November 2003 - Ifeffit - millenia.cars.aps.anl.gov

ifeffit and Mac OSX
by Matt Newville 03 Jul '04

03 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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Re: [Ifeffit] Scott's tutorial
by SCalvin100＠aol.com 28 Nov '03

28 Nov '03

Hi Tamas, You have a rather old version of Artemis (the current version is 0.6.009, and I wrote the tutorial with 0.6.008). Download the new version and you'll find that Artemis automatically generates a set of "Guess" variables that are reasonable to start with (unless someone changes the option described in your second paragraph.) Also, this is a good time to mention something Bruce pointed out to me. He said: "2. The first project is nice because it starts blank and walks the user through importing data and feff paths. The second project is a bit confusing because the data and feff path have to be changed from what they were on your computer to what they are on the users computer. It would be useful to start the journal with a note about that." To do this, highlight the FEFF calculation in the "Data & Paths" panel and use the option under the FEFF menu to "Change Path to FEFF", then highlight ZnO.chi and use the option under Data to "Change data file." --Scott In a message dated 11/26/03 4:29:53 PM, tamas.varga(a)chemistry.gatech.edu writes: > I'm doing Scott's posted tutorial on ZnO and found that the step-by-step > instructions in the journal for the first project part (very first fitting) > don't contain the step of creating guess parameters (amp, E0, etc.) and giving a > value to them. After selecting the R range, the tutorial goes right to > hitting the "Fit" button. I think this step (defining guess and path parameters) > is imporant to indicate for beginners. > Also, the tutorial says: > "If the fit does not appear to match what is described below, go to > Settings, then Edit Preferences, autoparams, do_autoparams, and check the red box. > Save changes for future sessions, then Quit Artemis without saving the project > and start again. If you are using a copy of Artemis which belongs to someone > else, change it back later so they don't yell at you." > I could not find the Edit Preferences option under Settings at all. Is this > a problem with my version (0.6.005)/copy? >

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Cu / CuO References?
by Norbert Weiher 26 Nov '03

26 Nov '03

Dear Friends, I am doing an XAS lecture and as example I would like to present Cu and CuO... Data for Cu I have - but not for CuO :( Can anyone give me Cu K edge spectra from this one? The Farrel Lytle DB is somehow down... Thanks for helping - and Bruce: Wish you a nice vacation if you still read this... Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)tech.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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FBox in newest horae
by Carlo U. Segre 26 Nov '03

26 Nov '03

Bruce: I have made a quick stab at packaging the newest version of horae. I noticed that FBox.pm is no longer included, however, the error in the ope file dialog now reappears. That is, the second time the open dialog routine is used, it begins at the root directory. I think that this was the reason you used a patched version of FBox. I think that I will re-include FBox.pm in my Debian packages. For documentation purposes, I am using perl-tk 800.024. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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new user contributions page
by Bruce Ravel 26 Nov '03

26 Nov '03

Hi folks, A couple weeks ago, Scott sent me a wonderful collection of Artemis project files which serve as a nifty tutorial on how to use Artemis. To quote from Scott's README file: "The tutorial is meant for people who understand the rudiments of EXAFS analysis, but have little practical experience. In other words, I assume you know what a "path" is, but are unsure of how to know what paths to include in a fit." For anyone just starting out using Artemis or anyone who would like some tips and hints from an expert user, Scott's tutorial should prove very helpful, indeed. I have started a page of user contributed materials. Here's the URL: http://leonardo.phys.washington.edu/~ravel/software/exafs/contrib.html Scott's tutorial is there. I'd certainly enjoy having more things to put on that page.... Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Scott's tutorial
by Tamas Varga 26 Nov '03

26 Nov '03

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vacation time!
by Bruce Ravel 25 Nov '03

25 Nov '03

Hi! This is my last message of the day to the mailing list. I promise! I wanted to let you all know that I will be taking some vacation time starting on Friday. I will not be near computers while I am gone (that's what makes it a vacation ;-) so I will not be responding to any email. Don't stop sending in bug reports and feature suggestions while I am away! I will read them all upon my return in mid-December. Regards, Bruce -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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phase corrections and saving files
by Bruce Ravel 25 Nov '03

25 Nov '03

Hi folks, I have received a few questions recently on the topic of saving data to column data files after doing a phase corrected Fourier transform. Both Athena and Artemis will do this. Let me explain how it works. ** In Athena, when you save chi(R) as a column data file for the current group it will save the phase corrected chi(R) if the button for central atom phase corrections is checked for that group. ** In Artemis, you can save chi(R) for the data, the fit, or any part of the fit. If a path has been chosen for the phase correction on the data page, then the Fourier transform will be done using that path's phase correction before writing out chi(R). ** Thus the rule for both programs is simple. If you select a phase correction, it will be applied before writing out chi(R). ** For both programs, chi(q) will likewise be written out with the phase correction is the phase correction is chosen. That is, if the phase correction is chosen, it will be applied to the forward transform and the backward transform will be done on that spectrum. ** Neither program writes out a phase corrected chi(k). ** Athena uses a central atom phase correction and no scattering atom correction. Artemis uses both a central and scattering atom phase correction, but only that of the path selected for the correction. The fit in Artemis is *always* done using the non-phase-corrected data and the non-phase-corrected feffNNNN.dat files. ** There was a recent discussion on the mailing list about doing phase *and* amplitude corrections. Neither Athena nor Artemis does that at this time. If you observe a situation where either program does not behave as advertised, let me know so I can fix it for the next release. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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Fwd: athena - Win 98 and Win NT
by Bruce Ravel 25 Nov '03

25 Nov '03

Brad, I am passing this along to the mailing list to see if anyone else has any better wisdom for you. But I'll take a stab. Win98: did you put "SHELL=C:\COMMAND.COM /E:4096 /P" into `config.sys', as the Win98 instructions on my and Matt's web sites suggest? Otherwise I am not familiar enough with Win98 to provide better guidance. WinNT: I have never seen the message you described and don't quite know what it means. What happens on NT if you install the stuff in to C:\Program Files\ rather than onto the F: disk? Again, I am not very familiar with NT (I've never actually haad it on a machine that I own.) Win2K: Whew! Using this seems like the path of least resistance. Anyone else have any wisdom? B ---------- Forwarded Message ---------- Subject: athena - Win 98 and Win NT Date: Tue, 25 Nov 2003 14:32:31 -0600 (CST) From: Brad Lindseth <bjl(a)ccrc.wustl.edu> To: ravel(a)phys.washington.edu Hi, We took some XAFS data a week ago at the APS. I installed athena to look at the data. Here is my report: 1. installed on Win 98: athena runs, but says "Error: Runtime exception" in the DOS window. And then a Microsoft Visual C++ Runtime library box says: Runtime Error! Program c:\ifeffit\grwnd.exe abnormal program termination. 2. installed on WinNT 4.0: in the DOS window it says: F:\PROGRA~1\Ifeffit>athena Can't load 'C:\TEMP\athena\{62B3D752-A76A-4C15-B621-8205B2665DBC}\/auto/Ifeffit/ Ifeffit.dll' for module Ifeffit: load_file:The paging file is too small for this operation to complete at DynaLoader.pm line 206. BEGIN failed--compilation aborted at athena line 59. 3. windows 2000 installation works just fine. Should I just use the win 2000 installation, or is there a simple fix for the other two? Thanks, Brad Lindseth # Brad Lindseth # Graduate Student # Washington University # Phone: (314) 977-0283 # E-mail: bjl1(a)cec.wustl.edu # Web: http://clarion.cec.wustl.edu/~bjl1/ ------------------------------------------------------- -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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new release of Athena and Artemis
by Bruce Ravel 25 Nov '03

25 Nov '03

Hi folks, I just posted a new tarball containing the source code for Athena 0.8.024 and Artemis 0.6.009. The Windows updater is not quite ready yet, but as soon as it is, Windows users will be able to update their computer. This is mostly a bug fix release, but I did add a new feature to Athena last week while I was at NSLS. You can now align data using a reference channel. The documentation has not yet been updated to reflect this new feature, but I describe it briefly on the News page for the latest release: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Alignment to a reference channel should work equally well if the reference spectrum is of the same edge as the data or of another element with a nearby edge. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 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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