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

Some thoughts on gifeffit
by Dr. Paul Fons 11 Mar '02

11 Mar '02

I just brought up gifeffit this morning -- and I can already say I like it. I was wondering about some simple changes (perhaps I can do some of these myself once I get a little more sophisticated) 1. It would be nice to have legends on the pgplot window -- colors are nice but if one is comparing different data sets, it is really hard to tell them apart (especially if the page is printed). Also one of the things I used to do with the unix environment was to set up a series of different autobak files with different rback settings so I could see the effect of moving the fit window. It was nice to be able to compare all of these in the same graphic window -- it doesn't seem like this can be done anymore (am I right about this?) 2. In terms of documentation, a nice intro would be to highlight the differences between gifeffit and the more traditional unix command line version to help new users get up to speed -- again I am willing to write some of this (if help is needed), but I still need to get up to speed myself! 3. I am not 100% sure of this, but it seemed that when, for example, I had the plotter open and subsequently read in a new data set in another window or defined a new array, the pop-up menus in the plotter window weren't aware of the new data set (at least not immediately). One last thing, on the ifeffit homepage, it is stated that feffit is included in the distribution, but is not stable -- what is unstable and what are the limitations of the feffit module within gifeffit currently, e.g. is it something I can use to fit data? Last thing -- but really should have been first. Thank you for putting all of this effort into ifeffit and then sharing it with the rest of the community. Many people are benefiting from your efforts. Bruce's course (which is still a developing entity I believe) is also of great help in learning more about the different approaches to data analysis. It is my impression that while there is a fairly good collection of knowledge regarding exafs (and less so for xanes), this information is scattered in many different locations (and some of it is very dated). Having a reference in a easy-to-find place is a real benefit to the community at large. It also would have the advantage of being dynamic in that it doesn't have the birth (and death) cycles of commercially published material. I guess all of this is obvious, but I just wanted to say thanks (again). Paul

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Athena runs
by Bruce Ravel 11 Mar '02

11 Mar '02

Chuck asked: CB> BTW, does Artemis have any requirements, other than its own perl CB> files, that are beyond ifeffit/atoms/athena? Nope. It works just like athena. There are a lot of widgets that are used to generate ifeffit text which gets piped to the ifeffit library. Then stuff gets plotted by pgplot. So if athena works, artemis will work. CB> Now to actually learn a bit about how to -use- ifeffit, tkatoms, CB> and athena! Matt's ifeffit tutorial (see the documents page on the ifeffit site) is quite nice and will give you an overview of all the main functions. The reference is also good -- I consult it all the time as I write my codes. It is, however, a bit behind the current version. Still, it's very useful. If you have ever used atoms, tkatoms will be quite straightforward. Athena is lacking documentation. I am going to post something this morning under a different subject line which will, I hope, get you started. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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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iFEFFit/PGPlot/AquaTerm
by Tsu-Chien Weng 11 Mar '02

11 Mar '02

> 3. Has anyone run ifeffit using aquaterm? > Yes, I just tried newplot() with PGPlot/AQT, not in rootless XFree86. Since I'm a new user, I've not tried many functions in iFEFFit. Has anyone tried to use Tcl/tk 8.4a4 with G.I.FEFFit? Tsu-Chien <Chien>001000</Chien> === PGPlot/AquaTerm === 1. cvs AquaTerm 0.3 from aquaterm.sourceforge.net. 2. cp AQTProtocol.h, aqdriv.m to /usr/local/src/pgplot/drivers 3. mkdir sys_macosx, then cp g77_cc_AQT.conf and iand.c to it. 4. mkdir /usr/local/pgplot and copy over drivers.list. Add a line: AQDRIV 0 /AQT 5. /usr/local/src/pgplot/makemake /usr/local/pgplot 6. Modify makefile: DRIVERS=nudriv.o aqdriv.o aqdriv.o: $(DRVDIR)/aqdriv.m $(MCOMPL) -c $(MFLAGC) $(XINCL) $(DRVDIR)/aqdriv.m 7. make === iFEFFit === 1. download readline-4.2a from GNU and install libreadline.a to /usr/local/lib. 2. modify ifeffit_1.0b/src/macosx/Makefile a. #X_LIBS b. READLINE_LIBS = -L/usr/local/lib -lreadline c. NSLIBS = -framework Foundation -framework AppKit d. PGPLOT_LIB = -L$(BASEDIR)/pgplot -lpgplot -L/usr/lib $(NSLIBS) Note: I downloaded gcc3.1/g77 from <http://floyd.liunet.edu/~gkhanna/g77.dmg.gz>. The version of /usr/bin/cc is 2.95.2 and it has problem like /usr/bin/ld: /usr/lib/crt1.o relocation overflow for relocation entry 33 in section (__TEXT,__text) (displacement too large)

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Mac OS X: athena, tkatoms, gifeffit all working!
by Matt Newville 09 Mar '02

09 Mar '02

OK, After installing perl/Tk, tkatoms (3.0beta5) installed without problems. Since I had already installed the ifeffit perl extension, and perl -e 'use Ifeffit;' was already working without complaint, the tkatoms interface to ifeffit ran fine. I also verified that a 'Powder' calculation ran and plotted to its canvas, and that the Chantler, Elam, and CL resources worked for absorption calcs. I couldn't get a plot in the DAFS window, but that could be operator error. After this, I reinstalled the ifeffit perl extension (though it may not have been necessary), and ... athena runs. It seemed to run perfectly, though I didn't try everything. There is a problem with athena saving hardcopies, but I think that will be easy to fix. In short, I believe everything is working on MacOS X. The necessary ingredients seem to be: From http://fink.sourceforge.net/ fink components: rootless X-windows, an X window manager (eg, orobus, sawfish, windowmaker), g77, python, and PGPLOT. From http://www.Lehigh.EDU/~sol0/Macintosh/X/ptk/ the perl/Tk fix for dyld follow instructions carefully!!! From http://cpan.perl.com/ perl's Tk800 build from source: > Perl Makefile.PL ; sudo make install From http://feff.phys.washington.edu/~ravel/software/exafs/ tkatoms build from source: > Perl Makefile.PL ; sudo make install From http://cars.uchicago.edu/ifeffit ifeffit.tar.gz, unpack and install: base lib: > tar xvzf ifeffit.tar.gz > cd ifeffit_1.0b/src/macosx > make > sudo make install perl extension + athena: > cd ../../wrappers/perl > perl Makefile.PL > sudo make install python extension + gifeffit: > cd ../../wrappers/python > sudo python setup.py install Edit .cshrc, adding if (! $?DISPLAY) setenv DISPLAY 0.0 setenv PGPLOT_DEV /xwindow # PGPLOT window dies with ifeffit setenv PGPLOT_DEV /xserve # PGPLOT window stays up. Then, with X-Darwin running, tkatoms, ifeffit, gifeffit, and athena should all run from a normal Terminal.app. I haven't tried these steps on a fresh MacOS X box, so there may be a missing step or two. Thanks Chuck, Francois, Paul, and Bruce for all the help. Now, can anyone else get all this to work? --Matt

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Athena runs
by Charles Bouldin 08 Mar '02

08 Mar '02

>From: Bruce Ravel <ravel(a)phys.washington.edu> > > >Well, it is certainly a step in the right direction to actually >install the perl interface to Ifeffit before attempting to use Athena ;-) Well, okay(!) :), I never said I knew what I'm doing here, although I certainly know a lot more than 2 weeks ago. I did what Matt said, and also cleaned up what may have been a small version difference in the ifeffit distribution, and then, as Matt suggested: > cd ..... src/macosx; make clean ; sudo make install > cd ../../wrappers/perl ; perl Makefile.PL ; sudo make install and it all works! At least I get the tk panel for Athena...I don't know how to drive it yet. So, I agree with Matt...ifeffit, atoms and tk interfaces seem to be working. We should now put our heads together and try to refine the directions for all this....I'm pretty sure I could repeat it all from scratch, but it would take a while. Now to actually learn a bit about how to -use- ifeffit, tkatoms, and athena! BTW, does Artemis have any requirements, other than its own perl files, that are beyond ifeffit/atoms/athena? Chuck

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Re: [Ifeffit] The road to Athena... (and Artemis too!)
by Bruce Ravel 07 Mar '02

07 Mar '02

The fact that the wrapper for python worked as it was occurred to me after I hit the send button. How does the loader work on BSD? Does it expect libraries to be in certain standard places? Perhaps Chuck ended up with the ifeffit library in some non-standard place and so needs to fix that, set an environment variable (like on SGI), or fix the loader configuration (like on linux). Anyway, I am glad to hear that such good progress is being made. I wish I could contribute more to the immediate problem. Do post the screen messages from the build, as Matt suggested. I mostly grok perl's strange and numerous messages (which must say something bad about me .... ;-) I wanted to mention that this week I made some good progress on Artemis (I had all of Monday at home watching a contractor poke holes in my walls!) There are still alot of clunky interface problems, but Artemis will run to completion a fit with one data set using any number of feff calculations and it will plot the results in a manner that rsembles Athena. That is, you can select the data, the fit, and/or any number of paths from the list in the skinny panel on the right and click a button for plotting in k, R, or q. Model building needs a lot of work, but its usable. I would love if the Mac effort could succeed soon -- that would somewhat increase the number of alpha testers ;-) B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b 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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The road to Athena...
by Charles Bouldin 07 Mar '02

07 Mar '02

Bruce sez to try this to test if things are in place for Athena: >#!/usr/bin/perl -w >use Tk; >use Ifeffit qw(get_scalar); >use Tk::Dialog; >my $x = get_scalar('etok'); >my $top=MainWindow->new(); >$top->Label(-text=>"Ifeffit sez etok=$x") ->pack(); >$top->Button(-text=>'Done', -command=>sub{exit})->pack(); >MainLoop; I tried it and got: >[h196132:~/Desktop] charlesb% perl test_ifeffit.pl >Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5/darwin >/sw/lib/perl5 /System/Library/Pe >rl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl >/Library/Perl /Network/Library/Perl >/darwin /Network/Library/Perl /Network/Library/Perl .) at >test_ifeffit.pl line 3. >BEGIN failed--compilation aborted at test_ifeffit.pl line 3. But then I realized I needed to At 12:01 PM -0600 3/7/02, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > cd ../../wrappers/perl > perl Makefile.PL > sudo make install So, I did that, but now I get >[h196132:~/Desktop] charlesb% perl test_ifeffit.pl >dyld: perl Undefined symbols: >_ifeffit_ >_iff_exec >_iff_get_array >_iff_get_echo >_iff_get_scalar >_iff_get_string >_iff_put_array >_iff_put_scalar >_iff_put_string >_iffgetarr_ >_iffgetecho_ >_iffgetsca_ >_iffgetstr_ >_iffputarr_ and I'm not sure why this is happening. However, this feels close to working. More suggestions?

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How to run ifeffit from terminal.app
by Charles Bouldin 07 Mar '02

07 Mar '02

Thanks to helpful folks on usenet, who seem amused that Maccies are starting to ask such basic questions, here is how to run ifeffit from terminal.app: >: Wow, this sounds close to a solution to something I've been puzzling >: over. I have Xwindows installed and I can use pgplot from an xterm >: running under XDarwin, but I can NOT run pgplot from Terminal.app. If I >: try I get a message: >: PGPLOT /xw: cannot connect to X server >: I tried putting the DISPLAY=:0.0 export DISPLAY into .xinitrc and >: .cshrc, to no avail. Basically, I don't know what I'm doing here :) and >: I am just blundering about. > >That command is for sh/bash, not tcsh. For tcsh, you want > setenv DISPLAY :0.0 > >If you're going to put it in your .cshrc file, then use > if( ! $?DISPLAY ) setenv DISPLAY :0.0 >so it won't override DISPLAY if it's already set, such as by >a forwarded X11 connection. There were several interesting replies, one of which was basically, "I know how to fix it, but I refuse to use c shells". What's -that- about?

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Status of ifeffit, atoms, athena, etc on MacOS X
by Charles Bouldin 06 Mar '02

06 Mar '02

This may be the first message on the mailing list? It is a message mostly composed of questions: I have ifeffit and atoms running just fine on MacOS X, thanks to Francois' hard work figuring some things out and Matt's quick port of ifeffit. 1. Does anyone have Athena running? 2. Is anyone able to run ifeffit from Terminal.app, as opposed to running it from an xterm? When I try this, I get an error message, "PGPLOT /xw: cannot connect to X server". When I do ps -aux | grep pgp I see a process charlesb 3239 0.0 0.1 67316 672 std- S 0:00.04 /sw/pgplot/pgxwin_server -display :0.0 so clearly I need to something to tell terminal.app about the pgplot server? Anyone have advice on this? I just don't know where to look beyond this point. Why do I care about this distinction? (1) Terminal.app supports cut/copy/paste, (2) terminal.app is scriptable, which means that you can define define macros, or use script menu to put in common command blocks. In principle, this means that you could use Applescript studio to control ifeffit from a mac-native gui. 3. Has anyone run ifeffit using aquaterm? I'm very heartened by the recent rapid progress and hope that it can continue.

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Ifeffit Mailing List
by Matt Newville 05 Mar '02

05 Mar '02

OK, after two short weeks waiting for the APS firewall to allow the mail server to work, it appears that the Ifeffit mailing list is now really open for business! You can join this list or read the archives from http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit/ Thanks, --Matt |= Matthew Newville mailto:newville@cars.uchicago.edu |= GSECARS, Bldg 434A voice: (630) 252-0431 / 1713 |= Argonne Natl Lab fax: (630) 252-0443 |= 9700 South Cass Ave http://cars9.uchicago.edu/~newville/ |= Argonne, IL 60439 USA

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