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

Re: Ifeffit Digest, Vol 20, Issue 11
by Michel Jaouen 13 Oct '04

13 Oct '04

>On Wednesday 13 October 2004 10:15 am, Stefano Ciurli wrote: >> Hello David, >> >> >I have tried horae_update... but it doesn't work... in fact, Artemis >> > remains stuck to version 0.7.007, Athena to version 0.8.029 and so on.. As >> > if there was no update! I really don't know what I can do to make Artemis >> > and Athena work. >> >> i confirm that the horae_update script (run yesterday on my G4, not >> G5 - lucky you) yields the same versions of Artemis and Athena that >> you mention here. >> Stefano > >David, Stefano, > >What you guys say confuses me. When I run horae_update (not on a Mac, >but I don't see why that should make a difference) it downloads >horae-045, which contains athena 0.8.033 and artemis 0.7.011. The >horae-update script writes a log file which may be useful to me in >figuring out why it is behaving differently for you than it does does >for me. > >If it is behaving somehow wrong for you, you could always go to >SourceForge, download the package, unpack it, and do the "perl >Makefile.PL; make; sudo make install" incantation by hand. (The >script just automates those steps, it does not do anything different.) I confirm what Bruce says: running horae_update_042 (sudo horae_update) on my G5 (I haven't yet installed 045) fixes all my previously mentioned problems. All run smoothly. However, what makes me more puzzeling is that I don't obtain the same results (using of course all the same parameters) from Artemis compared to those I have found using Feffit in command line (Unix version). Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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rpm packages of horae, ifeffit, sixpack
by Carlo U. Segre 10 Oct '04

10 Oct '04

Hello All: I realized that there was a low cost method for me to generate *.rpm packages from my *.deb packages. I make no promises on how these will install or work and I really won't be able to do much to fix them since they are generated automatically but please let me know if they are useful or not working. You can get all the programs in my x-ray software archive at: http://fermi.phys.iit.edu/debian/rpm/ If anyone knows how best to make these available in an automated way please let me know and I will try to implement it. BTW: all these packages are comversions from the Debian "unstable" tree, which has the latest libraries and files. This is most likely the best version to work with Fedora. Cheers, 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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Re: Iffefit for Mac OSX 10.3
by Matt Newville 08 Oct '04

08 Oct '04

Hi Ann, I think this should have been to the Ifeffit list: On Thu, 7 Oct 2004, Ann Liang wrote: > Hi Bruce or Matt, > > I encountered some problems with athena when I recently switched my > workstation from PC to Mac. The graphic window didn't show up at all which > made it impossible to process any data. Could you please provide me some > guidance on this issue? I assume you installed the Mac installer (ifeffit-1.2.6_Mac10.3.dmg). I'm not sure what the problem is, but I'd recommend these steps: First, install Aquaterm from http://aquaterm.sourceforge.net/ . That might 'just fix' the problem. If it doesn't, edit the file /Applications/Ifeffit/bin/iff_init.sh to read (line 7) export PGPLOT_DEV=/XS instead of export PGPLOT_DEV=/AQT (Make sure to leave no extra space around the = sign). That will tell Ifeffit to use X-Window graphics instead of Aquaterm. The Aquaterm device is a little bit nicer, but the X-Windows one should definitely work. If you're running athena by clicking the icon, that should be enough. If you're running athena by typing 'athena' in a Terminal, _and_ you're using the tcsh shell, you should also edit /Applications/Ifeffit/bin/iff_init.csh to read setenv PGPLOT_DEV /XS (Here, the space is necessary and there is no = sign!! The syntax for these two shells is different, but the meaning is the same). Hope that's enough, and sorry for the pain. If not let me know, --Matt

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New user to EXAFS
by William Bisson 07 Oct '04

07 Oct '04

Dear all, I am a new user to EXAFS and I am currently experimenting with the anaylsis software available. Does anyone know how to convert raw data collected from Daresbury, UK, station 7.1 to be read by IFEFFIT? I shall be grateful for any help Kind Regards William Bisson

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Athena bug?
by Carlo U. Segre 07 Oct '04

07 Oct '04

Bruce, Norbert: I tried to duplicate norbert's error with version 044 of horae. I used a multielement detector file frm MR-CAT and I noticed no problems or errors. I also tried Norbert's file and I noticed a couple of things. 1. Athena cannot find the column titles. In the MR-CAT data file, there is no problem with this. I tried removing the "#L " at the front of the title line in Norbert's file but still the titles cannot be parsed. 2. The first time I try to import the file, I have no errors apart form the warning that the data is not in order and must be sorted (the first line is the culprit). If I try to import the same file, the error occurs and the channel selection box is badly deformed (most buttons are missing and only 3 channels are noted). 3. I removed the out of order line (the first data line) and the imports worked fine more than once. There are still no titles. It looks like there are two issues here. One is that the out of order first line somehow messes up some internal variables in the program. In the past the "sort data" function seemed to work fine. The second issue is that Norbert's file is not compatible with Athena's parsing of column titles. I really don't know what the parameters are here so I can't say what the problem is but I will try to compare the MR-CAT multilelment files with this one to see what is going on. Norbert, it looks like you can prvent problems temporarily by jsut deleting the first data line. 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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Athena bug?
by Norbert Weiher 07 Oct '04

07 Oct '04

Bruce, I just upgraded to the newest package today - since then, athena does not like to import data files anymore... When I select a data set (which was possible to import with the older version), The "channel select" box appears totally small, and ATHENA dumps this error to the screen. I included a data file to test for your convenience. The channels to import are (10-22)/4 (fluorescence data). Hope its not a machine-typical thingie :) I still have the SuSE 8.2 installed and run on the latest IFEFFIT. Ah, sometimes importing the first set works (e.g. when reading multiple sets at once), but then it automatically crashes at the next set. Cheers, Norbert Nasty codebabbling follows... Athena0.8.033warn/home/weiher/.horae/stash/ATHENA.TRAPCODE(0x911ce90) at /usr/bin/athena line 1364 main::__ANON__('Tk::Error: Can\'t use string ("Sort data") as a HASH ref whil...') called at blib/lib/Tk.pm (autosplit into blib/lib/auto/Tk/Error.al) line 402 Tk::Error('MainWindow=HASH(0x9c14628)','Can\'t use string ("Sort data") as a HASH ref while "strict r...','main::read_raw at /usr/bin/athena line 3786','main::read_file at /usr/bin/athena line 3537','main::__ANON__ at /usr/bin/athena line 453','(command bound to event)') called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 eval {...} called at /usr/lib/perl5/site_perl/5.8.0/i586-linux-thread-multi/Tk.pm line 340 Tk::MainLoop() called at /usr/bin/athena line 1420 -- 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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horae 043 tarball
by Bruce Ravel 06 Oct '04

06 Oct '04

Hi folks, I just put a new tarball on SourceForge and on my web site. This new tarball will be of interest to the people following the development version of Artemis. There are only small changes to the stable codes in this tarball and I will not be building new Windows executables. This new tarball is really only about the development version of Artemis. I am almost finished with the features I am planning for this round of development. (See the Artemis page on my web site for the complete list of features planned for this round of the development branch.) Once I polish off the last major feature, we will go into a testing period. Once I am content, I'll build some trial Windows executables. Once I am content with that, I'll merge the new feature back into the stable branch. Among the new features in the development branch: 1. A revamped feff interpretation page with new functionality 2. A revamped atoms page with new functionality 3. Major improvements to the fit history system 4. Direct import of data from Athena project files 5. A new type of parameter on the GDS page -- an "after" parameter is like a def in that it takes a math expression, but it is not part of the fit and is evaluated only after the fit finishes and then is recorded in the log file 6. Lots of bug fixes and minor feature enhancements. Lots of neat new stuff. Have fun and let me know what goes splat. B P.S. Carlo, FYI, two new files: Ifeffit/lib/artemis.doc/artemis_fitinfo.pod and Tk/TextUndoQuiet.pm. -- 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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horae 044
by Bruce Ravel 06 Oct '04

06 Oct '04

Okee dokee. This time for sure! I fixed the bug in the install script. The TextUndoQuiet.pm file should end up in the right place now. New tarballs are at SF and on my web site. Let me know if it doesn't or if some other problem crops up. Thanks, Igor. Then... On Wednesday 06 October 2004 06:00 pm, Adam Webb wrote: > Bruce, > > FYI I get the same thing. Also the file permission is not set to > executable. I only mention it because the other files in the Tk directory > are set that way so TextUndoQuiet.pm stands out. That shouldn't matter, but thanks for letting me know, Adam. 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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horae 043
by Igor Frota de Vasconcelos 06 Oct '04

06 Oct '04

Hi Bruce, I just installed the newest version of Horae and when I try to start Diana it complains that: Can't locate Tk/TextUndoQuiet.pm in @INC (@INC contains: /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/Tk/widgets.pm line 14. at /usr/bin/diana line 61 BEGIN failed--compilation aborted at /usr/bin/diana line 67. I could a problem with my system but since the previous version was working fine, I thought I should report. I use Fedora Core 1 and Tk-800.024.tar.gz. Thanks, Igor -- IGOR F. VASCONCELOS Department of Physics University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556 USA phone: (1 574) 631 5650 fax: (1 574) 631 5952 e-mail: idevasco(a)nd.edu www.nd.edu/~idevasco

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Is artemis running on G5 Mac,
by Michel Jaouen 06 Oct '04

06 Oct '04

Hi, I'm trying to run artemis on my Mac on which one I have used Matt's installer (ifeffit-1.2.6_Mac10.3.dmg). Actually, I'm unable to run a two shells fit , even for Cu. Therefore, I go back to the 1st shell alone fit: it works (idem for Zr, a crazy stuff because for hcp we need two shells, but anyway. BUT EVEN for a ONE shell fit it returns an error: The following message was trapped by Artemis: Artemis0.7.007warn/Users/mjaouen/.horae/stash/ARTEMIS.TRAPCODE(0x1e3e9d4)/U sers/mjaouen/.horae/stash/artemis.pro ject.1/ at /Applications/Ifeffit/bin/artemis line 1564 main::__ANON__('Use of uninitialized value in numeric lt (<) at /Applications...') called at /Applicatio ns/Ifeffit/bin/artemis line 8988 main::check_path('HASH(0x1ddc568)') called at /Applications/Ifeffit/bin/artemis line 8861 main::write_paths('GLOB(0x140c07c8)','data0',1,'all','HASH(0x1de42e8)') called at /Applications/Ifeffit/ bin/artemis line 9602 main::generate_script(1) called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 247 Tk::__ANON__('Tk::Button=HASH(0x1eddaf4)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/B utton.pm line 111 Tk::Button::butUp('Tk::Button=HASH(0x1eddaf4)') called at /Library/Perl/5.8.1/darwin-thread-multi-2level /Tk.pm line 406 eval {...} called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 406 Tk::MainLoop() called at /Applications/Ifeffit/bin/artemis line 1766 This message was dumped to a file: /Users/mjaouen/.horae/stash/ARTEMIS.TRAP Please include that file along with your explanation when you make a bug report. What is strange is that I can save the project in such a condition, eg artemis behaves as if there is no error (the artemis palette is active while it is empty for a 2 shells fit and inactive, I cann't close it for exemple by cliquing on the red button: all windows are frozen)! Looking at the the monitor for activity, I see that Perl was using 99% of the CPU! In fact artemis crashes when trying to write the log file. The only way to go out from is to kill artemis in the X11 terminal window. I must say that I have asked to one of my friend in Paris (G. Hug) to make the install on his machine and he experienced exactely the same punition! Both we are using G5 based Mac. I suspect Perl and/or Tk to be not fully compatible with this CPU. Therefore my question is simple: has anybody been able to run artemis (version 0.7.007) on G5? Must I update horae and how to do it? Cheers Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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