October 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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Re: [Ifeffit] ... and lots of new stuff in Athena and Artemis, too!
by SCalvin100＠aol.com 31 Oct '03

31 Oct '03

Yippee!!! Many thanks to Matt and Bruce for the new releases! --Scott Calvin Sarah Lawrence College

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Ifeffit 1.2.4 Debian Linux packages
by Carlo U. Segre 31 Oct '03

31 Oct '03

Hello all: The latest version of Ifeffit is now available as a Debian packge. There is also an update package of horae 024 with a recompiled wrapper for Ifeffit 1.2.4. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)agni.phys.iit.edu http://www.iit.edu/~segre

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RE: [Ifeffit] relation between DW factors in uranyls
by Kelly, Shelly D. 30 Oct '03

30 Oct '03

> This is in response to Shelly's post for MS references. For > linear multiple scattering, I like to use this paper: > > Hudson, EA; et. al. (1996) Phys Rev B 54(1) 156-165 > > It uses the uranyl ion specifically in this example and has a > short section in the introduction about the relations between > single and multiple scattering D-W parameters. > > Hope this is vaguely what you were looking for.... > > > Sam Hi Sam and John, I just wanted to say thank-you to the ifeffit mailing list. Sam, the reference was indeed helpful. And thanks to John for his derivation. This is what I learned about relating sigma2 values for the uranyl. For a linear uranyl moiety (UO2), where the atoms are all in a line O1-U-O2, the sigma2 values can be approximated like this: U-O1-U: sigma2-s.s. (single scattering sigma2) U-O1-U-O1-U: sigma2 = 4 * sigma2-s.s. U-O1-U-O2-U: sigma2 ~ 2 * sigma2-s.s. U-O1-O2-U: sigma2 ~ 2 * sigma2-s.s. This information has been published in Hudson et al. PRB V54 n1, pg 156 (1996). Shelly

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Coordination number
by Dave Baker 30 Oct '03

30 Oct '03

I'm interested in extracting coordination numbers from the S02 parameter in Artemis, and, as the beginner, I'm lost as to what to do. I am using two FEFF paths to describe the first shell, and have given each path its own S02 parameter. Any suggestions? -Dave ------------------------------------------------------------------------ -- North Carolina State University Dept. of Physics 2700 Stinton Dr. Box 8202 Raleigh, NC 27695 Ph: 919-515-5017 Fax:919-515-7331 email: dabaker(a)unity.ncsu.edu ------------------------------------------------------------------------ --

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RE: reference
by Webb, Samuel M. 30 Oct '03

30 Oct '03

This is in response to Shelly's post for MS references. For linear multiple scattering, I like to use this paper: Hudson, EA; et. al. (1996) Phys Rev B 54(1) 156-165 It uses the uranyl ion specifically in this example and has a short section in the introduction about the relations between single and multiple scattering D-W parameters. Hope this is vaguely what you were looking for.... Sam

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reference
by Kelly, Shelly D. 30 Oct '03

30 Oct '03

Hello All, Does anyone know of a reference that explicitly shows that sigma2 for a linear backscattering path is approximately twice a single scattering path? My example is for a uranyl moiety (UO2). The structure of this moiety is symmetric and linear with a dumbbell shape with O1=U=O2 all in a row. I need a reference that does the calculation to show that the 4 leg path (U-O1-U-O2-U) has a sigma2 value that is twice the single scattering path (U-O1-U) from one of the oxygen atoms. Thanks for your help Shelly

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one more thing...
by Bruce Ravel 30 Oct '03

30 Oct '03

Hi folks, The one very obvious change in how Athena behaves is how it plots normalized mu(E) spectra. If you dislike this new feature and would prefer to always see the normalized data as they were previously plotted, it is easy to disable by going to the preferences dialog, selecting the variable Bkg -> flatten, and setting it to false. Below is the description of this new feature from the NEWS page on my web site. B 1. FLATTENED DATA. I added a new features for plotting normalized spectra which I call flattening. In short, this works by subtracting the linear and quadratic portions of the polynomial regressed to the post-edge region of the data from the normalized data after the edge. This has the effect of shifting the oscillatory portion of the spectrum such that it oscillates about 1. That is, the flattened spectrum is presented with its baseline at 0 and it's post-edge at 1. This is purely a plotting device and has no impact on the calculation of chi(k). It can be turned on and off for a data set using a toggle button in the background removal section of the main window. Whether flattening is on or off by default is configurable in preferences dialog. Flattening is sensitive to how the post-edge line is chosen, particularly in XANES data which have a limited energy range. The idea for this feature was blatantly swiped from SixPack. -- 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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... and lots of new stuff in Athena and Artemis, too!
by Bruce Ravel 30 Oct '03

30 Oct '03

Hey! As a followup to Matt's announcement, I wanted to mention that the brand new Ifeffit release contains the latest versions of Athena and Artemis, both of which contain lots of new features. Here is an explanation of the new goodies: http://leonardo.phys.washington.edu/~ravel/software/exafs/NEWS Windows users can just run the updater or the installer and you will get the latest codes. Linux and other unix users can grabthe latest tarball from my web site. Regards, 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 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 1.2.4
by Matt Newville 30 Oct '03

30 Oct '03

Hi Everyone, I've uploaded Ifeffit version 1.2.4 to the Ifefft web pages, and to Sourceforge.net. This version has a few long-promised fixes, and improvements. == Bug fixes: the bug of 'n_varys' not being correct is now fixed. Several of the program limits were increased (lengths of strings, number of Feff paths, etc) and better reporting of these limits. Long label lines should be handled better now in read_data() and athena. Feff6 now works on Windows. A few more bug fixes are mentioned in the ChangeLog file. == Feff6, Feffit, Autobk: these 'input-file' based programs can now all take the name of an input file with a name other than 'feff.inp', 'feffit.inp', and 'autobk.inp' as a command line argument (on Unix, Mac OS X, and Windows). On Windows, the batch files now pop up a file browser so that you can browse for a feff.inp file, and Feff6 will be run with that input file, in that directory (and similarly for feffit and autobk). == Diffkk: This has (finally!) been updated to allow f1->f2 transforms. This still needs testing, but works for a test case. Sorry for taking so long, Michel! == Mac OS X: There is now a disk image with a crude installer that will install the latest versions of ifeffit, feff6, feffit, autobk, athena, artemis, tkatoms, and a few other programs for Mac OS X (but not gifeffit or sixpack -- yet). Fink is NOT required to run these programs, but there are a few important caveats: This installer will work only with OS 10.2, requires X11 to run (the X11 beta3 from Apple works OK for me), and assumes the Apple-supplied perl 5.6 (it won't work with perl 5.8). I realize that OS 10.3 just came out (which ships with X11 and perl 5.8) -- I don't yet have it installed yet, but expect to support it relatively soon. If anyone gives this installer a try, please let me know how it works. If you want to get these programs to work with 10.3 and/or 10.2 with perl5.8, let us know: we can make it go much smoother now than in the past. == Windows: There is a full installer (30Mb) or an update (8Mb) from Ifeffit 1.2.3 that can be automatically installed. These include latest versions of athena and artemis (and ifeffit, feff6l, feffit, and autobk) are included. If you install from the update, make sure you double-click on make_bats.exe afterwards!!! == Other Announcements: As some of you may know, , my wife Julie had a baby two weeks ago. We're very happy, and everybody's doing well. But as a result I'm spending a lot less "extra time" at work these days, and it will probably stay that way. This will cut down on my ability to support Ifeffit, especially to build and fix the Windows versions which I have to do at work (though I do count it as real work, it's not always the highest priority). On the other hand, I can work on the source and Mac versions from home between diaper changes and other real work. The Windows installer and updater for 1.2.4 are much less tested than they should be: please report problems and be patient, as it will take time to fix any problems!!! I'd also like to repeat Bruce's plea for help earlier this week. It's likely that the level of support and ability to respond to problems will drop, and we really do need help. If you're using these programs as an integral part of your research, please consider what they're worth to you and what you would have to do if these programs didn't exist. If you can help, either with making releases for Windows or Macs, with program documentation or web pages, or in any other way, please contact us. As always, let us know if there are any questions or problems, --Matt

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