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

Ifeffit 1.2.8 installer for WinXP
by Leandro Langie Araujo 19 Sep '05

19 Sep '05

Greetings everybody, I'm another newcomer to the EXAFS world whose life was made much easier thanks to this wonderful software package. My sincere thanks to Matt, Bruce and everyone else involved in the "Ifeffit family" project. But, although the software is very nice, I'm having some trouble installing the newest version (1.2.8). I've been trying to install the Ifeffit 1.2.8 package on my WinXP, but there seems to be a problem with the files. I've downloaded the installers from both sourceforge and cars.uchicago.edu, but whenever I try to run any of them I get the following message: "The setup files are corrupted. Please obtain a new copy of the program." So, I'd like to ask if anyone from the mailing list managed to install Ifeffit 1.2.8 on WinXP or if anyone got the same kind of error message when trying to install. Thanks, Leandro

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Ifeffit 1.2.8
by Matt Newville 18 Sep '05

18 Sep '05

Hi Folks, Ifeffit 1.2.8 is now available. There are minor changes to the core library and new versions of horae (055: athena 0.8.043, and artemis 0.8.002) in the Windows and Mac installers. A few version notes are below, and I will be putting more information at http://cars9.uchicago.edu/iffwiki/ReleaseNotes128/ == Windows == For Windows, there is a new installer, but no update. The new installer has the latest versions of the programs and also has dramatic changes to how the programs are organized and run. The batch files and the old automatic updater are gone, replaced by a single program 'runner' that checks for updates and runs all of the applications. There is also a completely new layout of C:\Program Files\Ifeffit. Bruce and I have been working on this for a while, and we believe it will be a lot easier for us to maintain. We expect that the changes will be mostly invisible to users, except when you install it. A result of the new layout is that *** *** *** you must uninstall any previous version of *** *** Ifeffit before installing the new version. *** *** *** Really, we're not kidding. There is a potential problem with this, as you may have your own projects under C:\Program Files\Ifeffit, say in \horae\ or in \examples\. You probably don't want to delete these!!! We recommend that you either move C:\Program Files\Ifeffit\horae and any other folders you may have file in to somewhere safe *before* you remove Ifeffit, or simply rename C:\Program Files\Ifeffit to Ifeffit_OLD and leave it there for a few weeks. And of course, we recommend that you save your data somewhere outside of C:\Program Files and make regular backups ("Gee, thanks, Mom!"). Then use the Control Panel 'add/remove programs' to remove Ifeffit. This will try to delete everything that originally got installed (and so *should* leave your data, but I wouldn't bet on it!!), including the shortcuts in the Start Menu. Once the C:\Program Files\Ifeffit folder is gone or cleaned out, you can then safely install the new Windows installer. The older Windows version (1.2.7) will see one more update, which will simply remind you to install the new version of the full installer. All further updates will be available only to the new version. == Mac OS X == For Mac OS X (10.3), the binary installer includes the codes from horae-055. The previous attempt to support Aquaterm is now dropped -- plotting is done with the X Windows plotting terminal. Since Athena/Artemis require X, and since X11 now comes from Apple, the Aquaterm support was more trouble than it was worth. == Unix == For Linux/Unix users using the source kit, the 'where is termcap?' problems should be gone. In addition, building on 64-bit linux machines should be much easier. PGPLOT_install now has a '--with-64bit' option which is needed for 64bit linux. Ifeffit's normal './configure' should then work fine. It now warns if the termcap library cannot be found. Let us know if there are any questions or troubles with these new versions. --Matt

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Athena Bug in Peak Fitting
by Barton, David (DG) 16 Sep '05

16 Sep '05

Bruce, FYI: I recently installed Ifeffit v1.2.8 using the new Windows installer and it worked perfectly on a couple Win XP machines. After using the latest version of Athena 0.8.043 I noticed a bug in the Peak Fitting Routine and also have a couple of other minor suggestions. Description of Peak Fitting Bug: --The centroids that are reported on the screen and in the results file are not updating after a peak-fit is done. When the checkbox is marked to fit the centroid the fit appears to be changing the centroid because the resulting plot looks like a better fit, however the value of the centroid on the screen is not updating and the results file does not reflect any changes in centroid. Then if you push the "Plot Lineshapes" button it uses the centroid on the screen and the fit changes dramatically using the original value of the centroid. This bug can be reproduced by pulling up any spectra, setting the centroid of the arctan to something that results in a poor initial fit, check the box to fit centroid, run the fit....you should see that the fit moves the centroid however the value on the screen does not update and then if you "Plot Lineshapes" you will see the fit change to value of the original centroid. Other Suggestions for minor improvements to Athena: --In Compute Difference window it would be nice to have a checkbox that allows the user invert the difference (do spectra-ref instead of ref-spectra). This would be helpful for doing the difference of Marked spectra where we would like to do the spectra-ref. --in Compute Difference window it would be nice to have a checkbox to plot the components of the difference along with difference (similar to LCF window). Helpful for diagnostic checks of difference. --in your new Plot Style functionality it would be nice if Athena would automatically replot the last plot choice after a new Plot Style is chosen. This would save a few clicks as I click back and forth between two different plot ranges. --the link to the Plot Style POD documentation is broken. Let me know if you need any further clarification. Dave _________________________________ David Barton The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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Tip of the Week: Features of the Guess, Def, Set page in Artemis
by Bruce Ravel 16 Sep '05

16 Sep '05

Hi, This week's tip of the week is "Features of the Guess, Def, Set page in Artemis" http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek Enjoy, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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compiling Ifeffit and friends on a 64 bit linux machine
by Bruce Ravel 14 Sep '05

14 Sep '05

Hi, Some months ago -- see the thread that starts here: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-December/001550.html Jake from U. Calgary posted a message about trouble getting Ifeffit et al to compile on his 64 bit machine. Over the last few days I have been upgrading to SUSE 9.3 on my home computer, which has an Intel 64 bit processor. (2 of them actually, lucky me!) 9.3 is much better for a 64 bit machine than 9.2 was. (It's also the first OpenSUSE release, which is a development I am very happy about.) Initially I ran into the exact same problem that Jake described in his original post. At the time, Carlo suggested that the -fPIC flag ("Position Independent Code", whatever that is) would be important. That turned out to be the trick. When installing Ifeffit, it was necessary to do the configure step like this: ./configure CC="cc -fPIC" FFLAGS="-g -O2 -fPIC" After that, the rest of installing Ifeffit and all of installing the horae tarball proceded normally. BUT, there is one other caveat. I had to make a small change to the pgplot makefile to get it compiled for my 64 bit machine. Everyplace in the makefile where it said "/usr/X11R6/lib", I had to change that to "/usr/X11R6/lib64". Compiling pgplot requires a bit of voodoo. I have always relied on Matt's PGPLOT_install script, which comes with the ifeffit tarball. In this case, I ran the script. It did some stuff, the failed. I cd-ed to /usr/local/pgplot, which is where it gets installed, and edited the makefile in that directory as I indicated in the last paragraph. Then in that directory I did a "make" and the pgplot compilation went to completion. Of course, I had to be root run the PGPLOT_install script and to do the compilation in /usr/local/pgplot. Hope that helps! (I'd be interested to hear how it goes with your opteron, should you try this, Carlo.) Bruce -- 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://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Bug report for Artemis 0.8.000
by schmithals＠hmi.de 12 Sep '05

12 Sep '05

Hello Bruce, After a break I just started to use Artemis again and I am delighted about the new features, especially the ability to store and compare subsequent fits in one file. Below I want to submit the bugs that I came accross so far (on Win2000): - If one opens by mistake an input file that is unknown to Artemis (or Athena) this file will be destroyed and cut to about 4kB. Workaround: Just DON'T do this (or keep regular backups). - Funny things happen when one studies an atoms/feff calculation without having loaded an experiment file: I imported an atoms.inp, ran atoms and feff and did two summations (Sum | All included paths ..). For the first summation I included only the first path, for the second summation only the second path. The first summation seems fine, for the second summation Artemis obviously includes both paths. In subsequent summations this effect will continue: all paths used in the past are considered plus the paths currently included. Workaround: Load a 'dummy'-chi file even for just making summations. I was teaching the use of Artemis to a few colleagues. I recommend them to keep a copy of their atoms.inp-files at a separate place for re-use in later projects. If time permits maybe you could account for these issues: - If saving an atoms.inp file via Theory | Write special output | atoms the name 'artemis.stuff' will be provided. Is it possible to change that to 'atoms.inp'? - The link to TKAtoms is missing for newly installed systems. Cheers, Gerrit Schmithals

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new tip of the week
by Bruce Ravel 09 Sep '05

09 Sep '05

Hi! I just posted this week's Tip of the Week at http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek This weeks topic: Easily marking arbitrary groups in Athena Enjoy, 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://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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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

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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

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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/

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