June 2004 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Matt, as to the following question: QUESTION: I do not seem to have, in tcsh, the command "configure" I think I solved this one by entering the /Users/stefano/Tk-804.027/ifeffit-1.2.5 directory I am proceeding with the resto of the indicated protocol, so far not caring about the downloading directory (I am using my home directory right now). Please let me know whether I can change the Tk-804.027 directory from my home directory to where it is more right to move it (which I do not know). Thanks, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 15 Jun '04

15 Jun '04

Paul, this is my .cshrc file: bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source /Library/Scripts/iterminal_custom.tcsh source /sw/bin/init.csh source /Users/stefano/Programs/XtalView/XtalView.env setenv PATH `echo $PATH`:/usr/local/sparky/bin:/usr/local:/usr/local/molscript:/usr/local/bin:/Users/stefano/Programs/modeller6v2:/Users/stefano/Programs/o/bin/:/Users/stefano/Programs/autodock/dist305/bin:/Users/stefano/Programs/autodock/dist305/share/:/Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin/bin:/Users/stefano/Programs/XtalView/bin/powerpcDarwin5/ defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv RCSBROOT /Users/stefano/Programs/Validation_suite/validation-v0.904-beta-prod-bin-darwin setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT source /Library/Scripts/settitle.csh source /Users/stefano/Programs/NMRPipe/com/nmrInit.mac.com alias ono osx_ono ### begin MODELLER6v2 ###################################################### setenv MODINSTALL6v2 /Users/stefano/Programs/modeller6v2 setenv EXECUTABLE_TYPE6v2 mac10v2-absoft setenv LIBS_LIB6v2 $MODINSTALL6v2/modlib/libs.lib setenv KEY_MODELLER6v2 MODELIRANJE alias mod mod6v2 set path=($path $MODINSTALL6v2/bin) limit stacksize unlimited ### end MODELLER6v2 ######################################################## # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~ so I think I do have the instruction for aquaterm. It is not a very nasty bug. I just have to remember to start aquaterm first... and the only bugging idea is that it worked once... Ciao, Stefano > In my case, aquaterm opens automatically. I did set in my .cshrc >(shell script initialization file), the variable >PGPLOT_DEV=/AQT >I do know that aquaterm started even automatically even when I was >building horae using the pgplot in fink as well. > > Paul -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello Matt, after having installed 1.2.5a, the aquaterm is now opening ok: am currently trying artemis ZnO tutorials... Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Stefano Ciurli 13 Jun '04

13 Jun '04

Hello again, after running horae_update, and having now horae-036, I still do not get aquaterm to open.... SHould I reinstall ifeffit1.2.5a??? Trying to do so... Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI

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Re: PCA
by Webb, Samuel M. 12 Jun '04

12 Jun '04

Hi Ethan, Glad to hear you've been checking out the PCA routines in SixPACK. I'm away from the office until after the July 4th holiday, so email access will be a little impeded. Your're right, the "save component" menu feature doesn't work, much to my surprise. I'll have this fixed in my next release. However, until that time (I won't be able to make an improved version until post July 5th), here is a quick work-around. You can plot the components, then use the "copy plot data to clipboard" option in the plot menu. This will place all current plots on the clipboard, which can then be pasted into any other application you'd like for further examination. If you want to save the components for further use in Sixpack or Athena/Artemis, any 2 column ascii format will work. As for the target transform, I can put that information of that fit into the next relase as well. As a temporary fix again, you can take the saved components (saving each of the plots above into its own text file) and then do a linear combo fit to get that data, using the PCA components as the components and the target transform file as the sample. This should give you the same fit as the target transform does in the PCA routine. Thanks for the feedback. Its always good to get comments from other users -- particularly on things that I didn't think of on the first time around. I'll try to have those improvements in the PCA released when I get back to my office. Sam ******************************************** Sam Webb SSRL/SLAC Bldg. 137, MS 69 2575 Sand Hill Rd. Menlo Park, CA 94025 Phone: (650)-926-3734 FAX: (650)-926-4100 E-mail: samwebb(a)slac.stanford.edu *******************************************

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trying to run artemis again
by doug pease 11 Jun '04

11 Jun '04

Hi Scott, This may duplicate the essentials of another e mail I sent to an address I found at the Sarah Lawrence home page, which looks a little different from this address. I would be delighted if you could look at my problem with ARTEMIS, and thank you for the generous offer!. My computer is presently at my home on 140 Sawka Drive, East Hartford, Connecticut, 06118. My phone is 860 - 568 - 5055. Once the bugs are out of these programs enough so that I can do a basic analysis, and I know I won't need to download anything I will move this computer to U. Conn. (My U. Conn. computer will only support 98, whereas my home computer supports XP. The home computer is closer to working with these programs than the one at U. Conn.) My home is about 35 minutes further from Holyoke and 35 minute closer to New Haven than U. Conn. Anytime is great for me except during the work day on Friday next week the 18th, when I have TEM time. We will cook for you if you wish, and thank you so much! Let me know the best time for you. Sincerely, Doug

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RE: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Carlo, Bruce is away. I'm sure that he fix this bug when he gets back. Shelly > -----Original Message----- > From: Segre, Carlo U. > Sent: Friday, June 11, 2004 9:15 AM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Artemis: Error in laoding additional > FEFF paths? > > > > > Shelly: > > Reading them in all at once is not a problem. It is just > when you read 10 in at once and then try to add another one > that we get problems. Specifically, Scott's ZnO tutorial does > this and has given light to the bug. > > I think that if one does as you propose, there is no problem > and artemis is functional. > > Carlo > > On Fri, 11 Jun 2004, Kelly, Shelly D. wrote: > > >Hi Carlo, > > > >Here is something to try. Put all the feffxxxx.dat files > into a single > >directory. Rename them so that you do not have repeating numbers. > >Then try to read them in all at one time. > > > >Shelly > > > >> -----Original Message----- > >> From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > >> Sent: Thursday, June 10, 2004 3:12 PM > >> To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > >> Subject: Re: [Ifeffit] Artemis: Error in laoding additional FEFF > >> paths? > >> > >> > >> Carlo, > >> > >> I have been having consistent problems running the tutorials on my > >> MacOSX G4 portable PC. I have posted several times the tect of the > >> trap files I am getting. .Apparently, there is no definitve answer > >> (yet). I am sure Bruce will try to clean up things whenever he has > >> time. But, if for some reason, some of you out there knows > a way out, > >> I'll be one of the many to be happy to read it. > >> > >> Stefano. > >> > >> >One of my students is just trying Scott's ZnO tutorial and we are > >> >finding a consistent problem when trying to work with the > >> third project > >> >file. > >> > > >> >When we get to the point of adding an additional path, > >> (feff0011.dat), > >> >artemis crashes with the following message: > >> > > >> >--------------------------------- > >> > > >> >The following message was trapped by Artemis: > >> > > >> >Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0 > >> x9652e54)/ > >> >home/segre/.horae/stash/artemis.project.2/ > >> >at /usr/bin/artemis line 1562 > >> > main::__ANON__('Use of uninitialized value in > string eq at > >> >/usr/bin/artemis l...') called at /usr/bin/artemis line 7313 > >> > main::read_feff('^^') called at > >> /usr/lib/perl5/Tk.pm line 225 > >> > eval {...} called at /usr/lib/perl5/Tk.pm line 225 > >> > Tk::__ANON__('Tk::Menu=HASH(0x974a060)', > 'active') called > >> >at /usr/lib/perl5/Tk/Menu.pm line 531 > >> > Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) > called at > >> >/usr/lib/perl5/Tk.pm line 347 > >> > eval {...} called at /usr/lib/perl5/Tk.pm line 347 > >> > Tk::MainLoop() called at /usr/bin/artemis line 1707 > >> > > >> >-------------------------------- > >> > > >> >This is happening on all of my Linux machines. They are using my > >> >Debian packages and so I have not tried with the tarball > >> installation. > >> > > >> >Has anyone else had this problem? I hesitate to report > it as a bug > >> >until it is confirmed. In a previous version of horae, it > >> worked fine. > >> > > >> >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 > >> >_______________________________________________ > >> >Ifeffit mailing list > >> >Ifeffit(a)millenia.cars.aps.anl.gov > >> >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > >> -- > >> ____________________________________________ > >> > >> Stefano Ciurli > >> Professor of Chemistry > >> Department of Agro-Environmental Science and Technology > University of > >> Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy > >> Phone: +39-051-209-6204 > >> Fax: +39-051-209-6203 > >> > >> "Fatti non foste a viver come bruti, > >> ma per seguir virtute e canoscenza" > >> Dante Alighieri - Inferno - Canto XXVI > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit > >> > > > >_______________________________________________ > >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/listi> nfo/ifeffit >

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MacOS X 10.3 - Athena Starts...then Stops
by Christopher Derr 11 Jun '04

11 Jun '04

I'm attempting to install Ifeffit 1.25 on a new Powerbook G4 with MacOS X 10.3. I've downloaded the installer (actually I've tried the stable and test versions) and installed into Applications. Clicking on Athena, however, starts Athena (you see the menu at the top change) and then it just goes away. Same with Artemis. Feffit asks for a file to load, but then goes the same route as Athena and Artemis...just goes away. I'll supply more information as needed. It's a brand new laptop with nothing really untoward installed. Thanks for any thoughts whatsoever. Chris

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RE: [Ifeffit] Artemis: Error in laoding additional FEFF paths?
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Carlo, Here is something to try. Put all the feffxxxx.dat files into a single directory. Rename them so that you do not have repeating numbers. Then try to read them in all at one time. Shelly > -----Original Message----- > From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] > Sent: Thursday, June 10, 2004 3:12 PM > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Artemis: Error in laoding additional > FEFF paths? > > > Carlo, > > I have been having consistent problems running the tutorials on my > MacOSX G4 portable PC. I have posted several times the tect of the > trap files I am getting. .Apparently, there is no definitve answer > (yet). I am sure Bruce will try to clean up things whenever he has > time. But, if for some reason, some of you out there knows a way out, > I'll be one of the many to be happy to read it. > > Stefano. > > >One of my students is just trying Scott's ZnO tutorial and we are > >finding a consistent problem when trying to work with the > third project > >file. > > > >When we get to the point of adding an additional path, > (feff0011.dat), > >artemis crashes with the following message: > > > >--------------------------------- > > > >The following message was trapped by Artemis: > > > >Artemis0.7.006warn/home/segre/.horae/stash/ARTEMIS.TRAPCODE(0 > x9652e54)/ > >home/segre/.horae/stash/artemis.project.2/ > >at /usr/bin/artemis line 1562 > > main::__ANON__('Use of uninitialized value in string eq at > >/usr/bin/artemis l...') called at /usr/bin/artemis line 7313 > > main::read_feff('^^') called at > /usr/lib/perl5/Tk.pm line 225 > > eval {...} called at /usr/lib/perl5/Tk.pm line 225 > > Tk::__ANON__('Tk::Menu=HASH(0x974a060)', 'active') called at > >/usr/lib/perl5/Tk/Menu.pm line 531 > > Tk::Menu::Invoke('Tk::Menu=HASH(0x974a060)', 1) called at > >/usr/lib/perl5/Tk.pm line 347 > > eval {...} called at /usr/lib/perl5/Tk.pm line 347 > > Tk::MainLoop() called at /usr/bin/artemis line 1707 > > > >-------------------------------- > > > >This is happening on all of my Linux machines. They are using my > >Debian packages and so I have not tried with the tarball > installation. > > > >Has anyone else had this problem? I hesitate to report it as a bug > >until it is confirmed. In a previous version of horae, it > worked fine. > > > >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 > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > _______________________________________________ > 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] Running FEFF
by Kelly, Shelly D. 11 Jun '04

11 Jun '04

Hi Poorani, I believe that Athena and Artemis do not work properly when installed in the C:/program files/ifeffit directory. The installation proceedures say to specify C:/ifeffit instead. To fix if, but all of C:/program files/ifeffit into the trash and then re-install. Shelly -----Original Message----- From: Ssk0016(a)aol.com [mailto:Ssk0016@aol.com] Sent: Thursday, June 10, 2004 9:55 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Running FEFF Hello All, I"m a graduate student and trying to use Athena and Artemis for EXAFS analysis.I just follow the steps ,as mentioned in the manual,to do Cu example.this is what I did. * First I opened the Chi file * Then I imported the Atoms input file,and typed all the informations and pressed "run atoms". * It gave me Feffinput.Then I pressed "run Feff".Then the bar at the bottom of the screen blinked and in very short time it asked "how many paths I want",and I clicked the button. ....It supossed to give the message screen with all the details and then all the paths should be displayed at "data & Paths". But it didn't,insted the message screen was displayed with no messages.Also there was a warning at the bottom says "Message dumped to C:/program files/ifeffit/horae/stash/ARTEMIS.TRAP". So i went to file menu and clicked "import feff calculations" and import ARTEMIS.TRAP.then in the interpretation page ,there was a message screen saying "couldnot find feff.inp,files.dat,paths.dat". I don't know how to solve this problem.Can anyone help me to overcome this? NOTE: I'm using windows XP. thanks Poorani ' i opened th

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