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

Re: [Ifeffit] Re: ifeffit installation on Linux
by Matt Newville 09 Sep '05

09 Sep '05

Hi Peter, > Here's the output: > > src/cmdline/Makefile:TERMCAP_LIB = -ltermcap > src/cmdline/Makefile:# readline_LIB = -L$(top_srcdir)/readline > -lreadline $(TERMCAP_LIB) > src/cmdline/Makefile:readline_LIB = > $(top_srcdir)/readline/libreadline.a $(TERMCAP_LIB) > readline/Makefile:TERMCAP_LIB = -ltermcap > readline/Makefile: $(CC) $(CCFLAGS) -o $@ ./examples/rl.c > ../libreadline.a ${TERMCAP_LIB} > # locate termcap: > /usr/lib/libtermcap.so.2 > /usr/lib/libtermcap.so.2.0.8 > /usr/lib/termcap/libtermcap.a > /usr/lib/termcap/libtermcap.so > # locate curses: > /usr/lib/curses/libcurses.a > /usr/lib/curses/libcurses.so > /usr/lib/libcurses.so.1 > /usr/lib/libcurses.so.1.0.0 > Thanks for the report. That looks like the change to configure did what it was supposed to do: instead of having './lib/termcap/libtermcap.a', it now has '-ltermcap'. The odd things to me are that a) libtermcap.a seems to be in an odd location (/usr/lib/termcap), which makes me wonder how any readline applications work. b) you still end up with a './lib/termcap/libtermcap.a' somewhere in your Makefile, but *not* as TERMCAP_LIB=./lib/termcap/libtermcap.a I have no idea where that would be coming from. I don't think that an extra '-L./lib/termcap' is causing a problem (it's ok to have '-L' arguments that point nowhere) but that the linking can't find the right libtermcap.a with '-ltermcap' alone. If the Makefiles said TERMCAP_LIB= '-L/usr/lib/termcap -ltermcap' that would work for sure. I've been relying on a 'BASH_CHECK_LIB_TERMCAP' macro in autoconf, which apparantly doesn't know to look in /usr/lib/termcap. At this point, it may be easier to just write a function to look for the right termcap library. I think readline can use termcap, curses, or ncurses, and to be honest, I find the differences confusing. Anyway, thanks for the help! --Matt

1 0

ifeffit installation on Linux
by marco antoni alsina corvalan 08 Sep '05

08 Sep '05

Hi everyone, I'm currently making my way into Linux, so I decided to change most of my programs to this plattform, which obviously include ifeffit ;) I downloaded the ".tar" file, ran with success the PGPlot script for the graphics library installation (at least the demos run!!), and executed the "configure" script, getting the message "ready for the next step"...however I also get the following info: .... checking termcap.h usability... no checking termcap.h presence... no checking for termcap.h... no .... checking for tgetent... no checking for tgetent in -ltermcap... no .... Anyway then I executed the "run" command, getting the following error: .... cc: ./lib/termcap/libtermcap.a: No such file or directory make[3]: *** [ifeffit] Error 1 make[3]: Leaving directory `/home/user/Programas/ifeffit-1.2.7/src/cmdline' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/Programas/ifeffit-1.2.7/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/Programas/ifeffit-1.2.7' make: *** [all-recursive-am] Error 2 If anyone can help me overcoming this impasse I would be very greatful. Also if you need more info please let me know Regards, Marco ______________ Marco A. Alsina Estudiante de Magíster Departamento de Ingeniería Hidráulica y Ambiental Pontificia Universidad Católica de Chile Vicuña Mackenna 4860, Santiago, Chile (56 2) 3544873

5 14

Questions and answers
by Bruce Ravel 06 Sep '05

06 Sep '05

Good morning, Every week I receive a large amount of email regarding my software and XAS in general. I am sure that's no surprise to anyone reading this. While I certainly want to encourage people to feel free to contact me about XAS, the software, and any other topic, the time I have to address the needs and concerns of all the people contacting me is limited. In recent weeks I have received an unusual number of emails containing vague, ill-posed questions or requests for inordinate amounts of help. The other day I was frustrated by one such correspondent, so today I am indulging myself by ranting in a public forum ;-) Consider this message that I received the other day: > I have a sample with lead adsorbed onto manganese oxide and I have > its EXAFS. I want to study the Pb-Mn shell (including r(Pb-Mn) and > the number of Mn atom around Pb atom). How should I proceed? > > Awaiting your reply. Contrast that with an email I received from a user who had some questions along with a bug report regarding how e0 is determined by Athena: > I'm attaching an Athena project with a sample labeled Libethenite > and a Cu standard, along with an step by step explanation included > in the project journal. I trust the difference between these two is clear. I do not know either of these individuals except by their emails. Both are from places far away from Chicago. The first received a 5-line response while I spent two hours on a plane flight two weeks ago addressing the second one. I encourage people to contact me at any time with any question about XAS or my software. Indeed, if Athena and Artemis are useful data analysis tools today it is only because of the kind and generous feedback I have received from its users. But if a genie were to grant me a wish, it would be that more folks were like the second correspondent than the first. Thanks, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

1 0

RE: [Ifeffit] Ifeffit Wiki
by Barton, David (DG) 06 Sep '05

06 Sep '05

Bruce, >It makes me kind of sad to think that some of these neat-o features > are not widely used. If it makes you feel any better, I just used your linear combination module in Athena to fit 165 XANES spectra. Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Friday, September 02, 2005 4:10 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Wiki > > > On Wednesday 31 August 2005 17:22, Matt Newville wrote: > > Hi Folks, > > > > I've created and started a wiki for Ifeffit and related topics. > > Currently, this is at > > http://cars9.uchicago.edu/iffwiki > > I, for one, think the new Wiki is quite cool. Yet another > thing that we have to thank Matt for. > > My first use of the Wiki is to start a "Tip of the Week" web > page. Athena and Artemis have become sufficiently robust and > feature-full that there are a lot of interesting aspects of > the codes that are not widely known about or used. It makes > me kind of sad to think that some of these neat-o features > are not widely used. To keep a smile on my face, I've > decided to use the wiki to highlight some cool tidbit every > Friday afternoon. The first one is up at > > http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek > > Check it out. Feel free to send me suggestions for features > of A&A that you think would make a good Tip of the Week. My > plan is more or less to alternate between Athena and Artemis > and occassionally to throw in a Hephaestus tip as well. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > ravel(a)phys.washington.edu > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > 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 >

4 6

RE: [Ifeffit] Ifeffit Wiki
by Barton, David (DG) 06 Sep '05

06 Sep '05

Bruce, > So would it be useful to have some more automation in the LCF > utility. Automation is always appreciated, not required, but much appreciated. The data set that I was fitting was indeed the result of multiple fast scans performed during an in-situ catalysis experiment, similar to what Anatoly is planning for NSLS. My biggest challenge with the current Athena code. 0.8.041 in fitting many XANES spectra was not having a single report where all fitting results could be exported to. I would imagine if you automated the fitting routine you would produce some report that lists all fitting results including fitting statistics in a single file. In addition, in the current fitting utility there was a few wasted clicks and edits because the fitting range kept reverting back to -15 to 45 eV... My fitting range was different than the default and every time I choose another data set to fit the fitting range reverted back to the default which meant I had to choose each box and make the appropriate changes for each new data set. Regardless of these issues, the LCF module is fantastic. I truly appreciate the ease of use, the ability to view the fit along with components of the fit, and the ability to plot the residual. Thanks for another useful tool to make my life easier. Regards, Dave > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > Of Bruce Ravel > Sent: Friday, September 02, 2005 6:02 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Wiki > > > On Friday 02 September 2005 16:12, Barton, David (DG) wrote: > > >It makes me kind of sad to think that some of these neat-o > features > > >are not widely used. > > > > If it makes you feel any better, I just used your linear > combination > > module in Athena to fit 165 XANES spectra. > > Spectacularly so! Thanks for the big smiley at the end of the week. > > So would it be useful to have some more automation in the LCF > utility. What occured to me as I read this was to have a way > to fit a fixed set of standards to all the marked groups and > right a big report at the end. That is, play around with > spectrum #1 until you have decided which standards to use and > how to do the fit. Then mark spectra 2-165, press the > button, and go get a cup of coffee. That seems like a good > idea to me. > > B > > -- > Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- > > ravel(a)phys.washington.edu > > Environmental Research Division, Building 203, Room E-165 > Argonne National Laboratory phone and voice mail: > (1) 630 252 5033 > Argonne IL 60439, USA fax: > (1) 630 252 9793 > > 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 >

1 0

new source code release
by Bruce Ravel 04 Sep '05

04 Sep '05

Hi folks, I have released the latest source code tarball for my codes. Tarball 054 is now available on my web site and at Source Forge. I am continuing Matt's experiment providing an Ifeffit Wiki by posting the change log on my wiki page: http://cars9.uchicago.edu/iffwiki/BruceRavel Scroll to bottom of the page (after smiling at the photo of me and my adorable niece) to find the page documenting the new features and bug fixes in this release. Matt and I are getting close to having a completely new Windows installer prepared. The new package has a more sensible file structure, a much improved launching tool for the programs, and new executables of my codes made with PerlApp. This version of my codes will be in the first release of the new Windows installer. Hopefully that will be ready soon. Regards, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

1 0

Ifeffit Wiki
by Matt Newville 02 Sep '05

02 Sep '05

Hi Folks, I've created and started a wiki for Ifeffit and related topics. Currently, this is at http://cars9.uchicago.edu/iffwiki At this point, this should be considered experimental. I'm still ambivalent about the whole thing, but we definitely need *something* to allow outside people to add content. Please feel free to play with this wiki, and let me know what you think. If this is something we decide we want to keep, I'll have this become part of the main set of Ifeffit and XAFS pages. I'd like to give it a trial run first, and hear some feedback. For those who aren't familar with wikis, these are set of web pages that are editable and expandable by users. There are all sorts of features for adding content -- too many to explain here. The basic idea is that you log onto the system, and edit the web pages using a web browser in a simplified structured text -- NOT directly editing HTML. Anyway, it's pretty easy to use, and there's plenty of documentation on how to use it. --Matt

2 1

compilation problem under MacOSX 10.4 - again
by Hugh Harris 02 Sep '05

02 Sep '05

Hi all, I'm new to the list and ifeffit. I've tried to get ifeffit 1.2.7 installed (for the first time) under tiger (on a system upgraded from panther) according to the instructions posted in the FAQ and the following modification on the list; > Thanks Matt - installing g77 and then recompiling perl/Tk and horae > did the > trick! > > Bruce - sorry, I meant Perl/Tk... > > Paul, you may want to upgrade the installation notes to mention > that g77 has > to be installed first. Installion with Fink was a pleasure. > > Thanks again guys! > > JOEL I have Xcode installed, g77 via fink, and ran the ifeffit binary installer. Perl/Tk seemingly builds and installs ok but when I try to build horae 0.5.3 I get the following error; [harris:~/Desktop/horae-053] hugh% perl Makefile.PL === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is Mac OSX. Checking dependencies ... Dependencies ok. Cool! Reading configuration file: Ifeffit/lib/athena/athena.config Wrote Ifeffit/lib/athena/athenarc Ifeffit/lib/athena/athenarcw Ifeffit/lib/athena/athena.ini athena_parts/rc.pl Reading configuration file: Ifeffit/lib/artemis/artemis.config Wrote Ifeffit/lib/artemis/artemisrc Ifeffit/lib/artemis/artemisrcw Ifeffit/lib/artemis/artemis.ini diana_parts/rc.pl Assembled athena.pl from its parts (athena_parts/). Assembled artemis.pl from its parts (diana_parts/). Assembled hephaestus.pl from its parts (hephaestus_parts/). Fixing execution path in the Athena, Artemis, and Hephaestus executables... Changing athena.pl to /usr/bin/perl Changing artemis.pl to /usr/bin/perl Can't process diana.pl: No such file or directory Changing hephaestus.pl to /usr/bin/perl Changing ifeffit_shell.pl to /usr/bin/perl Changing horae_update to /usr/bin/perl Changing rdaj.pl to /usr/bin/perl Changing atoms.pl to /usr/bin/perl Ifeffit's installations directory is (found by capturing `ifeffit -i`) Could not open /config/Config.mak file for reading [harris:~/Desktop/horae-053] hugh% Trying to run athena from the xterm gives; Can't locate Ifeffit.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/ perl5/darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level / System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread- multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/ 5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/ Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread- multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /Applications/Ifeffit/bin/athena line 54. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 58. Any ideas? Am I missing something obvious? Cheers, Hugh -- ------------------------------------------------------------------ Hugh Harris ASRP Postdoctoral Fellow School of Chemistry, Building F11 University of Sydney, NSW, 2006, Australia Office: +612-9351-2745 -------------------------------------------------------------------

2 2

Re: Fitting an Extended R-range
by Michel Jaouen 31 Aug '05

31 Aug '05

>Shelly wrote: > >I was hoping that you could help me put together a list of EXAFS papers >that fit the R-space data out to at least 5 Angstroms. Hi Shelly, You can add to Scott's list the following entry: Mutiple-scattering EXAFS and EXELFS of titanium alloys T. Sikora, G. Hug, M. Jaouen, and J.J. Rehr, PRB 32, n°3, 1723 (2000) Best regards, M. Jaouen -- __________________________________________ 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] Fitting an Extended R-range
by Kelly, Shelly D. 30 Aug '05

30 Aug '05

Hi Scott, Thank you for the help. Have a good one. Shelly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Monday, August 29, 2005 10:10 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Fitting an Extended R-range Sorry, the first one should have been: > >"Estimating crystallite size in polydispersed samples using EXAFS," S. >Calvin, C. J. Riedel, E. E. Carpenter, S. A. Morrison, R. M. Stroud, & V. >G. Harris, Physica Scripta, T115, 744 (2005). >> --Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0