December 2003 - Ifeffit - millenia.cars.aps.anl.gov

ifeffit and Mac OSX
by Matt Newville 03 Jul '04

03 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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Using FEFF calc to create "data"?
by sej9＠cornell.edu 06 Jan '04

06 Jan '04

Dear all, Is there any way to create "data" using just a FEFF calculation? I mean, can I use Artemis to create a theoretical EXAFS spectrum from a FEFF calculation without fitting it to any actual data? After seeing my data (from messy environmental soil samples), I came up with another idea for a compound that might be in it (a compound that I hadn't thought of before and so do not have real data from having run it as a model compound), and am trying to figure out the best way to incorporate that new compound into my fit. Thanks, Sarah Johnson

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running feff - a problem
by Tamas Varga 05 Jan '04

05 Jan '04

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maximum argument length?
by Peter Southon 05 Jan '04

05 Jan '04

Hello all, Is there a limit on the total length of arguments that follow an Ifeffit command? If so, is there a way of expanding the limit? I've constructed a rather complicated model which uses 37 paths (mostly multiple scattering). Furthermore, quite a few of these paths are sensitive to scattering angle, so I have calculated FEFF files for three versions each of most paths (each for a different scattering angle), as suggested in the course "EXAFS Analysis with FEFF and FEFFIT" and the old Feffit manual. Thus the final Ifeffit command calls on a lot of FEFF paths, each specifically numbered according to path and angle. Unfortunately, after adding a few extra paths I get error messages when running the feffit command: "feffit:unknown key" followed by a list of paths about halfway through my list, and also "feffit: no chi(k) data array?". I assume that this is because ifeffit will only swallow half the command, which is: feffit(1-4,500,510,520,600,610,620,700,710,720,800,810,820, 9-13,15-16,1700,1710,1720,1800,1810,1820,1900,1910,1920,2000,2010,2020, 37, 3800,3810,3820,3900,3910,3920,4000,4010,4020,4100,4110,4120, 4200,4210,4220,4300,4310,4320,4400,4410,4420,4500,4510,4520, 4600,4610,4620,4700,4710,4720,4800,4810,4820,4900,4910,4920, 5000,5010,5020,5100,5110,5120,5200,5210,5220,5300,5310,5320, 5400,5410,5420,5500,5510,5520, chi = data15.chi, macro = plot_fit) Short of actually renumbering all my paths so that they run sequentially, is there any solution...? Have a merry Christmas, Peter Peter Southon Research Fellow - School of Chemistry University of Sydney, NSW 2006, Australia +61 2 9351 4425

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Installer for Mac OS 10.3
by Matt Newville 19 Dec '03

19 Dec '03

Hi Everyone, I think I have a reasonably well-tested installer for Mac OS 10.3 (ifeffit-1.2.4_Mac10.3.dmg) at the usual download sites (see http://cars.uchicago.edu/ifeffit/download.html) Please try it out, and let me know how it works. This disk image contains a normal Mac Installation package, which will install clickable Applications for Athena, Artemis, TkAtoms, PeriodicTable, Feffit, Autobk, and Feff6, putting them in /Applications/Ifeffit. The "Ravelware" programs all launch the GUIs directly (and X11 is automatically started if it is not running). Clicking on the applications for Feffit, Autobk, or Feff6 will open a file chooser for you to choose the appropriate input file, which will then run the corresponding program in that folder. For those interested in using the Unix command-line all of these programs, plus the ifeffit command-line program and diffkk can be run from a regular Terminal or xterm. This installer does not require any Fink-based software, but it does require OS 10.3 and X11 to be installed. (X11 can be installed from the OS 10.3 disks or from Apple's web pages). The installer here WILL NOT WORK with OS 10.2. If you're planning on using 10.2 for awhile and really need to get Ifeffit running, please contact me. I think this is possible, but a little more work than can easily put into a single installer. SixPack is not included in this distribution. This may be possible, but I have not gotten SixPack (more accurately, some of the python GUI tools that SixPack depends on) to run on 10.3. If you've been following along with the conversations with Paul Fons on getting Perl/Tk, Athena, etc running on 10.3 from sources, please be aware that this installation will _OVERWRITE_ many perl modules (Tk, Xray, Ifeffit, etc) in /Library/Perl. My experience is that it is perfectly safe to overwrite, rename, and move this folder, but you should be aware that this installer will write to /Library/Perl as well as /Applications/Ifeffit. The installer here assumes Perl 5.8.1 (that's the system-supplied one), and uses Tk-804_025_beta6. If you have Fink installed, there should be no conflict with that software. This Ifeffit distribution is _not_ using Fink's PGPLOT, but it shouldn't cause problems unless you are using that PGPLOT for another purpose. If you know _anything_ about AppleScript or Apple Programming or are just interested, please don't hesitate to play with the scripts in the Ifeffit/applescript folder and make suggestions. If you have any trouble or questions, please let me know. --Matt

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Noise Generation in FEFFIT
by Norbert Weiher 17 Dec '03

17 Dec '03

Dear Friends, I am still going with the chi^2-scan business and need a fast way to modulate white noise on a spectrum for some proof of principle. Has anyone a good idea how to do this (or would it be even possible in ifeffit)? Thanx for helping Cheers, Norbert -- Dr. rer. nat. Norbert Weiher (weiher(a)tech.chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32

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Re: upgrading iffefit and stuff on linux
by Bruce Ravel 11 Dec '03

11 Dec '03

On Thursday 11 December 2003 08:57 am, Gleb Pokrovski wrote: > Dear Bruce, > > I'm using your nice programs Athena & Artemis (+iffefit+tkatoms) on > linux Mandrake 9.1 (2.4.21-0.13mdk), and I currently have 1.2.1, > 0.8.020 and 0.6.005 versions of iffefit, athena and artemis, > respectively. I would like to update to more recent versions. Not > being an expert in linux (but rather a very beginner!), I'm asking > myself how the upgrading will happen. On the ifeffit websites I > did'nt find any instructions how to upgrade on unix, but probably my > questions are quite trivial and silly... > > When I installed the above versions I followed the instructions provided > with the package (unzip, configure, make, make install...) > and these versions and corresponding executables and libraries were built > in the default directories /usr/local/.../bin, lib, include etc... > > If now I redo these operations with the new packages, do they automatically > replace the old files and executables? > Or I have to do some preparations before upgrading? > > (I already have PGPLOT and perl-Tk (800.024) installed and running) Hi Gleb, I am always happy to see another linux convert! Your questions are most certainly not silly and trivial. I would be surprised if others would not benefit by my answer. So I am taking the liberty of CCing my response to the mailing list. To answer your principle question -- doing an update is just that. The new version will be written on top of the old version. [1] No further preparation is required. If you are a user of Debian linux, the problem of keeping up-to-date is very simple because Carlo Segre makes installation packages for Debian of ifeffit, atoms, and athena&artemis. No one is currently maintaining packages for other linux distributions, however. Assuming you have PGPLOT and perl/Tk [2] already installed, the updating is explained below. If you need to update both, do ifeffit first, then A&A. If you only need to update A&A, it is not necessary to reinstall ifeffit -- just build and install the new version of A&A on top of the existing version of ifeffit. To update ifeffit: download the latest source code tarball from Matt's website. Unpack it. [3] Next, in a terminal window, go to the directory that got unpacked and type the following three commands: ./configure make make install The last command will require either having root or having sudo permission to install software. To update A&A (on a computer connected to the net): this is very simple. For almost the last year, a program called "horae_update" has been installed alongside A&A. Simply type "horae_update". It will fetch the latest version from my web site, unpack it, build it, and install it. Again, you will need root to actually install it. [4] To update A&A (on a computer not connected to the net): download the latest horae tarball from my web site. Unpack it. [2] In a terminal window, go to the directory that got unpacked and type the following three commands: perl Makefile.PL make make install The last command will require either having root or having sudo permission to install software. I strongly encourage you to learn how to use the horae_update script. It really does make updating A&A much easier. It is a pretty smart script in that it does nothing if the version on my web site is not newer than the version on your computer. This means that you can make horae_update a cron [5] process and have A&A updated automatically. Hope that helps, B Notes: [1] A long time ago (more than a year ago) I was struggling with a bug in perl's build system which resulted in the end user (you!) having to worry about deleting old versions of the ifeffit library before building the new one. This problem was avoided (not solved, just sidestepped) by forcing you to install ifeffit first, then install my programs second. [2] The easiest way to install PGPLOT is to run the "PGPLOT_install" script that comes with the ifeffit package. To install perl/Tk for the first time, grab the tarball for version 800.024 from my web page and do "perl Makefile.PL; make; make install". Some linux distributions (SUSE does, but Red Hat does not) have a package for perl/Tk that you can install from your installation media. [3] At the command line, you can unpack it via the command "tar xvfz". Under KDE, you can use the program Ark, which is what Konqueror suggests for opening the file when you click on it. Under GNOME, File Roller does the same thing. Ark and File Roller both behave somewhat like the popular Windows program "WinZip". [4] Also, the first time you run horae_update, it may need to fetch some additional perl modules from the web. This is automated, but it does require root access. [5] A cron process is one that is scheduled to run periodically. For instance, you could have cron run horae_update every morning at 3 a.m. In that way, the freshest versions of A&A will always be waiting for you along with your morning coffee. Cron may prove a bit daunting for a linux newbie, though. Here's a decent explanation of what it is and how it works: http://www.gdn.net/help/howto/crontab_howto.html There is a KDE program called "kroneko" that serves as a GUI to making cron jobs. A GNOME program of the sort is called "gcrontab". Neither is a default part of the desktop but a google search should turn them up. -- 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 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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errors = 0?
by k-kupiecki＠northwestern.edu 09 Dec '03

09 Dec '03

Hi, I'm hoping someone out there has seen this before and can tell me what to do to remedy it... I've been using artemis at home all weekend on my Win 98 computer without incident.... now I'm working at home today with the same feff and data files working on fitting... and while Chi sq etc. is the same the +/- values on all my variables are now reading as 0, even though the values for the variables are what I would expect them to be. Any ideas about how I can fix this? Thanks, Kristine Witkowski Northwestern University

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Re: Ifeffit Digest, Vol 10, Issue 2
by Zhan Zhang 05 Dec '03

05 Dec '03

Matt, One thing I noticed is that the link below does not work on my computer. Both Netscape and IE have trouble to find the file. However, if the filename removed from the link, the correct directory showed and the file can be found there. I am not sure what is wrong but it seems the browsers do not like the filename (or something else). Once the file downloaded, and installed, it is relatively smooth-going. But I first did that a strange way: I freshly install the Iffefit 1.2.4 downloaded Nov. 9th 03. And I run the updater came with the version (dated Oct-12, 03). I was told two updates available and I decide to go with it. It seems working ok. Athena was launched. Then I quit Athena and install the updater-1.1. And it seems messed things up. First I noticed the new updater was named updater_old.exe (with a recent date). Then when I launched Athena, the old updater run again and did the two updates without progress bar. Upon finishing, Athena launched fine. Next I quit and tried to relaunch Athena--only found out the Path for the '.bat' files were all changed to C:\Program Files\Iffefit instead of my installation directory C:\Iffefit. I did not pursue this too far believing I was doing it wrong way. I deleted (rather rudely) all files in the installation directory and reinstalled Iffefit and then installed the new updater before launching any program. Everything is fine now and no weird thing happened. I would guess no one else will do it my way. But just let you know things might go out of control if run in wrong order. Thanks. Zhan >Hi Everyone, > >I've posted a new version of the Updater program for windows -- >the program that automatically looks for updates to the Ifeffit++ >distribution for Windows. This is distributed in the form of an >installer program, and can be downloaded from > > http://cars.uchicago.edu/ifeffit/src/ifeffit_updater-1.1.exe > >or from the Sourceforge.net site (see the Ifeffit Download page). > >Installing this (to the same directory as Ifeffit is installed in!) >will upgrade versions 1.2.1 and higher of Ifeffit to "the latest", >including a new version of the updater program and the latest >versions of athena and artemis. > >The new updater shows progress for downloading uppdate files so it >shouldn't appear to "just sit there and do nothing", and should have >a much better chance at successful downloads. This updater also >"remembers" the last time it looked for updates. Once it has looked >for an update, it won't even look for another day (and this 'wait >time' can be increased). > >I recommend all Windows users to install this updater. In a few >minutes I'll post a new 'update' as well. This should test wether >the new updater is working. Please do NOT install this with the old >updater, but rather install the new updater first, which should make >the updater should run the first time you run an Ifeffit program. > >Please let me know if there are problems!! > >--Matt > > > -- -------------------------- Zhan Zhang Northwestern University Argonne National Laboratory Materials Science & Engineering Dept. Environmental Research Division MLSB 1058 Building 203, C-137 2220 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 --------------------------

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Windows updates
by Matt Newville 05 Dec '03

05 Dec '03

Hi Everyone, I've posted a new version of the Updater program for windows -- the program that automatically looks for updates to the Ifeffit++ distribution for Windows. This is distributed in the form of an installer program, and can be downloaded from http://cars.uchicago.edu/ifeffit/src/ifeffit_updater-1.1.exe or from the Sourceforge.net site (see the Ifeffit Download page). Installing this (to the same directory as Ifeffit is installed in!) will upgrade versions 1.2.1 and higher of Ifeffit to "the latest", including a new version of the updater program and the latest versions of athena and artemis. The new updater shows progress for downloading uppdate files so it shouldn't appear to "just sit there and do nothing", and should have a much better chance at successful downloads. This updater also "remembers" the last time it looked for updates. Once it has looked for an update, it won't even look for another day (and this 'wait time' can be increased). I recommend all Windows users to install this updater. In a few minutes I'll post a new 'update' as well. This should test wether the new updater is working. Please do NOT install this with the old updater, but rather install the new updater first, which should make the updater should run the first time you run an Ifeffit program. Please let me know if there are problems!! --Matt PS: next up is a "real" installer for Mac OS 10.3. If there are any people who need or want to use Ifeffit with Mac OS 10.2, please let me know.

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