May 2002 - Ifeffit - millenia.cars.aps.anl.gov

Ifeffit: spline with a standard
by Bruce Ravel 23 May '02

23 May '02

Hi, Earlier today Michael Green asked Matt a question of the variety "How do you do ______?" Athena (and artemis) may provide some help with regards to questions like that. If you look in the Edit menu, you will see a item that says "Display Ifeffit buffer". This shows a text box which displays all text strings that have been sent by athena to ifeffit. This is useful to folks who want to learn ifeffit's syntax. To use the example that was just posted to the mailing list, one could read some data and a feff chi.dat file. Then plot the data in mu(E) and the background without a standard. Then tell athena to use the chi.dat file as a standard and replot in energy. Because the standard was changed, the spline will be redone using the newly chosen standard. All of the ifeffit commands to do this will be written to the ifeffit buffer for your examination. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/

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Ifeffit: spline with a standard
by Matt Newville 23 May '02

23 May '02

Hi Michael, This seems like a question that others might have, so I hope it's OK that I'm sending this reply to the ifeffit mailing list too. On Thu, 23 May 2002, Michael Green wrote: > I can't figure out how to use a standard for background > removal in G.I.FEFFIT or IFEFFIT. Is there a way to do > this? Table 4 of the Refman lists a chi_std data type, but > I didn't find any mention of it anywhere else. Yes. In ifeffit, it would go like this: #### # background-removal using known chi(k) data read_data(file= data.xmu, label= 'energy xmu', group= dat) read_data(file= standard.chi, label= 'k chi ', group= std) # without standard spline(energy= dat.energy, xmu= dat.xmu, kweight=1,rbkg=1) # with standard spline(energy= dat.energy, xmu= dat.xmu, kweight=1,rbkg=1, k_std=std.k, chi_std = std.chi) #### That is, you read in the spectra for the standard, and use it's "k" and "chi" arrays for "k_std" and "chi_std". Hope that helps, --Matt

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divorce and OSX
by Bruce Ravel 23 May '02

23 May '02

Hi, There are two more issues that I wanted to comment on, but my last message was really long, so I am writing a new one. 1. Matt suggested an amicable divorce as a way of trying to avoid many of the installation problems that we have been having recently. I would suggest a separation rather than a divorce. Ifeffit and the apps might resolve their marital issues in the future and choose to get back together. But for now, for the sake of the kids, I think a separation is a good idea. I freely confess that many of the installation problems are either due to programming mistakes I have made or due to inherent problems in how perl modules get built. It seems imprudent that Matt and Ifeffit should suffer for those reasons. And, as Matt pointed out, my codes are evolving and releasing faster than Ifeffit itself. While it is certainly less convenient for the end user to have to install several packages than a single one, it is even less convenient if the whole kit 'n' kaboodle fails because of an error in a single app. A separation is thus a very good idea. The separation works well for unix users, where it is a simple matter to grab, say, the athena source tarball and install it on top of a functional ifeffit. It is a little less convenient for the windows users. I suppose a solution is that *I* build a new windows installer package based off of Matt most recent ifeffit release when I release new source code tarball. That's not a complete solution because Sam will certainly have a different release schedule than I will. I vote that Matt, Sam, and I put off dealing with that until dealing is unavoidable. 2. Could Paul, Francois, or Chuck summarize for us the status of ifeffit + X + perl + tk + my codes on OSX? (Although I chuckled when I read it, I cannot bring myself to actually use the word Ravelware ;-) Specifically I am interested in a clear statement of how difficult it is to get my codes up an running on a virgin system and how much time it takes. I am also interested in the prospects for providing a click-n-install package for OSX users. I just gave a poster at the NSLS users meeting on my software and showed one of Francois's pictures of Atoms running on OSX. I presume that it will spark some interest. Also, NRL's beamlines at NSLS are Mac shops (thanks to Johnny Kirkland, deacon of the church of the mac) and I'll want to be running the codes there. Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/

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installation issues
by Bruce Ravel 23 May '02

23 May '02

Wow! I was gone for three days and a whole flurry of interesting issues came up. ;-) First off, I must thank Mark Jensen for these kind words: MJ> Ever since the Windows version of Athena was released, I've been MJ> hooked. I'm blushin'. Then Mark said: MJ> After an apparently successful installation, neither Athena nor MJ> Artemis ran, saying that they couldn't locate FileDialog.pm, MJ> widgets.pm, or Chemistry/Elements.pm (depending on the MJ> program). I was unsure where to get these files, or why they MJ> weren't where they were supposed to be, but the MJ> Chemistry/Elements.pm file made me wonder if that wasn't part of MJ> Atoms3.0. Indeed it is. After installing Atoms, Athena and MJ> Artemis both appear to be working correctly. So, Bruce might want MJ> to make a change in the intall.unix file to say that Athena (or MJ> Artemis) requires PGPlot, IFeffit, and Atoms. and Paul followed up with PF> Although I had "cleaned" and reinstalled several times athena and PF> Tk, I hadn't given a second thought to tkatoms -- it had no PF> relation to athena, right? wrong! Upon reintalling tkatoms, PF> athena worked. For starters, I am pleased that you both were able to solve your immediate problems. I am lucky to have such smart users. This exchange, though, underscores a serious problem. Eventually I intend to tie atoms, athena, and artemis (and a feff gui, should I or someone else ever get around to writing it) into a more cogent package. At the current stage both of the software development and of my understanding of the needs and challanges of GUI EXAFS software, it is a great convenience for them to be distinct programs. Still, as Paul pointed out, there are some ties between the codes. I use some object inheritance in athena and artemis, so they do share some code already. And one small feature of athena is only enabled if one of modules from Atoms is installed. So I have put myself in an awkward state of having neither a unified suite of programs nor three disjoint programs. Clearly what I need to do is to make a "clean room" for myself. That is, I need a place where I do not have any of my own software installed. Then I can install the tarballs individually or in any combination. If I do this, I should be able to avoid the problems that Paul and Mark reproted to this list. Thanks you both for the excellent feedback. I have said it before and I'll say it many times in the future -- this stuff is much better thanks to you guys providing feedback. Why having an out-of-date atoms resulted in the error that Paul described is a bizarre mystery to me. And why lacking atoms gave Mark an error about widget.pm is equally strange. I'll look into all of it and certainly will work on the installation scripts. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/

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Athena Run Time Error Solved!
by Dr. Paul Fons 22 May '02

22 May '02

I wrote earlier that upon trying to install athena on a colleagues powerbook, I ran into problems with an undefined value in a call to the perl standard routine configure. e.g. Tk::Error: Can't call method "configure" on an undefined value at /sw/bin/athena line 1775, <R> line 9. It turns out that the problem was related to an earlier windows-related post (aka the Ravel-ware post). Although I had "cleaned" and reinstalled several times athena and Tk, I hadn't given a second thought to tkatoms -- it had no relation to athena, right? wrong! Upon reintalling tkatoms, athena worked. There must be a perl module that is installed only with tkatoms that is required by athena. Consistent with this is the observation that artemis worked out-of-the-box (e.g. a simple make) without problem. In any case all is solved. It might be a good idea however to investigate this issue further as I am fairly sure that this problem will come up again (not with me though!). In my case (on my own machines), I installed all three programs (tkatoms, athena, and artemis) and never ran into the problem. Paul

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Run time error with athena
by Dr. Paul Fons 21 May '02

21 May '02

I have been using athena and just installed the latest version (5.16) on a colleagues G4 powerbook running Mac OSX (10.1.4). This machine is ostensibly running the same set of basic software, namely same version of perl, Tk, python, and pgplot, but he gets a runtime error when he attempts to read in some data while I don't. It would help if there were some suggestions as to how to narrow down the problem. Upon opening a prj file (the example file, ga.prj in the examples folder), the following gibberish appears: Tk::Error: Can't call method "configure" on an undefined value at /sw/bin/athena line 1775, <R> line 9. main::set_properties at /sw/bin/athena line 1775 main::fill_skinny at /sw/bin/athena line 923 main::read_record at /sw/bin/athena line 4306 main::read_file at /sw/bin/athena line 1973 [\&main::read_file,0] Tk callback for .frame.menubutton2.menu Tk::__ANON__ at /Library/Perl/darwin/Tk.pm line 228 Tk::Menu::Invoke at /Library/Perl/darwin/Tk/Menu.pm line 530 (command bound to event) It seems to be referring to a perl module called configure. Any ideas? Thanks. Dr. Paul Fons Senior Research Scientist National Institute for Advanced Industrial Science and Technology Optoelectronics Institute Energy Electronics Institute Umezono 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 paul-fons(a)aist.go.jp lines below are in Japanese: 〒305-8568茨城県つくば市梅園1-1-1 主任研究官ポール・フォンス

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GIFeffit, Athena and Artemis Installation
by Mark Jensen 21 May '02

21 May '02

Bruce, Matt, and everyone: Ever since the Windows version of Athena was released, I've been hooked. I couldn't wait for a Windows version of Artemis, so after a week of pondering the best way to re-introduce Linux to my PC, I have installed Linux, PGPlot, Ifeffit, Athena and Artemis this morning. I had a problem that others doing a "Ravel-ware" installation for the first time might run across. After an apparently successful installation, neither Athena nor Artemis ran, saying that they couldn't locate FileDialog.pm, widgets.pm, or Chemistry/Elements.pm (depending on the program). I was unsure where to get these files, or why they weren't where they were supposed to be, but the Chemistry/Elements.pm file made me wonder if that wasn't part of Atoms3.0. Indeed it is. After installing Atoms, Athena and Artemis both appear to be working correctly. So, Bruce might want to make a change in the intall.unix file to say that Athena (or Artemis) requires PGPlot, IFeffit, and Atoms. There is one other problem that I have not solved. Ifeffit runs fine, but when I try to run GIFeffit, the "splash window" pops up for a split second and then I get 2 error messages before the program shuts down. The errors are File "/usr/local/gin/gifeffit", line 3, in GIFeffit.GIFeffit (sys.argv[1]) File "/usr/lib/python1.5/site-package/Ifeffit/GIFeffit.py" line 285, in __init__ self.iff_dir = os.getenv('IFEFFIT_DIR) Attribute Error: getenv Does anyone have any thought? Have I missed something obvious in the installation? Mark Jensen ---------------------------------------- Mark Jensen Chemistry Division Argonne National Laboratory 9700 South Cass Avenue Argonne, Illinois 60439-4831 (630) 252-3670 (630) 252-7501 FAX mjensen(a)anl.gov

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New pgplot in fink unstable branch
by Dr. Paul Fons 17 May '02

17 May '02

There is a new version of pgplot in the unstable branch of fink which breaks the ifeffit install process. The only thing that needs to be changed is to include the two "library" like arguments: -framework Foundation -framework AppKit to the linking arguments (or compile arguments). The location of the pgplot library has also been changed to (the now standard location) /sw/lib/pgplot. I can see how to make the changed to the Makefile in src/macosx without trouble, but I am thrown a little by the python setup (it seems somewhat convoluted). What changes need to be made there to reflect the new link arguments and the new location of the pgplot library? Thanks.

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athena update
by Bruce Ravel 16 May '02

16 May '02

Hi folks, I guess I have been a busy boy this week. There's another release of athena on my web site. New stuff includes: 1. A couple bug fixes and several changes to the layout of the main window. 2. An automated alignment algorithm which works by varying an e0 shift to minimize the difference spectra of the derivative of two mu(E) spectra. I would not place great trust in this algorithm, but it think it will often provide a good first guess for the e0 shift. It works well for the EuTiO3 data that is included in the examples. You can use this algorithm from the alignment dialog or from the data preprocessing options in the file selection dialog. 3. Athena now checks to see if input data is monotonically increasing in energy (or wavenumber for chi(k) data). If it is not, Athena spits up an error message and refuses to read the data. This choice seems safe, but I am open to suggestions for other ways to treat the non-monotonic data. 4. A y-axis offset plotting parameter. This is most useful for stacked plots like in this screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ath… This was done by setting the y-axis offset for the first data group to 0.5 and to -0.5 for the third data group. Enjoy, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/

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uh oh!
by Bruce Ravel 15 May '02

15 May '02

So, has anyone downloaded the athena tarball I released yesterday and noticed that you cannot plot chi(k) with any k-weighting other than 1? Yikes! How embarassing! That bug will certainly be fixed in the next release. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu U.S. Naval Research Laboratory, Code 6134 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/

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