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

Re: [Ifeffit] XANES
by John J. Rehr 10 Mar '03

10 Mar '03

Regarding XANES fits, I'm glad to hear Bruce is working on adding a principal component analysis to IFEFFIT. Doing XANES fits ala Benfatto and Della Longa would also be desirable in the long run, i.e., fitting the XAS(x) with x standing for various parameters like interatomic distances. To do that would generally require looping over the FMS module in FEFF and could get time consuming. To avoid this, one needs something like a tensor XANES calculation, which computes d mu/ dx via multiple XAS calculations and hence permits fast linear interpolations. This is not implementable with IFEFFIT/ATHENA at present as far as I know. However, I don't see major difficulties in implementation (?). There are some other ways to go, including using the parallel version of FEFF8 (Bouldin for example has suggested using this approach for XANES fits). Also, one might even consider adding constraints ala Krappe and Rossner's Bayesean-Turchin approach for EXAFS analysis. John Rehr > From B. Ravel ... >My program, Athena, currently has the capability of fitting lineshapes >(i.e. an arctangent and a number of Gaussians or Lorentzians) to >normalized XANES data. In the not-too-distant future, Athena will be >able to fit a linear combination of standards to a XANES spectrum and >be able to do principle component analysis (PCA). >

4 5

Athena 0.8.014
by Bruce Ravel 06 Mar '03

06 Mar '03

Hi folks, I am pleased to announce a new version of Athena today. The source code tarball and windows executable are on my web site. Today's version offers three significant new features: 1. A fairly major user-interface change 2. The ability to fetch data files from web sites 3. An improved merging algorithm Please note that I am making use of a very recent feature of Ifeffit (the "nofx" array function) in the new merging algorithm. Windows users need to update to the version of the big Ifeffit installer from January 22, 2003. Linux, Unix and OSX users should be using Ifeffit version 1.0076 or later. The Windows installer and the ifeffit source code can be found at Matt's web site http://cars9.uchicago.edu/ifeffit/download.html If you are not running Ifeffit 1.0076 or later, then merging WILL NOT WORK in Athena 0.8.014. So, please, upgrade. I'll describe each of those features in detail below. I'd like to specifically thank Matt (who suggested the web thing) and Adam Web (who pointed out a problem with the merging algorithm). I'd also like to mention to all the people who have been asking for PCA in Athena that it's moving closer to the front of my TODO list. The change to the user interface is needed to be able to put PCA into Athena in a sensible manner. Regards B The details about each new feature: 1. Although the user interface change is pretty significant, I think it will be easy for current users to adapt to. Indeed, I think most people will appreciate the added functionality that the change allows. In earlier versions of Athena, data processing and analysis chores such as alignment, calibration, and log-ratio were done by interacting with a special dialog that popped up in a separate window. This separate window performed a grab, which means that you could not interact with the main window until you were done with the dialog and had dismissed it. Now, each of the various chores that previously used a pop-up dialog works by replacing the main part of the main window with the dialog specific to that analysis chore. Thus, when you, say, go to align data, the part of the main window where you specify background removal and Fourier transform parameters gets replaced by various menus and entry boxes relevant to that chore. If that's not clear, check out the new screenshots at http://leonardo.phys.washington.edu/~ravel/software/exafs/screenshots.html#… There are screenshots showing each of the eight alternate views in Athena. Not only does this reduce the number of windows that Athena throws up on the screen, it also allows you to use the groups list and the plotting buttons while one of the alternate views is displayed. For example, you can now view one or more data groups in R-space *while* aligning. Chores like alignment and difference spectra which require specifying a second data data group now work by selecting the second data group from the group list. 2. You can now read data files from web sites using an extremely primitive interface. In the File menu, there is an item which says "Open URL". When you select this, the Echo area at the bottom of the screen gets replaced by a bright orange text entry box. If you type in the fully resolved URL of a data file somewhere on the web, Athena will fetch and import that file. This is not extremely convenient because you have to type in the exact URL (or use cut and paste, of course). I have not (yet) implemented a mouse-driven browser of any sort. I may in the future if this feature proves popular. One helpful feature I did implement is that Athena keeps a history of files downloaded during the current Athena session. If you hit the up or down arrows while the URL text entry box has the focus, you will scroll up and down in the history of fetched data files. If you want to try it, I put some iron foil data on my web site. Enter this URL in the orange box: http://leonardo.phys.washington.edu/~ravel/misc/fe.060 This feature will work for Windows users. It will work for other platforms only if you have the LWP perl modules installed. Because that is a very large and frequently changing package, I am not comfortable distributing it with the horae package. If you are a linux, unix, or OSX user and the "Open URL" thing is greyed out, then you will need to install LWP. You can grab the latest version of the Bundle::LWP package from http://search.cpan.org/author/GAAS/libwww-perl-5.69/ Alternately, you can use perl's CPAN interface. At the command line, type perl -MCPAN -e shell then at the CPAN prompt type install Bundle::LWP 3. The merging algorithm has changed. Before, the marked data groups were merged after interpolating them onto the abscissa grid of the first marked group in the groups list. Now, Athena determines what is the longest abscissa range common to all marked groups. The reason for this change is that the prior algorithm would extrapolate if a marked group had a shorter abscissa range than the first group. Often this isn't a problem, but it can lead to very strange and undesirable results in the merged data. I am modestly confident that I have merging working correctly again in all cases. I encourage anyone using the merging algorithm to send me a project file if they suspect that bugs remain. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory 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/

3 12

[Ifeffit] ldd /usr/local/bin/ifeffit ldd: /lib/ld-linux.so.2 exited with unknown exit code (139)
by Jacques Roux 04 Mar '03

04 Mar '03

This is a short report of various successful installations of ifeffit (and companion programs athena, artemis etc...) on linux boxes running Mandrake 8.1 8.2 and 9.0. However I would like to report one nagging failure which is summarized in the subject line of the message. On my office DELL under Linux Mandrake 9.0 ifeffit core dump and ldd issues the rather terse error message "unknown exit code (139)". The very same code runs fine and (ldd gives a meaningfull answer!) on other machines running the very same version of linux (including gcc, ld, glib etc...). I checked on google and found other people running into very similar problem (OK on one machine, wrong on the other). I tried to recompile ifeffit.f using --static but I could not get the static version of libX11 so for the time being I gave up. BTW it is not too bad as I can use the software on the same computer booting an older version (mdk 8.1) and at home on a 9.0 ! I hope this information may be useful to someone sometime ? -- J. Roux, CNRS-Institut des Sciences de la Terre 1a rue de la Férollerie, 45071 ORLEANS cedex 2, France

3 2

:)
by Du Yonghua 04 Mar '03

04 Mar '03

Dear adaministrator: I have met some unknow problems that I cannot download the iffefit setup file. So I wonder whether you will be so kind to send me a copy of iffefit. The system of my computer is windows and the limination of my mail box is 100MB. Thank you very much! Du Yonghua Beijing Synchrotron Radiation Facility Institute of High Energy Physics Chinese Academy of Sciences P.O.Box 918 2-7 Tel: (86)01088235980 19(B) Road Yuquan Beijing China

3 2

XANES
by Ahmed M Shahin 03 Mar '03

03 Mar '03

I have some question. I have mixed oxidation states and I would like to fit XANES, to determine the ratio of the mixed oxidation states I have. I looked at the documentations in the Ifeffit website but I could not find it. I have a license of feff. Would you please help me in how to fit XANES. I appreciate your help Ahmed ***************************************************** Ahmed Shahin Chemistry Department University of Missouri-Rolla 142 Schrenk Hall, Rolla, MO 65409-0010 E-mail: shahin(a)umr.edu Phone (573) 341-4083 "Make yourself a better person and know who you are before you try and know someone else and expect them to know you." *********************************************************

2 1

feff8
by shahin 26 Feb '03

26 Feb '03

Bruce, I have recieved the liscence to install and use FEFF8. Would you please tell me how to upgrade the FEFF6 tiral version, so that, I can use ifeffit with FEFF8 instead of FEFF6. I appreciate your help. Ahmed

3 3

Fresh installations of linux and ifeffit
by Bruce Ravel 14 Feb '03

14 Feb '03

Hi folks, This message is partly in response to Norbert's post from last week and partly because I noticed some things today that may trip up others in my situation. I wanted to post something here so that the solution to a similar problem might be found in the mailing list's archive. Yesterday and today I have been entertaining myself by updating my desktop computer to SuSE's Office Desktop edition of SuSE 8.1 It's pretty nifty and the installation was a breeze. Installing Ifeffit and my programs was not a breeze, however, because of some issues related to a linux distribution with a name like "Office Desktop". Because this distribution is targeted at people who use office applications, it was pretty weak in terms of software development. I had to go to SuSE's online distribution to get rpms for such obviously necessary things as C and Fortran compilers and make! Once I installed all the obvious development stuff, I made a stab at compiling Ifeffit. I immediately saw the problem that Norbert reported, which was the configure script complaining about not being able to find the "tputs" function in any of the terminal libraries. I solved this problem by downloading and installing the ncurses development package. SuSE and Red Hat give names like "ncurses-devel" to these packages, which contain header files and the like. After that, no problem. Ifeffit compiled up just fine. As did Athena and Artemis. However, trying to start Athena it became obvious that I had forgotten to install PGPLOT. Matt's PGPLOT_install script did it's magic exactly as expected. However, to get the compilation of PGPLOT to finish, I had to install the development packages for the PNG, zlib, and X windows libraries. Again, my "Office Desktop" system was lacking the header files needed to compile software. Once those were installed, PGPLOT compiled fine. I recompiled Ifeffit and my codes and I was happy. To summarize: 1. Don't forget to install PGPLOT. 2. If you have a choice about which linux distribution to choose, go for one of the "professional" distributions and make sure to install development packages up front. 3. If your CDs did not have the development packages on them, go to your vendors website and download them. If you ever want to compiler other stuff from the web, you will want these anyway. 4. To compile Ifeffit and PGPLOT, you need the header files for -- ncurses (or whichever terminal library you have on your system) -- the PNG library -- the zlib library -- the X windows headers Hope that's helpful to someone sometime. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory 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/

1 0

Re: Ifeffit digest, Vol 1 #109 - 2 msgs
by Zhan Zhang 12 Feb '03

12 Feb '03

Matt, I tried on my Win98. Installing it into C:\Ifeffit solved this icon not run problem for me. In my case, I believe this make_bats.exe works fine all the time. It generates the right .bat files. I would believe that the two easy steps you listed below works well for me. Hope it is fine for all other Win98 users. Anyway, I am working primarily on Win2K or WinXP now. Thanks for the hard work maintaining this! Zhan >My guess is that make_bats.exe that is supposed to make >the *.bat files at the 'Finish installation' step may >also be choking on the space in 'C:\Program Files'. > >Could one or both of you try installing into 'C:\Ifeffit' >instead of 'C:\Program Files\Ifeffit'. That might get the >start menu and desktop icons to work better -- and >everything else is supposed to work fine. If that doesn't >work, we might have to figure out something better. > >In the end, it would be really nice to have a small list >of steps for getting Ifeffit installed on Win98. If it >was as easy as: > 1. put SHELL=C:\COMMAND.COM /E:4096 /P into config.sys > 2. run the installer, but install to C:\Ifeffit. > -------------------------- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Dept. Environmental Research Division MLSB 2017 Building 203, C-137 2225 N. Campus Drive 9700 Cass Ave. Evanston, IL 60208 Argonne, IL 60439 U.S.A U.S.A. Email address: zhanzhang(a)northwestern.edu Office: (630) 252-8629 Fax: (630) 252-5498 --------------------------

2 1

Procedure for Win 98 installation
by krk511＠casbah.it.northwestern.edu 11 Feb '03

11 Feb '03

Matt and Group, It appears that the following two steps should be all that is needed to install on Win 98 and make the desktop icons usuable. (THANKS!) I've tried this today on another computer in our lab, and it even managed to install the xxx.bat files without having to go to the Make bats application. (My guess is that when I originally tried this a couple of days ago I may have done the shell command with a number much smaller than 4096, and that was the difference between then and now.) The procedure below appears to work great, if someone has problems they should immediately look to see if the xxxx.bat files were generated, and if not use the Make bats application. -- Kristine MN> In the end, it would be really nice to have a small list MN> of steps for getting Ifeffit installed on Win98. If it MN> was as easy as: MN> 1. put SHELL=C:\COMMAND.COM /E:4096 /P into config.sys MN> 2. run the installer, but install to C:\Ifeffit. MN> MN> That would be good enough for now. MN> Thanks, MN> MN> --Matt

2 1

Problems compiling ifeffit
by Norbert Weiher 11 Feb '03

11 Feb '03

Hi folks, I just got a new computer and put SuSE Linux 8.1 on it. Now I started compiling ifeffit (which worked fine with the 7.3 version on my old one) and it produced the following error: ./configure worked. When I tried to do "make", it gave me loads of "undefined references" to some commands (mainly: tputs and so on). I examined the output of ./configure and found the following lines: checking for tputs in -lncurses... (cached) no checking for tputs in -lcurses... (cached) no checking for tputs in -ltermcap... (cached) no checking for tputs in -lterminfo... (cached) no checking for tputs in -ltermlib... (cached) no Anyone who can help me with this? Thanks in advance :) Regards, Norbert Weiher

2 2