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

Substrate material question
by Paul Fons 27 Apr '04

27 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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new versions of my programs
by Bruce Ravel 22 Apr '04

22 Apr '04

Hi folks, I have just finished the new release of my data analysis programs: Athena 0.8.027 and Artemis 0.7.003. This release contains mostly bug fixes and feature enhancements. As you may recall, last month's release of Artemis generated a very large amount of traffic on this list due to several problems surrounding the new project file format and other file management issues. I have addressed almost all of the problems that were reported and am cautiously optimistic that this release of Artemis will be much more solid than the last. There is one significant new feature in this release -- the program Hephaestus, which will be a permanent part of future releases. Hephaestus replaces the Atoms Periodic Table and expands greatly upon its functionality. I will describe Hephaestus in more detail in a message later this morning. Source code tarballs are already available on my web site and at SourceForge. The Windows updater package will be available soon. Change logs with all the details of the new features of Athena and Artemis are on my web site. Lots of people helped out this time with excellent suggestions and bug reports. Special thanks to Mauro Ravezzi, David Barton, Peter Pfalzer, Gerrit Schmithals, Stanislav Stoupin, and Shelly Kelly. Regards, 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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Re: Truncate, Post-edge Athena Issues
by Bruce Ravel 21 Apr '04

21 Apr '04

On Tuesday 20 April 2004 11:56 pm, Barton, David (DG) wrote: > One final question. I often see a strong discontinuity near the edge > energy in the background subtraction. The attached Athena project clearly > shows this discontinuity, any thoughts about this? Dave, I am CCing the answer to this one to the mailing list. The background spline is evaluated between the energies (or k values) specified. Outside that range the spline is not evaluated at all. To make the arrays conatining the data and background spectra easier to handle when interacting directly with Ifeffit, Matt wisely chose to make the background array the same length as the data array. At energies within the spline range, the background array contains the background spline. Outside the spline range, that background array contains the original data. Not only does this make the arays the same length, but it makes computation of chi(E) completely trivial -- you can just subtract the background array from the data array point by point. If the first or last few points of the spline are not near in value to the data (which can happen since a spline can be poorly constrained at the ends), then the plot of the data and background arrays will be as you described. The background array will have a discontinuity, but that is not a bug. Regardless of the constraint of the spline near its ends, the criterion for choosing the spline is met. That is, the spline is always chosen to minimize the low-R Fourier components (possibly with respect to a standard spectrum). Sometimes this minimization results in a spline that deviates from the data at the ends. Constraining that deviation is the purpose of the spline clamps. > I typically have ignored this since it is outside the EXAFS fitting > region and the XANES background subtraction routines are not > affected by it. That is completely correct. HTH, 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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Athena Minor Error
by Norbert Weiher 21 Apr '04

21 Apr '04

Hey Bruce, I found a minor error in athena: When want to select the spline range for my spectrum and accidentially press the "k" button (but have the spectrum plotted in E), athena crashes as soon as I click on the graph to select some value. Its not bothering much (actually I should be aware of pressing the right button - I know :)), just wanted to tell you. Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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noisy spectrum and AUTOBK
by gabriel rosenblum 20 Apr '04

20 Apr '04

Hi all. Sorry for not being specific. I am trying to do background removal with AUTOBK. The parameter emax is present at autobk.inp file under the UWEXAFS package. Emax � means the region after the edge in the xmu file to be taken by AUTOBK to perform the spline. For example, if emax is set to 400 eV, it means the spline and the subtraction will be carried 400 eV over the edge. After the subtraction I FT the data and observe chi(R ). I guess the noise problem is more pronounced 350 to 550 eV over the edge, and not near the edge. However I will sure try the recipe offered by Shelly. Still waiting for an answer. Thanks. Gabi. __________________________________ Do you Yahoo!? Yahoo! Photos: High-quality 4x6 digital prints for 25� http://photos.yahoo.com/ph/print_splash

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