone (and especially Bruce) has on the trade-off between tracking down every bug so as to give Bruce full reports and spending the time actually using this great software for analysis. --Scott Calvin Sarah Lawrence College

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RE: [Ifeffit] k range
by Kelly, Shelly D. 28 Apr '04

28 Apr '04

Hi Steven, > On Tue, 27 Apr 2004, Steven Sangyun Lim wrote: > > > My question is how low can I set the k range? Is there any minimum > > range for reliable result? Please let me get out of this dilemma... > Scott and Matt both answered this question differently than I would. I guess I am very practical. If I was asking this question I would want a set of rules that would help me figure it out the k-range. So here one way to do that. 1) Look at the data in Athena to determine a good k-range to use. Here is how. 1a) As Matt suggested find a node in the chi(k) data that is around 3 inverse angstroms and set that to the kmin value. 1b) make about 6 copies of the chi(k) data set, all with the same kmin value. All the other FT values should be as you used in Artemis. (k-weight, window, dk) 1c) highlight each data set choosing a larger and larger node for kmax. Start really safe value around 8 inverse angstroms. Then pick the next node for the next copy and so forth using up all the data. For example, the first copy of the data set has a k-range [3.2 to 8.2] the next copy has k-range [3.2 to 9.3] and so forth....until the last has a k-range of [3.2 to 14] 1d) Plot the FT of the first three data sets all together (using the purple buttons to select them and the purple R button). Look at the data with the magnitude and the real or imaginary part. With a small k-range the FT signal will be very smooth curve in the magnitude, real and imaginary parts. You will tend to see two types of changes as you increase the k-range. 1) peaks will become more resolved, larger amplitude and thinner. --this is a good kind of change 2) eventually you will see noise in the FT of the data. The noise will look like high frequency pulses in the real and imaginary part of the spectra all over in R. From one data set to the next random signals will appear and disappear as you include noise in the data. --this is the bad kind of change. Keep comparing three data sets, drop the first one then add another with slightly larger k-range. You should be able to find the cross over from the good kind of a change to the bad kind of a change. 1e) By using this comparison you should be able to choose a k-range that is large but not too large. It should result in a conservative k-range to use as a starting point for your modeling. Be careful about the k-weight that you use when you make this comparison. It needs to be the same that you are using in Artemis to model the data. Larger k-weights will have smaller "good" k-ranges for the data. 2) Pull your data into Artemis. Use the good k-range that you determined from step one. 2b) Determine a model that works and look at the results including the uncertainties. 2c) Increase the k-range and compare the results. Try to decrease kmin and increase kmax. Do one thing at a time and see how the results vary. You will need to make a lot of comparisons, see how your results and uncertainties change as you adjust these values. 2d) Decide on a k-range that gives you the "best" results. 3) You may want to go back into Athena and use a standard to adjust the low k region of the chi(k) data, depending on how your FT looks at low R. This can help you stretch the kmin value. HTH Shelly

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RE: [Ifeffit] k range
by Kelly, Shelly D. 28 Apr '04

28 Apr '04

Hi Steven, In general you can use as small of a k-range as you want but you loose the number of variable that you can determine and your uncertainty in those variable gets really big too. If those trade offs are acceptable then there is no problem. I assume that you want to determine a few variables so Scotts equation is all you need to determine the minimum k-range. Artemis also lists the number of independent points in the log file. That number has to be greater than the number of variables you can determine in the fit. In practice, you need about twice as many independent points as variables to get reasonable uncertainties. But if what you say about your data is true then the metal peak is not real. In the chi(k) data the signal for each peak starts at k=0 and goes until the sigma2 term damps it out, usually around 8 to 10 inverse angstroms for oxygen, but usually much larger values for atoms with more electrons. It is physically impossible for the signal of the metal peak to only exist between 6 and 8 inverse angstroms. I would compare the data set that you are having troubles with to the other data sets that you indicated gave a consistent peak in the FT. I would bet that the troubled data set has some artifact in it that is distorting the FT. Shelly -----Original Message----- From: Steven Sangyun Lim [mailto:steven.lim@yale.edu] Sent: Tuesday, April 27, 2004 6:31 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] k range Thank you all very much for the immediate help. One more question, may I??? What can the minimum kmax be? I think it can be about 8 according to Scott. If I use kmin=2, can it be 7 or 6? The reason why I ask this is that when I plot R space with my sample, which has been reduced and needs to be confirmed if there is any metal cluster, the metal peak shows at kmax=8, but it disappears at kmax=6 or 7. At kmax=10, it is hard to tell because the spectrum is very noisy (it shows split peak). When there are extremely small metal clusters (even at CN=0.6), I can see a distinct metal peak that does not change no matter what k range and weight I use. I wonder any further advice can be suggested. Thank you for your help in advance. Steven

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Substrate material question
by Paul Fons 28 Apr '04

28 Apr '04

OK, I admit this isn't an athena question (but it is about how to take the raw data for it!). I want to do biaxial strain measurements. The idea is to deposit a thin film of the material to be investigated on a substrate and then deform the plate with a form of cylindrical symmetry. One can then solve for the stress of a plate using elasticity theory. The twist is that I need a plate that is stiff and (surprise) x-ray transparent ... and heat resistant to about 250 C. Kapton would be a wonderful choice, but is only made in thicknesses up to 175 microns (hardly stiff enough). There must be someone out there in the collective iffeffit world who knows of an appropriate material. Doing some web surfing, I came across another product by DuPont called Vespar that *may* be available in thicker forms. The specs I am looking for are: a thin (semiconducting) film has to stick to the surface, heat resistant to <=250 C, thick enough to be elastically stiff, and x-ray transparent. Any suggestions? Thanks for any help that may come my way in advance! Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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k range
by Steven Sangyun Lim 27 Apr '04

27 Apr '04

Thank you all very much for the immediate help. One more question, may I??? What can the minimum kmax be? I think it can be about 8 according to Scott. If I use kmin=2, can it be 7 or 6? The reason why I ask this is that when I plot R space with my sample, which has been reduced and needs to be confirmed if there is any metal cluster, the metal peak shows at kmax=8, but it disappears at kmax=6 or 7. At kmax=10, it is hard to tell because the spectrum is very noisy (it shows split peak). When there are extremely small metal clusters (even at CN=0.6), I can see a distinct metal peak that does not change no matter what k range and weight I use. I wonder any further advice can be suggested. Thank you for your help in advance. Steven

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k range
by Steven Sangyun Lim 27 Apr '04

27 Apr '04

Dear all, I always appreciate the big useful help from everyone. I have a basic question. I think a similar question has been arose long time ago. (But I lost the mail..) My sample has very small amount (under 1 wt%) and cluster size (< 1nm). The spectrum is always noisy at high k range, so I use usually k=2 to 10 or 12. It depends on the noise of the spectrum. Of course, if I go further down, it is better. My question is how low can I set the k range? Is there any minimum range for reliable result? Please let me get out of this dilemma... Thank you always. Steven

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RE: Ifeffit Digest, Vol 14, Issue 23
by Aria 27 Apr '04

27 Apr '04

Hi, Bruce For the first question, after I answered 'yes'. Artemis will run well without problems. But after running fits for four (sometimes even three) times, it will crash again. And the next cycle begins. As for reproducible, only after I finished the updates, it will crash every four or three fits, no matter what fits I am running. The fits paths included might be around 100. By the way, I did not notice if Artemis posts a message or not before. But this time, it do pop up a message at the first time I run the fit (not at the time it crashes). This is the message I got: # This file created at 11:01:54 on 27 April, 2004 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.5 The following message was trapped by Artemis on a SIGWARN: ArtemiswarnC:\Program Files\Ifeffit\horae\stash\ARTEMIS.TRAPCODE(0x3525f58) at artemis line 1491 main::__ANON__('Tk::Error: Can\'t locate utf8.pm in @INC (@INC contains: C:\DOCU...') called at blib\lib\Tk.pm (autosplit into blib\lib\auto\Tk\Error.al) line 402 Tk::Error('MainWindow=HASH(0x394d430)', 'Can\'t locate utf8.pm in @INC (@INC contains: C:\DOCUME~1\VINCEH...', '[\&main::__ANON__]', '(menu invoke)') called at /PerlApp/Tk.pm line 340 eval {...} called at /PerlApp/Tk.pm line 340 Tk::MainLoop() called at artemis line 1627 Here attached is the file. Thanks a lot, Aria ------------------------------ Message: 2 Date: Mon, 26 Apr 2004 17:04:59 -0400 From: Bruce Ravel <ravel(a)phys.washington.edu> Subject: Re: [Ifeffit] Artemis Crashed too often To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200404261704.59318.ravel(a)phys.washington.edu> Content-Type: text/plain; charset="iso-8859-1" On Monday 26 April 2004 04:27 pm, Aria wrote: > I began to use the old version of Artemis in last September, and did not > update till days ago. But after the installation, Artemis crashed very > often. After running four fits, it will crash without any reasons (I did > not close the graphics window). And when I restart the Artemis, sometimes > it will give out information like: 'There seems to be a large number of > abandoned project folders. This might be due to past program crashes or > other past problems. I can clean these up at this time.' I am not sure if > it happens to others. I work in Windows XP platform. You seem to be reporting two different problems here, but have not given me enough information to do anything useful about either one. 1. What happens when you answer yes to the question about cleaning up abandoned project folders? Does Artemis crash again right after that? How about the next time you start Artemis? 2. It is really not adequate just to say "Artemis crashed very often." If you do not give me enough information to reproduce the problem myself, then I cannot fix whatever is causing the crash. Indeed, I cannot even begin to search for the problem because you haven't told me anything about it. Please read this page carefully: http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html and the consider trying your bug report again. If Artemis beeps and posts a message to the echo area about a TRAP file, please send me the specified file along with a description of how you got to the situation. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Artemis Crashed too often
by Aria 26 Apr '04

26 Apr '04

Hello, I began to use the old version of Artemis in last September, and did not update till days ago. But after the installation, Artemis crashed very often. After running four fits, it will crash without any reasons (I did not close the graphics window). And when I restart the Artemis, sometimes it will give out information like: 'There seems to be a large number of abandoned project folders. This might be due to past program crashes or other past problems. I can clean these up at this time.' I am not sure if it happens to others. I work in Windows XP platform. Regards, Aria

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Re: [Ifeffit] Re: A question about the new Artemis version
by Scott Calvin 22 Apr '04

22 Apr '04

Hi Matt, FYI, the path limit in the current version appears to be set to 256 paths. --Scott Calvin Sarah Lawrence College At 02:53 PM 4/1/2004 -0600, you wrote: >The latest version of the ifeffit_10.dll windows binary should >support 1024 paths, and 16 data sets. You can see what these >limits are for your system by typing > show &max_paths, &max_data_sets > >at the command line prompt. The limits are set to their current >values so that Ifeffit+Athena takes well under 64Mb RAM. But these >limits are set in one place in the source code (src/lib/consts.h) so >that you can easily change them and recompile if you need these >limits to be higher. max_paths can be increased easily up to 9999, >but going above that would take more work. >>

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