- 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

2 2

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

2 1

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 >

3 4

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 >

1 0

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

1 0

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/

4 4

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

4 5

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 __________________________________________

3 2

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

1 0

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

1 0