April 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

4 4

Athena - resetting working directory
by Carlo U. Segre 28 Apr '03

28 Apr '03

Hello Bruce: I am using the latest version of Athena on Linux and I have noticed a strange behavior. I cd to the directory where my data is located and run athena form the command line. When I want to open my first file, the dialog puts me in the same directory with no problem. However, any time I try to do another file operation (reading, writing, etc), the dialog starts at the filesystem root "/". Even if I move back to the initial directory the next time it is back at the root. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

3 3

Re: ifeffit window
by Matt Newville 25 Apr '03

25 Apr '03

Hi Frank, I Hope it's OK that I CC: this to the ifeffit mailing list. On Thu, 24 Apr 2003, Frank Haass wrote: > Hi Matt! > > I have worked on my data with the IFEFFIT for a few days now, and I think it > is quite a very good improvement from the autobk and feffit-Versions I used > bevor. Great! But, I have a question concerning the windows for FT which can > be used in IFEFFIT. > > In the "old" FEFFIT, the keyword ikwindo could be used to change the window > function from Hanning to Gau� etc. > > Using the keyword kwindow (kwindow = 1 etc.) in IFEFFIT, it was not possible > to do this. Have I taken the wrong keyword? Are the numbers uses for the > separate window-functions in IFEFFIT the same like in FEFFIT? The 'ikwindo' flags in Feffit were too hard for most of to remember, so Ifeffit uses character strings for the name of the window function as with fftf(data.chi, kmin=2,kmax=12,dk=1, kwindow='hanning') The feffit() and window() command use this keyword too, or it can set with the string $kwindow: set $kwindow = 'hanning' I'm not sure that's easier than it was in Feffit, but it doesn't seem worse. For back-transforms, use 'rwindow' in place of 'kwindow'. The supported window types are: hanning fhanning kaiser parzen welch sine gaussian Only the first 3 letters of these namew are really needed. The default is 'hanning', but 'kaiser' is often a good choice. Of course, the GUIs have drop-down lists for this. I see that this information is not in the on-line docs. Eeek! I would have sworn it was.... I'll be sure to add this when I post the next version. The good news is that I am actually working on this these days, and even though I keep finding more to add and fix, I'm optimistic that 1.0077 will be ready next week. --Matt

1 0

Reading in mu(E) data
by Carlo U. Segre 25 Apr '03

25 Apr '03

Bruce: i have been using our rebinning program to combine data before loading into Athena. The data produced is a two column file, E and mu(E). When I try to read it into Athena, the edge is not properly detected and I have to set it by hand before the background can be subtracted properly. I haven't seen any way to avoid this problem. Is there something funny about this kind of data which would cause this problem? Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

2 1

artemis updated (again!)
by Bruce Ravel 24 Apr '03

24 Apr '03

Hi folks! Well, it didn't take me very long to find several very serious bugs in the multiple-data-set version of artemis that I released the other day. I was able to fix most of them and have posted new tarballs and windows executables. One problem had to do with the first path in a fit sometimes being neglected by Artemis. Yikes! The other problem had to do with sving and rereading project files multiple data sets. Both of these and a few smaller problems are fixed in version 0.6.002. One problem which remains is in the brand new Project Assistant. Suppose that you want to fit several scans of the same material measured at different temparatures. In that case you would want to import several data files and then import the same feff calculation(s) for each data file. If you attempt to import the same feff calculation more than once with the Project Assistant, it will not do the right thing. Other uses of the Project Assistant, including single data set fits and multiple data set fits with *different* feff calculations, *will* work as intended. Also, if you import your data and feff calculations outside the Project Assistant (i.e. by using the appropriate entries in the File menu), then you can set up a multiple-temperature fit. So, if you want to do a fit with many data sets and a single feff calculation which is used repeatedly, you must set it up by hand and not by using the Project Assistant. This will be fixed in 0.6.003. 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, 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 2

artemis 0.6.001 and athena 0.8.016
by Bruce Ravel 21 Apr '03

21 Apr '03

Hi folks! Today I am pleased to announce the first version of Artemis that supports multiple data set fitting. That is, you can import 1 or more data sets along with all the relevant feff calculations and use parameters which impose constraints between the data sets. The second huge new feature in Artemis is something I call the Artemis Project Assistant. This is a wizard-like feature of the program which helps you walk through the steps necessary to import one or more data sets and one or more feff calculations and to set up fitting parameters. This will, I hope, reduce the difficulty and complexity of getting started with Artemis. I threw together a web page explaining the Project Assistant: http://feff.phys.washington.edu/~ravel/software/exafs/apa.html There are lots of pictures on that page as well as a step-by-step recipe using the copper example that comes with the distribution. The third big change has to do with how k-weighting is done for fitting and plotting. It is now possible to do a multiple k-weight fit, that is to simultaneously fit data using, for example, both k=1 and k=3 weighting. This is often helpful for distinguishing between correlated variables which have different k dependence, such as sigma^2 and S_0^2. To explain how to use the various k-weighting options in fits and in plots, see this web page: http://feff.phys.washington.edu/~ravel/software/exafs/kweight.html I am looking forward to getting some feedback on this new version of Artemis, both in terms of bug reports and in terms of suggestion for user interface improvements. The problem of organizing and presenting a fit with multiple data sets and multiple feff calculations is very difficult. I have tried to present it in a way that is tractable, but I am open to any suggestions any of you might have to make is better and more clear. As for Athena, 0.8.016 represents only a few small changes. The most important is that I fixed a very serious bug in the deglitching interface. As always, new tarballs and Windows executables are available on my web site. Please note that unix, linux, and OSX users must be running at least version 1.0076 of Ifeffit. If you have not updated the Ifeffit core recently, please do so before installing the latest tarball. Thanks this time to Adam Webb for pointing out the deglitching bug in Athena. And a huge pile of thanks to Shelly Kelly for testing Artemis last week and for making many great suggestions for improving the Project Assistant and multiple data set fitting in general. Regards, Bruce -- 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

a pgplot question
by Bruce Ravel 18 Apr '03

18 Apr '03

Hi Matt, The attachement is a screenshot of the PGPLOT window that was left lying around from the last time I fired up athena. My question is about the large white-space gutter around the plot. Is there some way that I don't know about of reducing the size of that gutter? That is, can I expand the bounding box around the plot to be much closer to the size of the window? Also, what exactly does the reset argument to plot() do? And what is the most reliable way to get pgplot to *not* write a legend entry for a plot? Is it plot(a.x, a.y, key="")? Thanks 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/

3 4

Re: Calculating Phase Corrected Re and Im
by Matt Newville 14 Apr '03

14 Apr '03

Dear Ian, On Thu, 10 Apr 2003, Ian Drake wrote: > ... I would like to calculate and plot the fourier transform > of the phase corrected chi function. Can I do this using > the UWXAFS software suit? If not, can you recommend other > software. I have Mathematica....do you recommend its use in > the analysis. My curiosity on this issue stems from the > work of Lee and Beni in PHYS. REV. B, 15, 1977, pg.2862. Thanks for the question. Yes, phase-corrected Fourier transforms can be done. I hope it's OK if I CC this reply to the Ifeffit mailing list, as this is a fairly common question about XAFS analysis... Also, since you asked about UWXAFS software, I'll point out that Ifeffit is the successor to the UWXAFS programs, and includes those programs and quite a bit more capability, including a few GUIs. See: http://cars.uchicago.edu/ifeffit/ for more details. The longer answer about Phase-corrected FTs: Phase-corrected FTs are not always as good as you might hope. They don't give real radial distribution functions. They do give somewhat cleaner XAFS FTs and put peaks in |chi(R)| closer to the corresponding distance. Of course, to do these, you need to know the phase. Also, since you can do only one phase-shift correction, you can't correct all shells or multiple-scattering contributions. Anyway, lots of people like phase-corrected FTs, especially for making plots to show non-XAFS people, and it usually work fine for the first-shell. With ifeffit, there are a couple ways to do phase-corrections. The simplest way is to name the central atom/edge (eg, 'Cu K') to the fftf() command. In ifeffit commands, this looks like: read_data(file= 'my_chi.dat', type='chi') fftf(my_chi.chi, kmin=2, kmax=15, dk=2, kweight=2, pc_caps = 'Cu K') ^^^^^^^^^^^^^^^^ (pc_caps is for Phase-Correction, Central Atom Phase Shift), This will do only the central-atom portion of the phase-shift, so will be incomplete, but is often most of the correction, will work for the whole spectra, and doesn't require knowing much about the system. Athena (the excellent GUI to ifeffit from Bruce Ravel) can do these central-atom phase-corrections very easily (ie, no typing commands). I think Sam Webb's SixPack doesn't do phase-corrected FTs, but I could be wrong. If you know have a Feff calculation for a scattering path, in the form of a feffNNNN.dat file, you can use this for a more-complete phase-corrected FT, like this: path(1, feffNNNN.dat) fftf(my_chi.chi, kmin=2, kmax=15, dk=2, kweight=2, pc_feff_path = 1) ^^^^^^^^^^^^^^^^ This version includes both central-atom and scattering-atom phase-shifts, which will give a much better phase-correction, but assumes you know quite a bit about the system. I think athena doesn't do this form of phase-correction, and I don't remember if artemis does this (yet??). Feffit will aslo write out phase-corrected FTS (the full kind, using the first feffNNNN.dat file listed in feffit.inp) if the keyword 'pcout=1' in in feffit.inp. Finally, some people use phase-corrected FTs for analysis, especially to pick R_NN at a place where Im[chi(R)] = 0. I'm not sure what the accuracies of this are, but pelase note that Ifeffit (and feffit) swaps real and imaginary parts for its FT, so that it is actually Re[chi(R)] that is ~=0 at R=R_NN for these FTs. Hope that helps, but don't hesitate to ask again if it's not clear enough. --Matt Newville

2 1

Debian packages
by Carlo U. Segre 01 Apr '03

01 Apr '03

Hello All: I have a first version of Debian Linux packages for IFEFFIT, Atoms and Horae. They now install with no conflicts and appear to work on my machines. I believe that all package dependencies are in place as well. Please feel free to test them out and let me know if there are any big errors. Sources are also on the archive. The apt/sources.list lines would be deb http://fermi.phys.iit.edu/debian binary/ deb-src http://fermi.phys.iit.edu/debian source/ The binary packages have been compiled for the stable (woody) distribution but seem to run fine on testing (sarge). Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

1 0