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

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/

2 1

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/

1 0

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

2 1

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 __________________________________________

3 3

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 __________________________________________

1 0

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/

1 0

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

4 5

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.

1 0

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

1 0

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

4 3