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

(no subject)
by Gael Poirier 19 Oct '04

19 Oct '04

Hello, I'm a new user of FEFFIT programs and actually I have some problems with Athena (version 0.8.032). In fact, when I try to import data files, the program apparently identificate the commas (,) as a column separator. I think that my input file is correct: ASCII data and each column separated by a space. What can I do to resolve it?? Thank you very much for your help Gaël Poirier Universidade Estadual Paulista (UNESP) Brazil

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RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 14 Oct '04

14 Oct '04

Hi I fear it doesn't work for me. I have untared the Horae-045.tar file in the Ifeffit directory. And when I type 'perl Makefile.PL', the installation script crashes and says 'Could not open /config/Config.mak file for reading'. The Greek gods may not be with me! I'll wait for the next tarball... Thanks a lot in adavance! David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Bruce Ravel > Envoyé : mercredi 13 octobre 2004 19:23 > À : XAFS Analysis using Ifeffit > Objet : Re: [Ifeffit] Is artemis running on G5 Mac, > > On Wednesday 13 October 2004 12:49 pm, Matt Newville wrote: > > Hi, > > > > OK, I agree that a simple 'horae_update' also did not work to > > update thes for me. It appears that the new codes are built > > but not installed. This definitely did work for me: > > tar xvzf horae-045.tar.gz > > cd horae-045 > > perl Makefile.PL > > make > > sudo make install > > > > I believe that 'sudo horae_update' will also work. > > > > --Matt > > > > PS: Oddly, without the 'sudo', horae_update did not give a > > warning about installing as root. I got largely the same log file > > as Stefano, and also got this on the screen: > > > > print() on closed filehandle OUT at /Applications/Ifeffit/bin/horae_update > > line 263. > > > > perhaps this is printed to STDERR not STDOUT?? it's not in > > horae_update.log. Anyway, this is where the warning about > > trying to install as someone other than root is. > > > > The horae_update could probably use other improvements, as > > horae_update --force --file=horae-045.tar.gz > > > > still attempts to download the tarball, requires it to > > be named 'horae-045.tar.gz' and then deletes it. > > What you said is exactly right. There was a problem that had > horae_update complain about a closed file handle and exit just before > doing the "make install" step. I think I fixed it and asked Stefano > to give it a try. > > I'll post a fix tomorrow (I hope) and the fix will be included in the > next tarball. > > 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/ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] delR and delE
by Kelly, Shelly D. 14 Oct '04

14 Oct '04

Ritika, delr and Eo are correlated. So you can (1) force delr to the same for two paths with different Eo-values, or (2) use two different delr-values with one Eo-value. Most prefer the second choice over the second choice. Also, Eo is important at low k-values. If you move your k-range that you use in the FT of your data you might find a different Eo value, or that only one Eo is needed with a shorter k-range than with a longer k-range. I do not think that you model is "okay" with three Eo values. How much does EO differ? Usually Eo is the last button I turn on when I try to make a model fit the data. Large Ezero values (> 10 eV) are common if you have a poor model. So use only one Eo at the beginning. Often I just set it to zero, and then when the model gets close, try to add one or two more to really get it right on. I would try only one Eo first. Let delr vary for all the paths and change the k-range. See how small the k-range needs to be before you can fit the data with only one E0 value. 1.9 Angstroms is a short distance. It would seem more reasonable to me that you might need two Eo values. One for this short shell and then one more for all the other shells. Give these things a try and tell us how it goes. Shelly > -----Original Message----- > From: ritika.uppal(a)yale.edu [mailto:ritika.uppal@yale.edu] > Sent: Wednesday, October 13, 2004 2:50 PM > To: Segre, Carlo U.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] delR and delE > > > > I have 3 different values of Eo for the fit. 2 for the first > shell and > the 3rd for the rest of the paths. Actually the bond distance > of the 6 > oxygens in the first shell differs. 3 of them have a bond length of > around 1.9 A and the other 3 around 2.2 A. So using one value of Eo > does not fit the second peak very well. > > Ritika > > > Quoting "Carlo U. Segre" <segre(a)iit.edu>: > > > > > delR is just the deviation from the distance you used in > the feff.inp > > file to generate the paths. It can be positive or negative > depending > > on > > > > whether these atoms are closer or further away from the > central atom. > > > > By delE, do you mean Eo? When you say two values, do you mean > > different values for two different shells? > > Carlo > > > > > > On Wed, 13 Oct 2004, ritika.uppal(a)yale.edu wrote: > > > > > Hi guys, > > > I have a few questions about the fitting parameters. the delR for > > my > > > fit has a negative value. Is that wrong or its possible to have a > > > negative value?? and also for the first shell, I have 2 values of > > del > > > E. Does that mean that the model I am using is not a good one?? > > > > > > Thanks for all your help > > > Ritika > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > -- > > 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 > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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RE: [Ifeffit] delR and delE
by Kelly, Shelly D. 13 Oct '04

13 Oct '04

See below for clarification.. > -----Original Message----- > From: Kelly, Shelly D. > Sent: Wednesday, October 13, 2004 3:10 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] delR and delE > > > Ritika, > > delr and Eo are correlated. So you can (1) force delr to the > same for two paths with different Eo-values, or (2) use two > different delr-values with one Eo-value. Most prefer the > second choice over the second choice. This should read "Most prefer the second choice over the first." > > Also, Eo is important at low k-values. If you move your > k-range that you use in the FT of your data you might find a > different Eo value, or that only one Eo is needed with a > shorter k-range than with a longer k-range. > > I do not think that you model is "okay" with three Eo values. > How much does EO differ? Usually Eo is the last button I > turn on when I try to make a model fit the data. Large Ezero > values (> 10 eV) are common if you have a poor model. So use > only one Eo at the beginning. Often I just set it to zero, > and then when the model gets close, try to add one or two > more to really get it right on. > > I would try only one Eo first. Let delr vary for all the > paths and change the k-range. See how small the k-range > needs to be before you can fit the data with only one E0 value. > > 1.9 Angstroms is a short distance. It would seem more > reasonable to me that you might need two Eo values. One for > this short shell and then one more for all the other shells. > > Give these things a try and tell us how it goes. > > Shelly > > > -----Original Message----- > > From: ritika.uppal(a)yale.edu [mailto:ritika.uppal@yale.edu] > > Sent: Wednesday, October 13, 2004 2:50 PM > > To: Segre, Carlo U.; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] delR and delE > > > > > > > > I have 3 different values of Eo for the fit. 2 for the first > > shell and > > the 3rd for the rest of the paths. Actually the bond distance > > of the 6 > > oxygens in the first shell differs. 3 of them have a bond length of > > around 1.9 A and the other 3 around 2.2 A. So using one value of Eo > > does not fit the second peak very well. > > > > Ritika > > > > > > Quoting "Carlo U. Segre" <segre(a)iit.edu>: > > > > > > > > delR is just the deviation from the distance you used in > > the feff.inp > > > file to generate the paths. It can be positive or negative > > depending > > > on > > > > > > whether these atoms are closer or further away from the > > central atom. > > > > > > By delE, do you mean Eo? When you say two values, do you mean > > > different values for two different shells? > > > Carlo > > > > > > > > > On Wed, 13 Oct 2004, ritika.uppal(a)yale.edu wrote: > > > > > > > Hi guys, > > > > I have a few questions about the fitting parameters. > the delR for > > > my > > > > fit has a negative value. Is that wrong or its possible > to have a > > > > negative value?? and also for the first shell, I have 2 > values of > > > del > > > > E. Does that mean that the model I am using is not a good one?? > > > > > > > > Thanks for all your help > > > > Ritika > > > > _______________________________________________ > > > > Ifeffit mailing list > > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > > -- > > > 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 > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit >

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RE: [Ifeffit] Is artemis running on G5 Mac,
by Stefano Luciano Ciurli 13 Oct '04

13 Oct '04

Hi all, sorry Bruce but I had to leave the office and have had no time to try your new script. I wil lgive it a try tomorrow afternoon (loaded with teaching around here). I'll let you know. Ciao, Stefano

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horae-045
by Bruce Ravel 13 Oct '04

13 Oct '04

Hey, It's been a busy week. I just posted another new tarball. This fixes: 1. The bug Norbert reported in Athena's file selection dialog (this bug does not exist in the current build of the windows executable, so there is not pressing need to update it) 2. The problem Igor reported with importing project files from the previous version of the development branch of Artemis 3. A bug in the build scripts that resulted in not being able to use the Atoms page in the development branch of Artemis. New tarballs are at SourceForge and at my web site. As before, this release is mostly intended for people following the development branch of Artemis. Thanks to Norbert, Igor, and Carlo for their help. Hopefully this one will work better than the last two...... ;-) 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 : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 13 Oct '04

13 Oct '04

Hi all 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. If anyone has any idea, one is welcome. David > -----Message d'origine----- > De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] De la part de Matt Newville > Envoyé : dimanche 3 octobre 2004 05:22 > À : XAFS Analysis using Ifeffit > Objet : Re: [Ifeffit] Is artemis running on G5 Mac, > > Michel, David, > > Have either of you tried upgrading Artemis using horae_update? I > don't know that it will help, but it might.... > > The message Michel sent looks like a Perl error that wouldn't be > processor dependent, so I'm not sure what's going on. All I can > say is that Artemis works for me on a G4. I'm perfectly willing > to believe that my system has something different from or not > included in the dmg (I try hard for this to not happen, but > realize that 'works for me' is not always sufficient). > > Can anyone else using a Mac report on how Artemis works for them? > Thanks, > > --Matt > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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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 05 Oct '04

05 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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RE : [Ifeffit] Is artemis running on G5 Mac,
by POGER David 202545 01 Oct '04

01 Oct '04

Hi I use a Mac IBook and I have the same problem. I can't use the Mac version of Artemis (I use Matt's installer as well, ifeffit-1.2.6_Mac10.3.dmg). Artemis crashes and the only way to close it is killing the job in the X11 window. Cheers David -----Message d'origine----- De : ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] De la part de Michel Jaouen Envoyé : vendredi 1 octobre 2004 16:09 À : ifeffit(a)millenia.cars.aps.anl.gov Objet : [Ifeffit] Is artemis running on G5 Mac, 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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Re: [Ifeffit] New user to EXAFS
by Bruce Ravel 30 Sep '04

30 Sep '04

On Thursday 30 September 2004 10:16 am, ritika.uppal(a)yale.edu wrote: > Hi Bruce, > Thanks for the reply. I have attached the artemis project file with > this email. Ritika, I'll add this to my list of things to look at today and get back to you when I have some information. 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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Fitting Problems via Artemis
by hsnuboy＠ksu.edu 27 Sep '04

27 Sep '04

Dear All, Greeting.This is Yu-Chuan. After struggling a long time, I just felt a little bit progress in the fitting program. However, there are still some questions confused me. 1. What's the meaning and purpose of "Fit Background" in Artemis? I know the backgound as "bare atom" in EXAFS theory. So, what kind of situation we need to use this function? 2. Is that possible for the Debye-Waller factor(sigma^2) be negative? Actually, I am not so sure about the physical meaning for that. Just know its a kind of thermal vibration. 3. Sometimes, The results obtained from Artemis seems not the same. Says, the guess parameters and uncertainties may be varied even if you input the same data for different time.Has anyone met this problem before? Sincerely yours, Yu-Chuan Lin Graduate Student and Reseach Assistant Kansas State University

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RE: [Ifeffit] Fitting Problems via Artemis
by hsnuboy＠ksu.edu 24 Sep '04

24 Sep '04

Dear Norbert, Thank you for your reply. About the DW factor, I think the problem may be another scatterer. Due to the self adsoption, I use Dr. Booth's correlation equation to correlate my data. Is that the way I obtain minus DW factor? The other parameters work great, except DW factor for about -0.001(the uncertainties is +/- 0.00094). Do you thinnk is that possible cause by self absorption or other effects? Thank you for your time. Sincerely, Yu-Chuan On Fri, 24 Sep 2004, nobert.weiher(a)chem.ethz.ch wrote: >Concerning the DW factor, you are right that it accounts for >vibrational disorder in the sample (in the ideal case). If, however, >your material has a high structural disorder by itself, DW factors >might become high due to this. The general behaviour is that they >should increase with temperature of the measurement. A negative value >is physically not possible, and usually means that something is wrong >with your fitting path. Possible things to check are >- did you use proper reference paths (i.e. were they correctly >computed by feff) >- is it maybe another scatterer which contributes to the EXAFS at this >part.

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RE: [Ifeffit] Fitting Problems via Artemis
by Weiher, Norbert 24 Sep '04

24 Sep '04

Dear Yu-Chuan, I quickly comment on the last two points you mentioned in your message. Concerning the DW factor, you are right that it accounts for vibrational disorder in the sample (in the ideal case). If, however, your material has a high structural disorder by itself, DW factors might become high due to this. The general behaviour is that they should increase with temperature of the measurement. A negative value is physically not possible, and usually means that something is wrong with your fitting path. Possible things to check are - did you use proper reference paths (i.e. were they correctly computed by feff) - is it maybe another scatterer which contributes to the EXAFS at this part. Concerning fit stabilities: I never encountered the problem you mentioned, i.e. when I use the same starting values for a fit (even for a bad one), the results are the same. A good fit should by definition converge to the same fitting parameters even when starting from slightly different points on the chi2 surface. However, it is possible that you obtain different results from different starting values. Possible things to do if your fit is not stable: - dont fit all parameters at one run (at least not in the first place) - start fitting all parameters independently, then grabbing the values of the former fits and slowly approach a stable point in the fit - if you have a stable result, try freeing all parameters and see if you reach the same point again. This is a quite good indication that you are on a good way. - if you include another shell, fix all first shell parameters and just fit the second one. Afterwards, vary all parameters again. Finally, the background refinement is a feature of ARTEMIS to correct the background spline you are using. Unfortunately, I have not much experience with it, so I leave it to the other IFEFFITers in the world to comment on this... Hope my suggestions help you to have more productive sessions with these great software packages. Cheers, Norbert

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Re: ? about l_scmt etc.
by k-kupiecki＠northwestern.edu 15 Sep '04

15 Sep '04

Matt & IFEFFIT group, This is actually a feff.inp question.... but I'm hoping someone might be able to clarify this for me... I was wondering what appropriate values are for l_scmt, l_fms, and stoichiometry for the feff.inp I'm working with regarding Au on a Ni surface (I'm fitting with feff calculations with either a single Au atom in the first Ni layer or two Au atoms in the first Ni layer)? Should they all be the same for each potential? I just wanted to check if my values were appropriate. I've used some values based off of an example file all along... but I'm not sure if I used them appropriately for my scenerio. I've read the FEFF8.10 manual but I'm still unclear as to the proper values... (i.e. in the past I have used the following for 2 Au's in the surface) POTENTIALS * ipot z element l_scmt l_fms stoichiometry 0 79 Au 3 3 0.001 1 28 Ni 2 2 4 2 79 Au2 3 3 4 Oh... one more question... I haven't been using the ellipticity card in the feff.inp file, even though I've been using "POLARIZATION 1 0 0"... is this OK? Thanks, Kristine

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Artemis and atoms.inp/feff.inp files
by Bruce Ravel 14 Sep '04

14 Sep '04

Hi folks, This morning, a user pointed out an interesting problem in any version of Artemis up to and including 0.7.010. I thought I should mention it on the list because I would be surprised if no one else runs into this particular issue. Artemis currently does no error checking to determine if an atoms.inp file is actually an atoms.inp file. Similarly Artemis does no error checking to confirm the feff-ness of a feff.inp file. This is a problem because there are separate menu entries in the File menu for importing atoms.inp and feff.inp file. Different things happen when you select these two items. If you choose the wrong kind of file, Artemis will get confused trying to read one file type as the other file type. This will lead to lots of error messages and may result in project files that cannot be saved and re-read by Artemis. Currently there is no better solution than to be sure that, when you intend to import a feff.inp file. you select a feff.inp file and, when you intend to import an atoms.inp file, you select an atoms.inp file. If you make this mistake, the best solution may be to quit Artemis and try again. Clearly this is an untenable situation. Building enough intelligence into Artemis to distinguish between atoms.inp and feff.inp files is now high on my to-do list. 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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iPot Exceeded
by Barton, David (DG) 09 Sep '04

09 Sep '04

Thanks to Bruce for releasing the new versions. He has been extremely responsive to dealing with most of my bug reports and suggestions for change. The implementation of reading CIF files directly into Artemis and Atoms makes going from crystal structures in a database to simulated EXAFS patterns almost trivial. O.K. enough padding Bruce's ego...now for a question. Artemis 0.7.010, with FEFF6L on WinXP machine: What is the best way to deal with a crystalline compound in Artemis/FEFF that has 9 unique elements? Attached is a CIF file containing a Au cluster that has nine different elements, which is easily imported in to Artemis using Bruce's new import feature. When imported this compound has ~150 distinct atomic positions in the unit cell. Running FEFF within Artemis with this Atoms.inp file results in the error message: "Feff 6L.02 Unique potential 8 not allowed. Must be between 0 and 7 8 15 P Fatal Error: at RDINP" It appears that FEFF can only handle 8 unique elements at a time. No problem, I would like to ignore the H atoms anyway. Any suggestions on how to handle this within Artemis/FEFF? Otherwise, there is the obvious workaround, I can manually edit the CIF or Atoms.inp and eliminate the H atoms from one of those files and then run FEFF. It would be helpful if the Atoms input page would allow the user to sort the atomic positions by element and then select a range of these atomic positions and delete them all. Thanks Dave ipot Z element 0 79 Au 1 7 N 2 6 C 3 5 B 4 9 F 5 8 O 6 1 H 7 79 Au 8 15 P <<Au5N.cif>> David Barton The Dow Chemical Company Email: dgbarton(a)dow.com

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