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

ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 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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Feff6l on Windows
by Matt Newville 29 Sep '03

29 Sep '03

Hi Everyone, The Feff6l executable included with the Ifeffit 1.2.3 windows installer is broken. The source is OK (and I expect the version of feff6l in Carlo's new debian packages too), but it looks like an older, broken version of the binary got included with the 1.2.2 windows distribution in late August. Anyway, I have a fixed version of feff6l.exe that runs correctly. But since running feff on Windows has always been a pain -- requiring you to use the DOS command shell -- so I also added a program (runfeff6l.exe) that pops up a file browser pops up so that you can select a feff.inp file (doesn't need to be called feff.inp, either) and will run feff6l for you. This is not a complete Feff GUI, but it is easier to use than the older executable. The feff6l.bat file and the 'feff' shortcut now point to this program. Since there were questions about (and problems with) the automatic updater, I have not yet made this an 'update'. I'd like to hear some feedback (either here or by private email) on how to deal with such small changes. Forcing people to downlod an install another 28Mb setup.exe seems sort of silly. Some of the options I see are: 1. assume the updater is working for most people, and just make this an automatic update. 2. scrap the automatic updater altogether, and just make this a new Ifeffit version. 3. make a separate installer for Feff6L. Any other suggestions are welcome. If you have Ifeffit 1.2.3 installed and want to try the new Feff6l, follow these instructions: 1. download http://cars9.uchicago.edu/ifeffit/updates/ifup_002.zip 2. unzip this into your main Ifeffit directory (probably C:\Program Files\Ifeffit or C:\Ifeffit ) 3. IMPORTANT: after unzipping this file, double-click on make_bats.exe This will re-make the batch files and shortcuts that run the programs. 4. If you're interested, more details can be found in IFEFFIT_DIR\updates\readme_002.txt For now, I'll leave this version of Feff6 in this zip file, so that you can test it out if you want but aren't forced to do so. If the consensus is to make this a regular update, I can do that easily. If having feff6l is important to you, please let me know whether these binaries work for you. Any feedback will be greatly appreciated. Thanks, --Matt

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new ifeffit and horae packages
by Carlo U. Segre 29 Sep '03

29 Sep '03

Hello All: After some time being unable to work on this (I skipped a few releases), I have Debian/Linux binary and source packages for ifeffit 1.2.3 and horae 024 for both the stable and testing releases of Debian. I can also make rpms of the two even though I have not tested these. The Debian packages can be accessed with the following lines in the /etc/apt/sources.list file. # X-Ray Software Archive deb http://fermi.phys.iit.edu/debian/woody binary/ #deb http://fermi.phys.iit.edu/debian/sarge binary/ deb-src http://fermi.phys.iit.edu/debian/woody source/ #deb-src http://fermi.phys.iit.edu/debian/sarge source/ Note, the testing archive has been commented out. Just uncomment it and comment the stable (woody) lines. Cheers, -- 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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IFEFFIT error messages
by SCalvin100＠aol.com 26 Sep '03

26 Sep '03

Hi Matt, Bruce, et al., Does Artemis somewhere provide any clue as to where the error was found when it says "Fit aborted due to errors in parameters and math expressions"? FEFFIT used to highlight the last line successfully read, which was helpful for finding unbalanced parentheses and the like. But I don't see an equivalent message here. --Scott

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ifeffit 1.2.3
by Matt Newville 19 Sep '03

19 Sep '03

Hi Everyone, I've just posted Ifeffit version 1.2.3. As with earlier versions in the 1.2.x series, this is a bug-fix release. The changes are: 1) setting 'path_index' now causes the given path to be the 'current path', so that 'reff', 'degen', and any parameters that might depend on them are automatically updated. 2) spline() now passes all of the arguments to pre_edge() correctly. There is now an updater program for Windows is now available. If you already have 1.2.2 installed, you do not need to download the 30Mb full installation, just the 2Mb program ifeffit_update-1.0.exe from either http://cars9.uchicago.edu/ifeffit/download.html or https://sourceforge.net/project/showfiles.php?group_id=80919 Once installed, the updater program will automatically run just before all Ifeffit applications, checking whether updates are available and installing them if desired. This should make it a lot easier to keep up-to-date with the latest versions of Ifeffit, athena, artemis, sixpack, etc... If you have any questions or trouble, let me know, --Matt

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Re: Ifeffit Digest, Vol 7, Issue 4
by Charles Bouldin 17 Sep '03

17 Sep '03

Just and FYI for the Mac OS X crowd: IBM has released their splendid optimizing C and Fortran compilers for OSX. See http://www-3.ibm.com/software/awdtools/fortran/ These are -great- compilers, and best of all, you can trivially modify standard makefiles and compile fortran programs. Definitely worth investigating. I can send a makefile for Feff to anyone interested. Haven't tried feffit or ifeffit yet, but thought others would be interested to know this, if you don't know it already.

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integrating difference spectra
by Bruce Ravel 16 Sep '03

16 Sep '03

Hi folks, In response to a request from an Athena user, I am incorporating a feature that will allow the user to integrate difference spectra. I suspect that this will prove most useful for XANES studies and for XMCD studies. I was wondering if someone on the mailing list would be so kind as to send me some sample XMCD data, either in the form of raw data or as an Athena project file, so I can test this. The most useful example at this stage would be a model system -- i.e. something that demonstrates a large dichroic effect. It would also be useful if your data set has a well known value for the integral of the difference spectrum. That way I'll have a bit of confidence that my algorithm is working. Thanks in advance! 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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path-sensitive math expressions
by Bruce Ravel 05 Sep '03

05 Sep '03

Hi Matt, I have some questions about a subtle detail in ifeffit. It is possible to make a def parameter which is path sensitive in the sense that it will evaluate differently for different paths. Any def parameter which includes reff, eins(), or debye() in its math expression will be that way. Here is a simple, if slightly silly, example: def rrr = reff/10 path(1, feff=feff0001.dat, dr=rrr) path(2, feff=feff0002.dat, dr=rrr) Then show rrr will report 1/10 the R_eff of the *second* path. So here are my questions: 1. Are all def parameters reevaluated every time a new path is evaluated? Or only if the path uses the def parameter in one of its math expressions? (I think the answer is the former.) 2. Is it possible to ask ifeffit which def parameters are path sensitive? Of course, I can scan the def parameters at the level of perl to see if any of them obviously are, but ifeffit might already know that. 3. If you do show ss the value is the value of the last path evaluated. Doing show @path N show ss will indeed display the value of the def parameter appropriate to the Nth path. Is there another way of forcing ss to be evaluated appropriate to a desired path? 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/

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how Atoms builds clusters
by Bruce Ravel 04 Sep '03

04 Sep '03

Hi everyone, I have twice recently been asked about how Atoms converts from its input data, which is the minimal set of positions necessary to describe the crystal, to the cluster that gets reported in the feff.inp file. Since there seems to be some interest in this question, I thought I would send a message to the mailing list with the answer. That way it'll be archived and anyone can go back and look at the answer. If you've ever wondered about this, read on. If the thought never crossed your mind, this is a good moment to go on to your next email message ;-) Here is the broad outline: 1. Atoms fills out the unit cell in the first octant. By "first octant" I mean that all fractional coordinates of all positions are non-negative and less than 1. 2. Enough unit cells are stacked up like blocks to make a rhomboid large enough to entirely encompass a sphere of the radius specified by the Rmax parameter. (If you poke hard enough at Atoms, you will find a situation where it fails to create a large enough rhomboid. It's an odd situation, though, and you won't run into it if your space group is orthogonal.) 3. The fractional coordinates are converted to their Cartesian equivalents. 4. All the atoms within the rhomboid but outside the sphere are tossed. 5. The atoms are translated such that the absorber is at the origin and the list is sorted by distance from the absorber. The non-obvious part of this algorithm is the first step. To fill out the unit cell, these steps are taken: a. For each atomic position given to Atoms, apply the symmetry operations associated with the point group. These are the operations reported in the symmetry.dat output file. They are also given in the International Tables of Crystallography for each space group. b. For each position found from the point group, apply the Bravais translations, if any. c. Some of the coordinates found from applying the point and Bravais operations will fall outside the first octant, that is, there may be coordinates smaller than 0 or larger than or equal to 1. Translate those positions back to the first octant by adding the appropriate integer to the offending coordinate. d. Weed through the list of positions and throw away any repeats. For high symmetry groups, the vast majority of generated positions will be repeats. For FCC copper, for example, you will find that the point and Bravais operations generate the same point 96 times. At the end of step 1, you have the contents of the P1 output file. That is, you have a description in fractional coordinates of the entire contents of the unit cell. For step 2 above, it is much easier to use the fractional coordinates to stack up unit cells to make the rhomboid. The unit cell in the +x direction is made by adding 1 to all the x coordinates. The unit cell in the -y direction is made by subtracting 1 from all the y coordinates. And so on. The conversion to Cartesian coordinates is where the lattice constants and angles come into play. This is a tensor transform where the non-zero elements of the metric tensor are functions of a, b, c, alpha, beta, and gamma. This tensor is discussed in Volume A of the International Tables and in many crystallography textbooks. The geometrically inclined could probably derive it on the back of an envelope. Or see the subroutines Xray::Xtal::Cell::make and Xray::Xtal::Cell::metric in the file Xtal.pm from the Atoms distribution. The last interesting detail is how the absorber atom is chosen. In a space group of high symmetry, there may well be several examples of the absorber in the unit cell. Atoms chooses the one that is closest to the center of the unit cell, i.e. the one closest to (1/2, 1/2, 1/2). This choice minimizes the size of the rhomboid needed to encompass the sphere of radius Rmax. Now, wasn't that fascinating? 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/

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