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

trouble, trouble, trouble
by Bruce Ravel 10 Jan '03

10 Jan '03

Hi folks, The release I made yesterday seems to be the buggiest one I have released in quite some time. I have been getting lots of reports of problems with the latest source code tarball. Sigh. I am working on a new release -- hopefully things will be looking better on Monday. If anyone needs a copy of the previous release, you can grab it at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/horae-00… The entire archive of old versions is at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/ Sorry for the confusion and thanks especially to Jeff Terry, Paul Fons, and Shelly Kelly who have been very generous with their time and their useful bug reports. 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/

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Athena 0.8.009
by Bruce Ravel 09 Jan '03

09 Jan '03

Hi Folks, Since it has been almost a month since my last release of software and since I expect to be busy for the next couple of week, I decided to release all the stuff I worked on over the holidays. There are no changes to Artemis this time, but lots of changes to Athena. A new tarball and a new Windows executable for Athena are on my website. Lots of bug fixes this time, so I recommend that everyone upgrade. Check out the change log on my web page for all the new stuff. The highlights are 1. Fixed the problem involving long file names. Now the group name used by Ifeffit is constrained to 8 characters and is different from the string displayed in the groups list. This solves a number of recent complaints about mysterious misbehavior. It has the additional benefit of allowing you to change the string displayed in the group list to something that has spaces or non-alphanumeric characters. 2. Implemented a "recent files" feature under the File menu. This remembers the 8 most recent files that you read into Athena and allows you to reread them quickly. It uses an external file, so it "remembers" between sessions with Athena. 3. Added a dialog accessible from the Plot menu which allows you to quickly and easily set the y-offset values for marked groups in a way that is suitable for stacked plots. There are several other bug fixes and small improvements. And the documentation lags ever farther behind -- sigh! Extra thanks this time around to Dale Brewe. He pointed out an alarming number of problems one December afternoon while I was working at his beamline. I think I fixed all of them. Regards, B P.S. I have not yet addressed the problem in Artemis which Michel Schlegel pointed out earlier this week. What's mpre, command line users will notice that Artemis spits up a cryptic warning about an "Un-named file" as it starts up. I believe that warning can be safely ignored. -- 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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athena, OS X, and Apple's new X11
by Jeff Terry 09 Jan '03

09 Jan '03

Hi All, I just wanted to let everyone know that Artemis, Athena, and tkAtoms work with Apple's new implementation of X11. Jeff

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a problem with windows on Windows ...
by Bruce Ravel 07 Jan '03

07 Jan '03

Hi all, Michel Schlegel pointed out that there is a problem in the most recent version of Artemis wherein the Fourier transform window does not get properly displayed. Oddly, I could only reproduce this problem on Windows and not on my linux machine. So, for you Windows users -- you will either have to live without plots of window functions until I can get around to finding and fixing the bug or you may want to consider not upgrading Artemis until the next version. This window problem does *not* seem to be an issue for Athena either on Windows or on linux. When I release a version of Artemis that fixes this problem, I will, as usual, make an announcement here. Happy New Year! 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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RE: Plots of apodization Windows in Athena 0.8.005 and artemis.0. 5.004
by SCHLEGEL Michel 177447 07 Jan '03

07 Jan '03

Hello, > I hope you don't mind that I am sending my responses to your questions > to the Ifeffit mailing list. They seem of sufficiently general > interest that I think the Ifeffit list would be interested. I don't. :) > MS> Another detail which kind of puzzles me: whenewever I use a > MS> Kaiser-Bessel window and increase the weight, the *plotted* > MS> limits of the apodization window shift away from the positions > MS> defined in the command window (e.g., for positions set to 2 and > MS> 13 Å-1 in the command window and a weight dk = 1, the plotted > MS> apodization limits are shifted to 1 and 14 Å-1). > > I am a bit confused by the numbers you give in that they are not > consistent with what I observe when I make a plot displaying a > Kaiser-Bessel window. Here is what I observe: > > For a window defined by kmin=2, kmax=18, and dk=2, the first > non-zero value of the window is at k=1 and the last non-zero value > is at k=19. In general terms, the first non-zero value of the > Kaiser-Bessel window is at kmin-dk/2 and the last is at kmax+dk/2. OK, I wanted to make the distinction between the first and last non-zero values as they *appear* in the graphic window, and the numerical values as stored as internal values in the software. I assumed that these values were not the same. This assumption, but was -partly - justified by the wollowing reason: If I keep kmin and kmax constant and increase dk, I increase the k-range covered by the K.B. window, and this should result in an increase of the number of independent points. What I observe is that the number of independent points calculated by artemis is *not* affected by dk, suggesting that the FT range remains limite to [kmin, kmax]. > The bottom line is that you may want to set kmin a bit higher so that > kmin-dk/2 is at the point where you want the window to start. Note > that setting dk to 0 is probably *not* what you want to do, although > it is probably worth doing so just once to see what happens to the K-B > window. I did: the first and last non-zero values plot exactly at kmin and kmax. > MS> A final 'cosmetic' suggestion: would it be possible in future > MS> versions of artemis, to plot both the amplitude and real part, or > MS> amplitude and imaginary parts of experimental and simulated > MS> chi(R) together? > > > You are not the first person to ask for this, Michel, but the last > time this came up, Artemis was much less far along. Sorry for being late... > So, let me put it up to discussion among the folk on this mailing > list. What should Artemis do? > > 1. Allow the user to select one or more parts of chi(R) (or chi(q) > for that matter) and plot each of those parts for each of the > things selected in the "Paths" list. > 2. Allow the user to somehow specify which parts of chi(R) to plot > for the data, the fit, and each path individually. (This would > make the interface somewhat more complex.) > 3. Continue to work exactly as it works now. > 4. Something else entirely. Basically in a simulation, both the amplitude and the phase of selected paths may be (shoud be?) compared. Therefore, I would select (1) (but let me reiterate that this is not a priority to me). Thanks in advance, and happy new year, Michel Schlegel

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Plots of apodization Windows in Athena 0.8.005 and artemis.0.5.004
by Bruce Ravel 06 Jan '03

06 Jan '03

Michel, I hope you don't mind that I am sending my responses to your questions to the Ifeffit mailing list. They seem of sufficiently general interest that I think the Ifeffit list would be interested. MS> I used artemis.0.5.004 to open a project created with MS> artemis.0.5.002. I noticed that the apodization window didn't MS> plot correctly in the R-space (i.e., it is just a red flat line MS> instead of a cathedral door-like shape), eventhough I checked the MS> 'Window' box as a plotting option. Hmm... that certainly seems like a problem, but I am not certain which problem. Unlike the Athena project files, the Artemis project files do not currently contain the data, they only contain a pointer to the data. It is possible that the data moved, that you are on another computer, or for some other reason the path and file listed in your project file just don't point to the correct thing. If you select "Change data file" from the "Data" menu and refresh the location of the data, does that solve the problem? If not, you should prepare a bug report as described at http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html so I can figure out what is really going on. MS> Another detail which kind of puzzles me: whenewever I use a MS> Kaiser-Bessel window and increase the weight, the *plotted* MS> limits of the apodization window shift away from the positions MS> defined in the command window (e.g., for positions set to 2 and MS> 13 Å-1 in the command window and a weight dk = 1, the plotted MS> apodization limits are shifted to 1 and 14 Å-1). I am a bit confused by the numbers you give in that they are not consistent with what I observe when I make a plot displaying a Kaiser-Bessel window. Here is what I observe: For a window defined by kmin=2, kmax=18, and dk=2, the first non-zero value of the window is at k=1 and the last non-zero value is at k=19. In general terms, the first non-zero value of the Kaiser-Bessel window is at kmin-dk/2 and the last is at kmax+dk/2. The ultimate reference is, I suppose, the source code. In the src/lib/ folder of the ifeffit source directory, you will find the source code file "window.f". The first and last non-zero values for this and several other window types are defined around line 123. (Note that the comments at the top of the file regarding the K-B window are incorrect in that they contradict the code around lines 123.) The exact shape of the window and whether it falls all the way to zero is determined by some parameters computed from kmin, kmax, and dk and by the evaluation of a Bessel's function. This is all around line 167. The comments in window.f suggest this as a reference for the K-B window: 'Digital Filter' by J.F. Kaiser in 'System Analysis by Digital Computers' edited by F.F. Kuo and J.F. Kaiser, (New York; Wiley) 1966 The bottom line is that you may want to set kmin a bit higher so that kmin-dk/2 is at the point where you want the window to start. Note that setting dk to 0 is probably *not* what you want to do, although it is probably worth doing so just once to see what happens to the K-B window. MS> A final 'cosmetic' suggestion: would it be possible in future MS> versions of artemis, to plot both the amplitude and real part, or MS> amplitude and imaginary parts of experimental and simulated MS> chi(R) together? You are not the first person to ask for this, Michel, but the last time this came up, Artemis was much less far along. I suppose that it is time to revisit this issue. The reason that Artemis does not currently let you plot more than one part of chi(R) at a time is because it is so very easy to plot the data, the fit, the background spline, and any number of paths with a single mouse click. Already, that can make for an absurdly busy plot. If Artemis plotted *two* parts of each item, the plot would be twice as busy and twice as much of a mess. I suppose, though, that I should not be worried about that. That is, I shouldn't put too many limitations on what you can plot. If you choose to plot an unreadable number of traces, I should certainly let you do so! However, the situation gets more confusing as you allow more possible combinations of traces. For example, it might be reasonable to plot the amplitude and real part of the data and fit along with just the real parts of some of the paths. And so on... So, let me put it up to discussion among the folk on this mailing list. What should Artemis do? 1. Allow the user to select one or more parts of chi(R) (or chi(q) for that matter) and plot each of those parts for each of the things selected in the "Paths" list. 2. Allow the user to somehow specify which parts of chi(R) to plot for the data, the fit, and each path individually. (This would make the interface somewhat more complex.) 3. Continue to work exactly as it works now. 4. Something else entirely. Let me know! Happy New Year to all! B -- Bruce Ravel ----------------------------------- ravel@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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Athena 0.8.008 and Artemis 0.5.004
by Bruce Ravel 13 Dec '02

13 Dec '02

Hi Folks, I just uploaded new source code tarballs and new windows executables for the two programs to my web site. This release is mostly about bug fixes. You can read about those in the change logs. Athena has two big new features. 1. A dialog for fitting Gaussians/Lorentzians and an arctangent to near-edge peaks. See the "Analysis" menu. It is currently undocumented, but you should be able to figure it out by poking at the buttons. Here's a screenshot: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/pea… 2. An option at the bottom of the "Edit" menu for generating reports about the background removal and FT parameters for all the data groups. The options for these reports are plain text, Excel spreadsheet files, or comma-separated-value (csv) spreadsheets. The other new thing, which is relevant to Unix and Mac OSX users is a change to the build scripts. I have modified the Makefile.PL to incorporate a suggestion Matt had for avoiding the problems that several people reported this week regarding difficulties finding the PGPLOT library during the build of the ifeffit wrapper. The new build script works for me. I trust you will let me know if you have any problems. Special thanks this time to Adam Webb and Paul Fons who both found ways to crash Athena this week. Happily, they will both now have to start searching for new ways. 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/

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Re: [Ifeffit] Max OS X woes -- Solution ?
by Paul Fons 12 Dec '02

12 Dec '02

Some observations. In conjunction with the initialization file from fink there are path variables set that tell where the fink pgplot directory is (presumably on other Unixes as well). In terms of moving away from pgplot, I have been using a crystallographic library that uses blt (written in tcl) that is an extension to tcl/Tk. This is free and has scientific graphics functionality and also is being continually updated. The web site is: http://sourceforge.net/projects/blt/. The advantage here is that this is a write-once use everywhere library. The downside is that it is in tcl/Tk so you would have to interface via some intermediate code from fortran, but I suspect Bruce knows a lot more about Tk than I. The blurb on sourceforge states: The BLT Toolkit is an extension to Tcl and Tk. It adds new commands and widgets to the Tcl interpreter. Included widgets are 2D graph, barchart, stripchart, tab notebook, and tree viewer. Also in looking over the fink list, there is a gnu library called plotlibs (http://www.gnu.org/software/plotutils/) which is a device independent library that outputs in just about every format available. This is callable from fortran or c and also would seem to support a format a windows viewer could use (I think other than a blt/java route windows will always have to be different -- Bill Gates wants it that way) (from the web site) GNU libplot and libplotter support all the output formats mentioned above (X11, SVG, PNG, PNM, pseudo-GIF, WebCGM, Illustrator format, idraw-editable Postscript, PCL 5, Fig format, HP-GL/2, ReGIS, Tektronix, and GNU Metafile). They can produce animated pseudo-GIFs, and smooth, double-buffered animations on any X Window System display. The libplot imaging model is similar to Postscript's. In any output format, they can draw the following. • Graphical objects such as lines, circles and ellipses, points, and marker symbols; also paths. A path is defined as in Postscript as a sequence of line segments, arcs (either circular or elliptic), or Bezier curve segments (either quadratic or cubic). Paths may be open or closed, and they may be dashed. The filling of paths is supported (fill color, as well as pen color, may be set arbitrarily). • Text strings, in many fonts. Text strings may include subscripts and superscripts, and may include characters chosen from more than one font in a typeface. The X11, SVG, WebCGM, Illustrator, Postscript, and xfig drivers support the 35 standard Postscript fonts, and the SVG, Illustrator, PCL 5 and HP-GL/2 drivers support the 45 standard PCL 5 fonts. All drivers support a set of 22 Hershey vector fonts. This includes HersheyCyrillic, a Russian font that uses the KOI8-R encoding, and HersheyEUC, a Japanese font that uses the 8-bit EUC-JP encoding. Japanese text strings may include both syllabic characters (Hiragana and Katakana) and ideographic characters (Kanji). A library of over 600 Kanji is built in. When using libplot or libplotter, a programmer draws vector graphics in a `user frame', rather than in the device frame. As in Postscript, the user frame may be transformed into the device frame by an arbitrary affine map. Scaling, rotation, shearing, and translation are all supported. On Friday, December 13, 2002, at 08:17 AM, Matt Newville wrote: > Bruce, Paul, > >> Solving the problem at the level of ifeffit's build doesn't quite >> address the horae problem. The whole point of putting Ifeffit.pm and >> the wrapper in the horae tarball was one-stop shopping for perl-y >> goodness. However, it may suffice if the ifeffit C program, when >> invoked with a --pgplot_dir command line flag, writes the location of >> pgplot to STDOUT and exits. Then I could use perl's exec command in >> the Makefile.PL to set the compiler's -L flag properly. I normally >> avoid exec because I don't understand how it works on Windows. But I >> don't have Makefile.PL compile the wrapper on Windows, so it should be >> ok. > > See, I think ifeffit's build *should* solve horae's problem on > Unixes (Mac OS X included). Windows is inherently different. On > Unix, the issue of how to link to Ifeffit lib, PGPLOT lib (any > extra libs like X, png, ...) and generic C libs on any particular > machine are all fully determined when Ifeffit's Makefile is run. > > So Ifeffit's build can write all the needed build info without > relying on ExtUtils::F77, OS-specific switches, or any hardwired > values. In fact, an easily parsed Config.mak is built and > installed. In perl, this could be used like this: > > $iff_path = `ifeffit -i`; > chomp $iff_path; > $iff_path =~ s/ $//g; > $file = "$iff_path/config/Config.mak"; > open(F,$file) or die "no file $file .. Ifeffit not installed?\n"; > my @keys = ('LIB_IFF','LIB_PLT','LIB_F77','INC_IFF'); > my %build; > while(<F>){ > chomp; > foreach $i (@keys) { > if (/^$i[ ]*=(.*)/) { $build{$i} = $1;} > } > } > close(F) > foreach $i (@keys){ print "$i: $build{$i}\n";} > > I'm sure it could be done more elegantly... But Ifeffit's build > should be fixed to make sure it finds /sw/lib/pgplot and not > /sw/pgplot for PGPLOT on MacOS X. > >> Actually fink is way better than RPM. (More precisely, debian's >> apt-get is way better than RPM. Fink's cleverness was to use apt-get >> but the credit for an amazing packaging system goes to those clever >> debian folks.) > > I can agree that Fink is clever, and that apt is more clever than > RPM. I may even agree that apt is _better_ than RPM. That's not > high praise. All binary package systems are painful. Like, Fink > can just up and decide to move PGPLOT, and we're screwed. > >> And, yes, pgplot is a thorn in my side. Adam Webb at the U of >> Alberta had the linux equivalent of this problem the other day. > > What was the linux problem? PGPLOT_install should work fine on > all linuxes. Or did Adam do something silly like rely on a > binary package from debian... Oh, wait a second. > > I'd much prefer a plotting lib that could be built with ifeffit, > not relying on a separate library, and worked better on Windows. > I'd be willing to use python/blt myself, but some people still > like perl, so something that works in C/Fortran is needed. > PLPLOT is a possibility, so is using R, or wxWindows. PLPLOT is > the most like PGPLOT, but less stable than PGPLOT (no, really), > but at least they're working on it. R is straight C (GPL'ed), > and probably a LOT of work to use, but makes lovely plots. > > --Matt > > Paul Fons, Ph.D. Senior Staff Researcher Photonics Institute National Institute for Advanced Industrial Science & Technology Tsukuba, JAPAN 305-8568 email: paul-fons(a)aist.go.jp tel. +81-298-61-5636 fax: +81-298-61-5615 The lines below are in Japanese 主任研究官　ポール・フォンス産業技術総合研究所光技術研究部門つくば市茨城県　 305-8568

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more Max OS X woes!
by Matt Newville 12 Dec '02

12 Dec '02

Maurizio, Patrick, everyone, It appears there are some serious problems getting the latest 'Ifeffit/Athena' running on Max OS X -- both 10.1 and 10.2. The sympton is gettting messages like dyld: perl Undefined symbols: _pgarro_ _pgask_ which means the Ifeffit perl module is no longer able to find the PGPLOT library. When this happens, older versions of athena are also broken. My guess is that this is related to the changes in horae's Makefile.PL for horae-007, but I haven't looked into it any further. I believe the workaround is to go back to the Ifeffit source distribution and reinstall the ifeffit perl module from there: cd ...../ifeffit_1.0b/wrappers/perl perl Makefile.PL make make install and then back-tracking to horae-006.tar.gz: http://feff.phys.washington.edu/~ravel/software/exafs/packages/horae-006.ta… At least, this worked on Patrick's laptop last week. It might be enough to simply backtrack to horae-006. Sorry for all the trouble, --Matt On Wed Dec 11, Maurizio Aiello <aiello(a)ge.cnr.it> wrote: > > Dear Matt, > I tried to install ona fresh Mac-osX 10.1.4 athena. I followed all steps > necessary, (it required ten hours of continuous compilation) for installing > everything. I replaced dynamic loader with the patched one, and in fact > now I dont' have multiple definition error. But when i run perl -e "use > ifeffit" or I run from within an xterm in Xdarwin the command athena the > answer is: > > [localhost:~] marzia% perl -e "use ifeffit" > dyld: perl Undefined symbols: > _pgarro_ > _pgask_ > ..... > > > If I substitute dyld with the original one now the error is (of course) > [localhost:~] marzia% athena > dyld: perl multiple definitions of symbol _LangExit > /Library/Perl/darwin/auto/Tk/Event/Event.bundle definition of _LangExit > /Library/Perl/darwin/auto/Tk/Tk.bundle definition of _LangExit > > > If I run ifeffit directly from command line it seems to work correctly. > > Can you help me? > Thanks a lot. > > P.S. I am a Unix-Network programmer, I'm doing this job for my wife, she is > a researcher. I don't have any knowledge on what these programs do, I only > compile and debug and so on :-)))) > > Thanks a lot > > Maurizio Aiello On Wed Dec 11, Patrick Allen <allen42(a)llnl.gov> wrote: > > This is entirely FYI: I couldn't resist and got Jaguar 10.2.2 going now. > I reinstalled nearly every package I could think of and got very close > with Athena and get the message: > > dyld: perl Undefined symbols: > _G77_getenv_0 > _pgarro_ > _pgask_ > _pgband_ > _pgbbuf_ > _pgbox_ > etc..... > Trace/BPT trap > > So for the moment, I chickened out and downloaded the whole darn thing > onto my Virtual PC partition on OSX. It works and I can play with my > PNC-CAT files with the latest programs. I'm looking forward to coming out to > Chicago more now. Seasons greetings!

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occupancy numbers vs stochiometry with TkAtoms
by John J. Rehr 11 Dec '02

11 Dec '02

Hi Bruce, I have an inquiry about the Li XANES of a Li silicate Li4SiO4 with the following atoms.inp input file: ------------------------------------------------- title name: Li4SiO4 monoclinic structure title sites1: Si, O1-3, Li1-6 space = P 21/M a=5.14 b=6.10 c=5.30 beta=90.5 core = Li atoms # elem. x y z tag occ Si 0.6640 0.25 0.3252 Si 1. O 0.7737 0.0303 0.1842 O1 1. O 0.3526 0.25 0.3178 O2 1. O 0.7677 0.25 0.6210 O3 1. Li 0.165 0.009 0.174 Li1 0.667 Li 0.398 0.25 0.711 Li2 0.50 Li 0.164 0.25 0.644 Li 0.50 Li 0.398 0.964 0.150 Li4 0.333 Li 0.048 0.034 0.449 Li5 0.333 Li 0.057 0.25 0.981 Li6 0.334 ------------------------------------------------- The "confusing" thing, to me at least, is how TkAtoms interprets the occupation numbers, since the feff8 template gives the wrong stoichiometry for Li (should be identical to that for O, i.e. 8). POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 3 Li 1 1 0.001 1 14 Si 2 2 2 2 8 O 1 1 8 3 3 Li 1 1 18 Questions: 1) what is the recommended procedure for lattices with non-integer occupation? The Atoms documentation seems not very specific on this point, though it does emphasize the "confusing" aspects of the problem and the fact that it is easy to generate nonsense feff.inp. For example I could edit the feff.inp file that is generated and cut out *arbitrarily* some fraction of the atoms of a given tag, e.g., 2/3 of the Li1s, 1/2 of the Li2s, etc. But I also must edit the stoichiometry so the potentials come out right. But this procedure does seem arbitrary. Also, it appears that the Li atoms in this material are not all distinguishable so one has to take a linear combination FEFF runs for the different input Li sites. 2) can TkAtoms take the occupancy into account in determining the stoichiometry? Thanks much for your comments on this. Cheers, John Rehr The full feff.inp file is attached: * This feff8 input file was generated by TkAtoms 3.0beta7 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE name: Li4SiO4 monoclinic structure TITLE sites1: Si, O1-3, Li1-6 * Li K edge energy = 54.70 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 4.11922 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 10.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 3 Li 1 1 0.001 1 14 Si 2 2 2 2 8 O 1 1 8 3 3 Li 1 1 18 ATOMS * this list contains 720 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Li6 0.00000 0 0.55510 1.47010 1.01806 3 Li1 1.87237 1 0.55510 -1.47010 1.01806 3 Li1 1.87237 2 0.54996 0.00000 -1.79090 3 Li 1.87344 3 -1.14104 1.57990 -0.81154 3 Li1 2.11108 4 -1.14104 -1.57990 -0.81154 3 Li1 2.11108 5 0.87017 1.70983 -0.88315 2 O1 2.11203 6 0.87017 -1.70983 -0.88315 2 O1 2.11203 7 -1.45611 1.34017 1.08967 2 O1 2.25913 8 -1.45611 -1.34017 1.08967 2 O1 2.25913 9 1.75267 0.00000 -1.44630 3 Li2 2.27236 10 1.51933 0.00000 1.77178 2 O2 2.33400 11 -1.48695 0.00000 -1.89502 2 O3 2.40876 12 1.75267 1.74460 0.88040 3 Li4 2.62500 13 1.75267 -1.74460 0.88040 3 Li4 2.62500 14 -2.01994 0.00000 1.84189 1 Si 2.73363 15 -2.33861 1.30540 -0.67389 3 Li4 2.76176 16 -2.33861 -1.30540 -0.67389 3 Li4 2.76176 17 -0.04626 1.31760 2.48080 3 Li5 2.80938 18 -0.04626 -1.31760 2.48080 3 Li5 2.80938 19 -0.53968 1.73240 -2.27429 3 Li5 2.90944 20 -0.53968 -1.73240 -2.27429 3 Li5 2.90944 21 -0.04626 1.31760 -2.81920 3 Li5 3.11225 22 -0.04626 -1.31760 -2.81920 3 Li5 3.11225 23 -0.58594 3.05000 0.20651 3 Li6 3.11263 24 -0.58594 -3.05000 0.20651 3 Li6 3.11263 25 2.80119 1.30540 -0.71875 3 Li4 3.17291 26 2.80119 -1.30540 -0.71875 3 Li4 3.17291 27 -0.53968 1.73240 3.02571 3 Li5 3.52808 28 -0.53968 -1.73240 3.02571 3 Li5 3.52808 29 0.54996 0.00000 3.50910 3 Li 3.55193 30 3.11986 0.00000 1.79703 1 Si 3.60040 31 -3.38713 0.00000 -1.40144 3 Li2 3.66561 32 -1.48695 0.00000 3.40498 2 O3 3.71549 33 1.43401 3.05000 -1.63537 1 Si 3.74611 34 1.43401 -3.05000 -1.63537 1 Si 3.74611 35 0.90101 3.05000 2.10154 2 O3 3.81193 36 0.90101 -3.05000 2.10154 2 O3 3.81193 37 -1.13590 3.05000 1.99741 3 Li 3.81869 38 -1.13590 -3.05000 1.99741 3 Li 3.81869 39 1.51933 0.00000 -3.52822 2 O2 3.84144 40 -3.38713 1.74460 0.92526 3 Li4 3.92076 41 -3.38713 -1.74460 0.92526 3 Li4 3.92076 42 -2.01994 0.00000 -3.45811 1 Si 4.00484 43 -2.10526 3.05000 -1.56527 2 O2 4.02302 44 -2.10526 -3.05000 -1.56527 2 O2 4.02302 45 -3.62048 0.00000 1.81664 2 O2 4.05068 46 3.68370 1.34017 1.04481 2 O1 4.05676 47 3.68370 -1.34017 1.04481 2 O1 4.05676 48 3.65286 0.00000 -1.93988 2 O3 4.13600 49 -2.33861 3.05000 1.65281 3 Li2 4.18370 50 -2.33861 -3.05000 1.65281 3 Li2 4.18370 51 1.75267 0.00000 3.85370 3 Li2 4.23354 52 3.99877 1.57990 -0.85640 3 Li1 4.38402 53 3.99877 -1.57990 -0.85640 3 Li1 4.38402 54 2.80119 3.05000 1.60795 3 Li2 4.44238 55 2.80119 -3.05000 1.60795 3 Li2 4.44238 56 0.90101 3.05000 -3.19846 2 O3 4.51049 57 0.90101 -3.05000 -3.19846 2 O3 4.51049 58 0.55510 1.47010 -4.28194 3 Li1 4.56118 59 0.55510 -1.47010 -4.28194 3 Li1 4.56118 60 0.87017 4.39017 -0.88315 2 O1 4.56188 61 0.87017 -4.39017 -0.88315 2 O1 4.56188 62 3.03454 3.05000 -1.61012 2 O2 4.59385 63 3.03454 -3.05000 -1.61012 2 O2 4.59385 64 -1.13590 3.05000 -3.30259 3 Li 4.63679 65 -1.13590 -3.05000 -3.30259 3 Li 4.63679 66 -1.45611 1.34017 -4.21033 2 O1 4.65223 67 -1.45611 -1.34017 -4.21033 2 O1 4.65223 68 -4.26964 1.70983 -0.83830 2 O1 4.67505 69 -4.26964 -1.70983 -0.83830 2 O1 4.67505 70 3.11986 0.00000 -3.50297 1 Si 4.69087 71 -1.14104 4.52010 -0.81154 3 Li1 4.73200 72 -1.14104 -4.52010 -0.81154 3 Li1 4.73200 73 0.55510 4.62990 1.01806 3 Li1 4.77290 74 0.55510 -4.62990 1.01806 3 Li1 4.77290 75 1.75267 4.35540 0.88040 3 Li4 4.77666 76 1.75267 -4.35540 0.88040 3 Li4 4.77666 77 0.87017 1.70983 4.41685 2 O1 4.81552 78 0.87017 -1.70983 4.41685 2 O1 4.81552 79 -1.14104 1.57990 4.48846 3 Li1 4.89329 80 -1.14104 -1.57990 4.48846 3 Li1 4.89329 81 -4.58985 0.00000 -1.74605 3 Li 4.91074 82 -4.58471 1.47010 1.06291 3 Li1 4.93057 83 -4.58471 -1.47010 1.06291 3 Li1 4.93057 84 -0.53968 4.36760 -2.27429 3 Li5 4.95374 85 -0.53968 -4.36760 -2.27429 3 Li5 4.95374 86 3.65286 0.00000 3.36012 2 O3 4.96324 87 1.43401 3.05000 3.66463 1 Si 4.97879 88 1.43401 -3.05000 3.66463 1 Si 4.97879 89 -3.62048 0.00000 -3.48336 2 O2 5.02411 90 -3.70580 3.05000 -1.59052 1 Si 5.05620 91 -3.70580 -3.05000 -1.59052 1 Si 5.05620 92 1.75267 1.74460 -4.41960 3 Li4 5.06442 93 1.75267 -1.74460 -4.41960 3 Li4 5.06442 94 -1.45611 4.75983 1.08967 2 O1 5.09545 95 -1.45611 -4.75983 1.08967 2 O1 5.09545 96 -5.13980 0.00000 0.04485 3 Li6 5.14000 97 5.13980 0.00000 -0.04485 3 Li6 5.14000 98 -3.38713 0.00000 3.89856 3 Li2 5.16444 99 -2.10526 3.05000 3.73473 2 O2 5.26145 100 -2.10526 -3.05000 3.73473 2 O2 5.26145 101 -2.33861 3.05000 -3.64719 3 Li2 5.29845 102 -2.33861 -3.05000 -3.64719 3 Li2 5.29845 103 0.00000 0.00000 5.30000 3 Li6 5.30000 104 0.00000 0.00000 -5.30000 3 Li6 5.30000 105 -0.53968 4.36760 3.02571 3 Li5 5.34061 106 -0.53968 -4.36760 3.02571 3 Li5 5.34061 107 -2.33861 1.30540 4.62611 3 Li4 5.34547 108 -2.33861 -1.30540 4.62611 3 Li4 5.34547 109 -2.33861 4.79460 -0.67389 3 Li4 5.37693 110 -2.33861 -4.79460 -0.67389 3 Li4 5.37693 111 -0.04626 4.78240 2.48080 3 Li5 5.38775 112 -0.04626 -4.78240 2.48080 3 Li5 5.38775 113 4.00391 3.05000 1.95256 3 Li 5.39873 114 4.00391 -3.05000 1.95256 3 Li 5.39873 115 4.60012 1.73240 -2.31914 3 Li5 5.43514 116 4.60012 -1.73240 -2.31914 3 Li5 5.43514 117 4.55387 3.05000 0.16166 3 Li6 5.48328 118 4.55387 -3.05000 0.16166 3 Li6 5.48328 119 2.80119 1.30540 4.58125 3 Li4 5.52618 120 2.80119 -1.30540 4.58125 3 Li4 5.52618 121 2.80119 3.05000 -3.69205 3 Li2 5.54801 122 2.80119 -3.05000 -3.69205 3 Li2 5.54801 123 -0.04626 4.78240 -2.81920 3 Li5 5.55170 124 -0.04626 -4.78240 -2.81920 3 Li5 5.55170 125 -3.38713 4.35540 0.92526 3 Li4 5.59449 126 -3.38713 -4.35540 0.92526 3 Li4 5.59449 127 2.80119 4.79460 -0.71875 3 Li4 5.59924 128 2.80119 -4.79460 -0.71875 3 Li4 5.59924 129 -4.23880 3.05000 2.14639 2 O3 5.64596 130 -4.23880 -3.05000 2.14639 2 O3 5.64596 131 3.03454 3.05000 3.68988 2 O2 5.66799 132 3.03454 -3.05000 3.68988 2 O2 5.66799 133 4.60012 1.73240 2.98086 3 Li5 5.74873 134 4.60012 -1.73240 2.98086 3 Li5 5.74873 135 3.68370 1.34017 -4.25519 2 O1 5.78553 136 3.68370 -1.34017 -4.25519 2 O1 5.78553 137 5.09355 1.31760 2.43595 3 Li5 5.79777 138 5.09355 -1.31760 2.43595 3 Li5 5.79777 139 -3.38713 1.74460 -4.37474 3 Li4 5.80126 140 -3.38713 -1.74460 -4.37474 3 Li4 5.80126 141 -4.58985 0.00000 3.55395 3 Li 5.80494 142 -5.18606 1.31760 2.52566 3 Li5 5.91695 143 -5.18606 -1.31760 2.52566 3 Li5 5.91695 144 5.69490 1.47010 0.97320 3 Li1 5.96156 145 5.69490 -1.47010 0.97320 3 Li1 5.96156 146 -0.58594 3.05000 -5.09349 3 Li6 5.96569 147 -0.58594 -3.05000 -5.09349 3 Li6 5.96569 148 5.68976 0.00000 -1.83575 3 Li 5.97858 149 5.09355 1.31760 -2.86405 3 Li5 5.99025 150 5.09355 -1.31760 -2.86405 3 Li5 5.99025 151 -5.18606 1.31760 -2.77434 3 Li5 6.02730 152 -5.18606 -1.31760 -2.77434 3 Li5 6.02730 153 4.00391 3.05000 -3.34744 3 Li 6.04476 154 4.00391 -3.05000 -3.34744 3 Li 6.04476 155 -3.70580 3.05000 3.70948 1 Si 6.06594 156 -3.70580 -3.05000 3.70948 1 Si 6.06594 157 3.99877 4.52010 -0.85640 3 Li1 6.09548 158 3.99877 -4.52010 -0.85640 3 Li1 6.09548 159 0.00000 6.10000 0.00000 3 Li6 6.10000 160 0.00000 -6.10000 0.00000 3 Li6 6.10000 161 -4.23880 3.05000 -3.15361 2 O3 6.10042 162 -4.23880 -3.05000 -3.15361 2 O3 6.10042 163 3.68370 4.75983 1.04481 2 O1 6.10878 164 3.68370 -4.75983 1.04481 2 O1 6.10878 165 -4.26964 4.39017 -0.83830 2 O1 6.18111 166 -4.26964 -4.39017 -0.83830 2 O1 6.18111 167 3.99877 1.57990 4.44360 3 Li1 6.18319 168 3.99877 -1.57990 4.44360 3 Li1 6.18319 169 0.87017 4.39017 4.41685 2 O1 6.28803 170 0.87017 -4.39017 4.41685 2 O1 6.28803 171 6.00997 1.70983 -0.92801 2 O1 6.31700 172 6.00997 -1.70983 -0.92801 2 O1 6.31700 173 -0.58594 3.05000 5.50651 3 Li6 6.32199 174 -0.58594 -3.05000 5.50651 3 Li6 6.32199 175 0.55510 4.62990 -4.28194 3 Li1 6.33081 176 0.55510 -4.62990 -4.28194 3 Li1 6.33081 177 -5.67948 1.73240 -2.22944 3 Li5 6.34256 178 -5.67948 -1.73240 -2.22944 3 Li5 6.34256 179 0.54996 6.10000 -1.79090 3 Li 6.38120 180 0.54996 -6.10000 -1.79090 3 Li 6.38120 181 -4.26964 1.70983 4.46170 2 O1 6.40781 182 -4.26964 -1.70983 4.46170 2 O1 6.40781 183 -4.58471 1.47010 -4.23709 3 Li1 6.41355 184 -4.58471 -1.47010 -4.23709 3 Li1 6.41355 185 -1.14104 1.57990 -6.11154 3 Li1 6.41475 186 -1.14104 -1.57990 -6.11154 3 Li1 6.41475 187 1.75267 4.35540 -4.41960 3 Li4 6.44781 188 1.75267 -4.35540 -4.41960 3 Li4 6.44781 189 -1.14104 4.52010 4.48846 3 Li1 6.47144 190 -1.14104 -4.52010 4.48846 3 Li1 6.47144 191 0.87017 1.70983 -6.18315 2 O1 6.47396 192 0.87017 -1.70983 -6.18315 2 O1 6.47396 193 -5.72574 3.05000 0.25137 3 Li6 6.49229 194 -5.72574 -3.05000 0.25137 3 Li6 6.49229 195 1.75267 6.10000 -1.44630 3 Li2 6.50950 196 1.75267 -6.10000 -1.44630 3 Li2 6.50950 197 0.55510 1.47010 6.31806 3 Li1 6.51054 198 0.55510 -1.47010 6.31806 3 Li1 6.51054 199 -1.45611 4.75983 -4.21033 2 O1 6.51944 200 -1.45611 -4.75983 -4.21033 2 O1 6.51944 201 -6.28084 1.57990 -0.76669 3 Li1 6.52172 202 -6.28084 -1.57990 -0.76669 3 Li1 6.52172 203 1.51933 6.10000 1.77178 2 O2 6.53128 204 1.51933 -6.10000 1.77178 2 O2 6.53128 205 -2.33861 1.30540 -5.97389 3 Li4 6.54680 206 -2.33861 -1.30540 -5.97389 3 Li4 6.54680 207 -1.48695 6.10000 -1.89502 2 O3 6.55836 208 -1.48695 -6.10000 -1.89502 2 O3 6.55836 209 -4.58471 4.62990 1.06291 3 Li1 6.60191 210 -4.58471 -4.62990 1.06291 3 Li1 6.60191 211 1.75267 1.74460 6.18040 3 Li4 6.65679 212 1.75267 -1.74460 6.18040 3 Li4 6.65679 213 5.68976 0.00000 3.46425 3 Li 6.66141 214 -2.01994 6.10000 1.84189 1 Si 6.68451 215 -2.01994 -6.10000 1.84189 1 Si 6.68451 216 -5.67948 1.73240 3.07056 3 Li5 6.68477 217 -5.67948 -1.73240 3.07056 3 Li5 6.68477 218 -1.45611 1.34017 6.38967 2 O1 6.68911 219 -1.45611 -1.34017 6.38967 2 O1 6.68911 220 4.60012 4.36760 -2.31914 3 Li5 6.75393 221 4.60012 -4.36760 -2.31914 3 Li5 6.75393 222 2.80119 1.30540 -6.01875 3 Li4 6.76580 223 2.80119 -1.30540 -6.01875 3 Li4 6.76580 224 -6.59591 1.34017 1.13452 2 O1 6.82563 225 -6.59591 -1.34017 1.13452 2 O1 6.82563 226 6.65913 0.00000 1.72693 2 O2 6.87941 227 -6.62675 0.00000 -1.85017 2 O3 6.88018 228 1.75267 0.00000 -6.74630 3 Li2 6.97025 229 4.60012 4.36760 2.98086 3 Li5 7.00875 230 4.60012 -4.36760 2.98086 3 Li5 7.00875 231 -3.38713 4.35540 -4.37474 3 Li4 7.04134 232 -3.38713 -4.35540 -4.37474 3 Li4 7.04134 233 6.89248 0.00000 -1.49115 3 Li2 7.05193 234 0.54996 6.10000 3.50910 3 Li 7.05877 235 0.54996 -6.10000 3.50910 3 Li 7.05877 236 -2.33861 4.79460 4.62611 3 Li4 7.06103 237 -2.33861 -4.79460 4.62611 3 Li4 7.06103 238 6.04081 3.05000 2.05668 2 O3 7.07275 239 6.04081 -3.05000 2.05668 2 O3 7.07275 240 3.11986 6.10000 1.79703 1 Si 7.08328 241 3.11986 -6.10000 1.79703 1 Si 7.08328 242 0.54996 0.00000 -7.09090 3 Li 7.11219 243 -3.38713 6.10000 -1.40144 3 Li2 7.11665 244 -3.38713 -6.10000 -1.40144 3 Li2 7.11665 245 -1.48695 6.10000 3.40498 2 O3 7.14247 246 -1.48695 -6.10000 3.40498 2 O3 7.14247 247 6.89248 1.74460 0.83555 3 Li4 7.15877 248 6.89248 -1.74460 0.83555 3 Li4 7.15877 249 2.80119 4.79460 4.58125 3 Li4 7.19880 250 2.80119 -4.79460 4.58125 3 Li4 7.19880 251 1.51933 6.10000 -3.52822 2 O2 7.20879 252 1.51933 -6.10000 -3.52822 2 O2 7.20879 253 1.51933 0.00000 7.07178 2 O2 7.23315 254 -6.27570 3.05000 2.04227 3 Li 7.27034 255 -6.27570 -3.05000 2.04227 3 Li 7.27034 256 -2.01994 6.10000 -3.45811 1 Si 7.29717 257 -2.01994 -6.10000 -3.45811 1 Si 7.29717 258 -3.38713 1.74460 6.22526 3 Li4 7.29864 259 -3.38713 -1.74460 6.22526 3 Li4 7.29864 260 5.69490 1.47010 -4.32680 3 Li1 7.30166 261 5.69490 -1.47010 -4.32680 3 Li1 7.30166 262 -3.62048 6.10000 1.81664 2 O2 7.32243 263 -3.62048 -6.10000 1.81664 2 O2 7.32243 264 -1.48695 0.00000 -7.19502 2 O3 7.34707 265 5.13980 0.00000 5.25515 3 Li6 7.35079 266 -5.13980 0.00000 -5.25515 3 Li6 7.35079 267 3.65286 6.10000 -1.93988 2 O3 7.36997 268 3.65286 -6.10000 -1.93988 2 O3 7.36997 269 3.68370 4.75983 -4.25519 2 O1 7.37104 270 3.68370 -4.75983 -4.25519 2 O1 7.37104 271 5.09355 4.78240 2.43595 3 Li5 7.39928 272 5.09355 -4.78240 2.43595 3 Li5 7.39928 273 5.69490 4.62990 0.97320 3 Li1 7.40372 274 5.69490 -4.62990 0.97320 3 Li1 7.40372 275 -7.15975 0.00000 1.88674 1 Si 7.40417 276 -5.13980 0.00000 5.34485 3 Li6 7.41519 277 5.13980 0.00000 -5.34485 3 Li6 7.41519 278 -2.01994 0.00000 7.14189 1 Si 7.42204 279 1.75267 6.10000 3.85370 3 Li2 7.42515 280 1.75267 -6.10000 3.85370 3 Li2 7.42515 281 6.57381 3.05000 -1.68023 1 Si 7.43913 282 6.57381 -3.05000 -1.68023 1 Si 7.43913 283 3.68370 1.34017 6.34481 2 O1 7.45804 284 3.68370 -1.34017 6.34481 2 O1 7.45804 285 -6.62675 0.00000 3.44983 2 O3 7.47095 286 -5.18606 4.78240 2.52566 3 Li5 7.49303 287 -5.18606 -4.78240 2.52566 3 Li5 7.49303 288 3.99877 4.52010 4.44360 3 Li1 7.49447 289 3.99877 -4.52010 4.44360 3 Li1 7.49447 290 6.00997 4.39017 -0.92801 2 O1 7.50030 291 6.00997 -4.39017 -0.92801 2 O1 7.50030 292 -5.67948 4.36760 -2.22944 3 Li5 7.50352 293 -5.67948 -4.36760 -2.22944 3 Li5 7.50352 294 6.04081 3.05000 -3.24332 2 O3 7.50420 295 6.04081 -3.05000 -3.24332 2 O3 7.50420 296 -3.38713 0.00000 -6.70144 3 Li2 7.50879 297 3.99877 1.57990 -6.15640 3 Li1 7.50916 298 3.99877 -1.57990 -6.15640 3 Li1 7.50916 299 4.55387 3.05000 -5.13834 3 Li6 7.51284 300 4.55387 -3.05000 -5.13834 3 Li6 7.51284 301 5.09355 4.78240 -2.86405 3 Li5 7.55105 302 5.09355 -4.78240 -2.86405 3 Li5 7.55105 303 6.65913 0.00000 -3.57307 2 O2 7.55717 304 -4.26964 4.39017 4.46170 2 O1 7.57695 305 -4.26964 -4.39017 4.46170 2 O1 7.57695 306 -5.18606 4.78240 -2.77434 3 Li5 7.58047 307 -5.18606 -4.78240 -2.77434 3 Li5 7.58047 308 -7.47842 1.30540 -0.62904 3 Li4 7.61751 309 -7.47842 -1.30540 -0.62904 3 Li4 7.61751 310 6.00997 1.70983 4.37199 2 O1 7.62611 311 6.00997 -1.70983 4.37199 2 O1 7.62611 312 0.87017 4.39017 -6.18315 2 O1 7.63297 313 0.87017 -4.39017 -6.18315 2 O1 7.63297 314 0.55510 7.57010 1.01806 3 Li1 7.65839 315 0.55510 -7.57010 1.01806 3 Li1 7.65839 316 -1.45611 7.44017 1.08967 2 O1 7.65923 317 -1.45611 -7.44017 1.08967 2 O1 7.65923 318 -4.26964 1.70983 -6.13830 2 O1 7.67020 319 -4.26964 -1.70983 -6.13830 2 O1 7.67020 320 -1.14104 4.52010 -6.11154 3 Li1 7.68663 321 -1.14104 -4.52010 -6.11154 3 Li1 7.68663 322 3.11986 6.10000 -3.50297 1 Si 7.69508 323 3.11986 -6.10000 -3.50297 1 Si 7.69508 324 -6.27570 3.05000 -3.25773 3 Li 7.70063 325 -6.27570 -3.05000 -3.25773 3 Li 7.70063 326 1.43401 3.05000 -6.93537 1 Si 7.71092 327 1.43401 -3.05000 -6.93537 1 Si 7.71092 328 4.55387 3.05000 5.46166 3 Li6 7.73757 329 4.55387 -3.05000 5.46166 3 Li6 7.73757 330 3.11986 0.00000 7.09703 1 Si 7.75251 331 1.75267 4.35540 6.18040 3 Li4 7.76136 332 1.75267 -4.35540 6.18040 3 Li4 7.76136 333 -4.58471 4.62990 -4.23709 3 Li1 7.77229 334 -4.58471 -4.62990 -4.23709 3 Li1 7.77229 335 -6.28084 4.52010 -0.76669 3 Li1 7.77612 336 -6.28084 -4.52010 -0.76669 3 Li1 7.77612 337 -0.53968 1.73240 -7.57429 3 Li5 7.78860 338 -0.53968 -1.73240 -7.57429 3 Li5 7.78860 339 -5.67948 4.36760 3.07056 3 Li5 7.79492 340 -5.67948 -4.36760 3.07056 3 Li5 7.79492 341 -2.33861 7.40540 -0.67389 3 Li4 7.79507 342 -2.33861 -7.40540 -0.67389 3 Li4 7.79507 343 -2.10526 3.05000 -6.86527 2 O2 7.80170 344 -2.10526 -3.05000 -6.86527 2 O2 7.80170 345 -1.14104 7.67990 -0.81154 3 Li1 7.80650 346 -1.14104 -7.67990 -0.81154 3 Li1 7.80650 347 -0.04626 7.41760 2.48080 3 Li5 7.82159 348 -0.04626 -7.41760 2.48080 3 Li5 7.82159 349 -4.58985 6.10000 -1.74605 3 Li 7.83105 350 -4.58985 -6.10000 -1.74605 3 Li 7.83105 351 0.55510 4.62990 6.31806 3 Li1 7.85251 352 0.55510 -4.62990 6.31806 3 Li1 7.85251 353 3.65286 6.10000 3.36012 2 O3 7.86408 354 3.65286 -6.10000 3.36012 2 O3 7.86408 355 6.89248 0.00000 3.80885 3 Li2 7.87487 356 -0.04626 1.31760 7.78080 3 Li5 7.89171 357 -0.04626 -1.31760 7.78080 3 Li5 7.89171 358 -3.62048 6.10000 -3.48336 2 O2 7.90264 359 -3.62048 -6.10000 -3.48336 2 O2 7.90264 360 -6.28084 1.57990 4.53331 3 Li1 7.90544 361 -6.28084 -1.57990 4.53331 3 Li1 7.90544 362 0.87017 7.80983 -0.88315 2 O1 7.90763 363 0.87017 -7.80983 -0.88315 2 O1 7.90763 364 -6.59591 1.34017 -4.16548 2 O1 7.91538 365 -6.59591 -1.34017 -4.16548 2 O1 7.91538 366 -7.15975 0.00000 -3.41326 1 Si 7.93173 367 -0.04626 7.41760 -2.81920 3 Li5 7.93541 368 -0.04626 -7.41760 -2.81920 3 Li5 7.93541 369 -2.33861 3.05000 6.95281 3 Li2 7.94438 370 -2.33861 -3.05000 6.95281 3 Li2 7.94438 371 2.80119 7.40540 -0.71875 3 Li4 7.95005 372 2.80119 -7.40540 -0.71875 3 Li4 7.95005 373 -5.13980 6.10000 0.04485 3 Li6 7.97682 374 -5.13980 -6.10000 0.04485 3 Li6 7.97682 375 5.13980 6.10000 -0.04485 3 Li6 7.97682 376 5.13980 -6.10000 -0.04485 3 Li6 7.97682 377 -4.58471 1.47010 6.36291 3 Li1 7.97918 378 -4.58471 -1.47010 6.36291 3 Li1 7.97918 379 -3.62048 0.00000 7.11664 2 O2 7.98463 380 -1.13590 3.05000 7.29741 3 Li 7.99031 381 -1.13590 -3.05000 7.29741 3 Li 7.99031 382 -3.38713 6.10000 3.89856 3 Li2 7.99259 383 -3.38713 -6.10000 3.89856 3 Li2 7.99259 384 -7.24507 3.05000 -1.52041 2 O2 8.00657 385 -7.24507 -3.05000 -1.52041 2 O2 8.00657 386 -2.33861 4.79460 -5.97389 3 Li4 8.00904 387 -2.33861 -4.79460 -5.97389 3 Li4 8.00904 388 2.80119 3.05000 6.90795 3 Li2 8.05413 389 2.80119 -3.05000 6.90795 3 Li2 8.05413 390 0.90101 3.05000 7.40154 2 O3 8.05587 391 0.90101 -3.05000 7.40154 2 O3 8.05587 392 0.00000 6.10000 5.30000 3 Li6 8.08084 393 0.00000 -6.10000 5.30000 3 Li6 8.08084 394 0.00000 6.10000 -5.30000 3 Li6 8.08084 395 0.00000 -6.10000 -5.30000 3 Li6 8.08084 396 7.94100 1.30540 -0.76360 3 Li4 8.08372 397 7.94100 -1.30540 -0.76360 3 Li4 8.08372 398 1.75267 7.84460 0.88040 3 Li4 8.08608 399 1.75267 -7.84460 0.88040 3 Li4 8.08608 400 -1.45611 4.75983 6.38967 2 O1 8.09963 401 -1.45611 -4.75983 6.38967 2 O1 8.09963 402 6.57381 3.05000 3.61977 1 Si 8.10063 403 6.57381 -3.05000 3.61977 1 Si 8.10063 404 3.65286 0.00000 -7.23988 2 O3 8.10921 405 3.03454 3.05000 -6.91012 2 O2 8.14007 406 3.03454 -3.05000 -6.91012 2 O2 8.14007 407 -0.53968 7.83240 -2.27429 3 Li5 8.17375 408 -0.53968 -7.83240 -2.27429 3 Li5 8.17375 409 2.80119 4.79460 -6.01875 3 Li4 8.18903 410 2.80119 -4.79460 -6.01875 3 Li4 8.18903 411 6.89248 4.35540 0.83555 3 Li4 8.19597 412 6.89248 -4.35540 0.83555 3 Li4 8.19597 413 -6.59591 4.75983 1.13452 2 O1 8.21274 414 -6.59591 -4.75983 1.13452 2 O1 8.21274 415 -5.72574 3.05000 -5.04863 3 Li6 8.22042 416 -5.72574 -3.05000 -5.04863 3 Li6 8.22042 417 -0.04626 1.31760 -8.11920 3 Li5 8.22554 418 -0.04626 -1.31760 -8.11920 3 Li5 8.22554 419 -7.47842 3.05000 1.69766 3 Li2 8.25295 420 -7.47842 -3.05000 1.69766 3 Li2 8.25295 421 -3.38713 4.35540 6.22526 3 Li4 8.31841 422 -3.38713 -4.35540 6.22526 3 Li4 8.31841 423 3.68370 7.44017 1.04481 2 O1 8.36764 424 3.68370 -7.44017 1.04481 2 O1 8.36764 425 6.89248 1.74460 -4.46445 3 Li4 8.39531 426 6.89248 -1.74460 -4.46445 3 Li4 8.39531 427 -3.70580 3.05000 -6.89052 1 Si 8.39730 428 -3.70580 -3.05000 -6.89052 1 Si 8.39730 429 -4.58985 0.00000 -7.04605 3 Li 8.40913 430 -0.53968 7.83240 3.02571 3 Li5 8.41384 431 -0.53968 -7.83240 3.02571 3 Li5 8.41384 432 -4.58985 6.10000 3.55395 3 Li 8.42065 433 -4.58985 -6.10000 3.55395 3 Li 8.42065 434 8.25967 0.00000 1.75218 1 Si 8.44347 435 5.69490 4.62990 -4.32680 3 Li1 8.51992 436 5.69490 -4.62990 -4.32680 3 Li1 8.51992 437 -0.53968 1.73240 8.32571 3 Li5 8.52114 438 -0.53968 -1.73240 8.32571 3 Li5 8.52114 439 -5.72574 3.05000 5.55137 3 Li6 8.53840 440 -5.72574 -3.05000 5.55137 3 Li6 8.53840 441 5.68976 6.10000 -1.83575 3 Li 8.54128 442 5.68976 -6.10000 -1.83575 3 Li 8.54128 443 -3.38713 7.84460 0.92526 3 Li4 8.59456 444 -3.38713 -7.84460 0.92526 3 Li4 8.59456 445 5.69490 1.47010 6.27320 3 Li1 8.59920 446 5.69490 -1.47010 6.27320 3 Li1 8.59920 447 3.99877 4.52010 -6.15640 3 Li1 8.62106 448 3.99877 -4.52010 -6.15640 3 Li1 8.62106 449 6.00997 4.39017 4.37199 2 O1 8.63178 450 6.00997 -4.39017 4.37199 2 O1 8.63178 451 -8.52694 0.00000 -1.35659 3 Li2 8.63417 452 7.94100 3.05000 1.56310 3 Li2 8.64900 453 7.94100 -3.05000 1.56310 3 Li2 8.64900 454 -4.26964 4.39017 -6.13830 2 O1 8.67076 455 -4.26964 -4.39017 -6.13830 2 O1 8.67076 456 -1.45611 7.44017 -4.21033 2 O1 8.67198 457 -1.45611 -7.44017 -4.21033 2 O1 8.67198 458 3.99877 7.67990 -0.85640 3 Li1 8.70083 459 3.99877 -7.67990 -0.85640 3 Li1 8.70083 460 0.55510 7.57010 -4.28194 3 Li1 8.71491 461 0.55510 -7.57010 -4.28194 3 Li1 8.71491 462 -7.24507 3.05000 3.77959 2 O2 8.72232 463 -7.24507 -3.05000 3.77959 2 O2 8.72232 464 3.68370 4.75983 6.34481 2 O1 8.74541 465 3.68370 -4.75983 6.34481 2 O1 8.74541 466 -8.52694 1.74460 0.97011 3 Li4 8.75748 467 -8.52694 -1.74460 0.97011 3 Li4 8.75748 468 -0.53968 4.36760 -7.57429 3 Li5 8.75997 469 -0.53968 -4.36760 -7.57429 3 Li5 8.75997 470 6.00997 1.70983 -6.22801 2 O1 8.82221 471 6.00997 -1.70983 -6.22801 2 O1 8.82221 472 0.54996 0.00000 8.80910 3 Li 8.82625 473 4.00391 3.05000 7.25256 3 Li 8.82799 474 4.00391 -3.05000 7.25256 3 Li 8.82799 475 -1.48695 0.00000 8.70498 2 O3 8.83106 476 -7.47842 3.05000 -3.60234 3 Li2 8.84342 477 -7.47842 -3.05000 -3.60234 3 Li2 8.84342 478 -6.28084 1.57990 -6.06669 3 Li1 8.87411 479 -6.28084 -1.57990 -6.06669 3 Li1 8.87411 480 8.17434 3.05000 -1.65498 2 O2 8.88039 481 8.17434 -3.05000 -1.65498 2 O2 8.88039 482 -7.47842 4.79460 -0.62904 3 Li4 8.90565 483 -7.47842 -4.79460 -0.62904 3 Li4 8.90565 484 -7.47842 1.30540 4.67096 3 Li4 8.91340 485 -7.47842 -1.30540 4.67096 3 Li4 8.91340 486 -4.58471 7.57010 1.06291 3 Li1 8.91379 487 -4.58471 -7.57010 1.06291 3 Li1 8.91379 488 -4.26964 7.80983 -0.83830 2 O1 8.94013 489 -4.26964 -7.80983 -0.83830 2 O1 8.94013 490 -8.76028 0.00000 1.86149 2 O2 8.95587 491 1.51933 0.00000 -8.82822 2 O2 8.95800 492 -1.14104 7.67990 4.48846 3 Li1 8.96823 493 -1.14104 -7.67990 4.48846 3 Li1 8.96823 494 -6.28084 4.52010 4.53331 3 Li1 8.96834 495 -6.28084 -4.52010 4.53331 3 Li1 8.96834 496 8.82350 1.34017 0.99996 2 O1 8.98054 497 8.82350 -1.34017 0.99996 2 O1 8.98054 498 -2.01994 0.00000 -8.75811 1 Si 8.98803 499 8.25967 0.00000 -3.54782 1 Si 8.98939 500 8.79266 0.00000 -1.98473 2 O3 9.01388 501 0.87017 7.80983 4.41685 2 O1 9.01439 502 0.87017 -7.80983 4.41685 2 O1 9.01439 503 5.68976 6.10000 3.46425 3 Li 9.03241 504 5.68976 -6.10000 3.46425 3 Li 9.03241 505 -2.33861 7.40540 4.62611 3 Li4 9.03935 506 -2.33861 -7.40540 4.62611 3 Li4 9.03935 507 4.60012 1.73240 -7.61914 3 Li5 9.06718 508 4.60012 -1.73240 -7.61914 3 Li5 9.06718 509 0.90101 3.05000 -8.49846 2 O3 9.07404 510 0.90101 -3.05000 -8.49846 2 O3 9.07404 511 -4.23880 3.05000 7.44639 2 O3 9.09498 512 -4.23880 -3.05000 7.44639 2 O3 9.09498 513 -4.58471 4.62990 6.36291 3 Li1 9.10726 514 -4.58471 -4.62990 6.36291 3 Li1 9.10726 515 5.68976 0.00000 -7.13575 3 Li 9.12647 516 -0.04626 4.78240 7.78080 3 Li5 9.13315 517 -0.04626 -4.78240 7.78080 3 Li5 9.13315 518 -6.59591 4.75983 -4.16548 2 O1 9.13856 519 -6.59591 -4.75983 -4.16548 2 O1 9.13856 520 2.80119 7.40540 4.58125 3 Li4 9.14738 521 2.80119 -7.40540 4.58125 3 Li4 9.14738 522 -0.58594 9.15000 0.20651 3 Li6 9.17107 523 -0.58594 -9.15000 0.20651 3 Li6 9.17107 524 1.75267 7.84460 -4.41960 3 Li4 9.17292 525 1.75267 -7.84460 -4.41960 3 Li4 9.17292 526 6.65913 6.10000 1.72693 2 O2 9.19436 527 6.65913 -6.10000 1.72693 2 O2 9.19436 528 -6.62675 6.10000 -1.85017 2 O3 9.19494 529 -6.62675 -6.10000 -1.85017 2 O3 9.19494 530 -1.13590 3.05000 -8.60259 3 Li 9.19768 531 -1.13590 -3.05000 -8.60259 3 Li 9.19768 532 7.94100 1.30540 4.53640 3 Li4 9.23810 533 7.94100 -1.30540 4.53640 3 Li4 9.23810 534 1.75267 6.10000 -6.74630 3 Li2 9.26252 535 1.75267 -6.10000 -6.74630 3 Li2 9.26252 536 7.94100 3.05000 -3.73690 3 Li2 9.29120 537 7.94100 -3.05000 -3.73690 3 Li2 9.29120 538 6.89248 4.35540 -4.46445 3 Li4 9.29554 539 6.89248 -4.35540 -4.46445 3 Li4 9.29554 540 7.94100 4.79460 -0.76360 3 Li4 9.30756 541 7.94100 -4.79460 -0.76360 3 Li4 9.30756 542 -6.59591 1.34017 6.43452 2 O1 9.31156 543 -6.59591 -1.34017 6.43452 2 O1 9.31156 544 9.13857 1.57990 -0.90125 3 Li1 9.31782 545 9.13857 -1.57990 -0.90125 3 Li1 9.31782 546 1.75267 0.00000 9.15370 3 Li2 9.31999 547 5.09355 7.41760 2.43595 3 Li5 9.32196 548 5.09355 -7.41760 2.43595 3 Li5 9.32196 549 6.89248 6.10000 -1.49115 3 Li2 9.32415 550 6.89248 -6.10000 -1.49115 3 Li2 9.32415 551 3.68370 7.44017 -4.25519 2 O1 9.32911 552 3.68370 -7.44017 -4.25519 2 O1 9.32911 553 3.11986 0.00000 -8.80297 1 Si 9.33947 554 5.09355 1.31760 7.73595 3 Li5 9.35549 555 5.09355 -1.31760 7.73595 3 Li5 9.35549 556 0.54996 6.10000 -7.09090 3 Li 9.36981 557 0.54996 -6.10000 -7.09090 3 Li 9.36981 558 4.60012 7.83240 -2.31914 3 Li5 9.37476 559 4.60012 -7.83240 -2.31914 3 Li5 9.37476 560 6.89248 1.74460 6.13555 3 Li4 9.39121 561 6.89248 -1.74460 6.13555 3 Li4 9.39121 562 -8.52694 0.00000 3.94341 3 Li2 9.39463 563 -5.18606 7.41760 2.52566 3 Li5 9.39654 564 -5.18606 -7.41760 2.52566 3 Li5 9.39654 565 8.79266 0.00000 3.31527 2 O3 9.39691 566 3.65286 0.00000 8.66012 2 O3 9.39899 567 1.43401 9.15000 -1.63537 1 Si 9.40496 568 1.43401 -9.15000 -1.63537 1 Si 9.40496 569 -8.76028 0.00000 -3.43851 2 O2 9.41095 570 -0.53968 4.36760 8.32571 3 Li5 9.41725 571 -0.53968 -4.36760 8.32571 3 Li5 9.41725 572 -0.04626 4.78240 -8.11920 3 Li5 9.42310 573 -0.04626 -4.78240 -8.11920 3 Li5 9.42310 574 0.90101 9.15000 2.10154 2 O3 9.43137 575 0.90101 -9.15000 2.10154 2 O3 9.43137 576 -1.13590 9.15000 1.99741 3 Li 9.43411 577 -1.13590 -9.15000 1.99741 3 Li 9.43411 578 5.09355 7.41760 -2.86405 3 Li5 9.44287 579 5.09355 -7.41760 -2.86405 3 Li5 9.44287 580 8.17434 3.05000 3.64502 2 O2 9.45561 581 8.17434 -3.05000 3.64502 2 O2 9.45561 582 1.51933 6.10000 7.07178 2 O2 9.46195 583 1.51933 -6.10000 7.07178 2 O2 9.46195 584 -5.18606 7.41760 -2.77434 3 Li5 9.46641 585 -5.18606 -7.41760 -2.77434 3 Li5 9.46641 586 -5.18606 1.31760 7.82566 3 Li5 9.48010 587 -5.18606 -1.31760 7.82566 3 Li5 9.48010 588 -8.84560 3.05000 -1.54567 1 Si 9.48347 589 -8.84560 -3.05000 -1.54567 1 Si 9.48347 590 -3.62048 0.00000 -8.78336 2 O2 9.50028 591 -2.10526 9.15000 -1.56527 2 O2 9.51865 592 -2.10526 -9.15000 -1.56527 2 O2 9.51865 593 5.69490 7.57010 0.97320 3 Li1 9.52289 594 5.69490 -7.57010 0.97320 3 Li1 9.52289 595 -1.48695 6.10000 -7.19502 2 O3 9.54931 596 -1.48695 -6.10000 -7.19502 2 O3 9.54931 597 5.13980 6.10000 5.25515 3 Li6 9.55218 598 5.13980 -6.10000 5.25515 3 Li6 9.55218 599 -5.13980 6.10000 -5.25515 3 Li6 9.55218 600 -5.13980 -6.10000 -5.25515 3 Li6 9.55218 601 4.60012 7.83240 2.98086 3 Li5 9.55998 602 4.60012 -7.83240 2.98086 3 Li5 9.55998 603 1.43401 3.05000 8.96463 1 Si 9.57723 604 1.43401 -3.05000 8.96463 1 Si 9.57723 605 -2.33861 9.15000 1.65281 3 Li2 9.58767 606 -2.33861 -9.15000 1.65281 3 Li2 9.58767 607 -5.67948 1.73240 -7.52944 3 Li5 9.58906 608 -5.67948 -1.73240 -7.52944 3 Li5 9.58906 609 -7.15975 6.10000 1.88674 1 Si 9.59332 610 -7.15975 -6.10000 1.88674 1 Si 9.59332 611 -9.40944 1.70983 -0.79345 2 O1 9.59639 612 -9.40944 -1.70983 -0.79345 2 O1 9.59639 613 -3.38713 7.84460 -4.37474 3 Li4 9.59941 614 -3.38713 -7.84460 -4.37474 3 Li4 9.59941 615 -5.13980 6.10000 5.34485 3 Li6 9.60183 616 -5.13980 -6.10000 5.34485 3 Li6 9.60183 617 5.13980 6.10000 -5.34485 3 Li6 9.60183 618 5.13980 -6.10000 -5.34485 3 Li6 9.60183 619 -2.01994 6.10000 7.14189 1 Si 9.60712 620 -2.01994 -6.10000 7.14189 1 Si 9.60712 621 -8.52694 4.35540 0.97011 3 Li4 9.62389 622 -8.52694 -4.35540 0.97011 3 Li4 9.62389 623 4.60012 1.73240 8.28086 3 Li5 9.62990 624 4.60012 -1.73240 8.28086 3 Li5 9.62990 625 -7.47842 1.30540 -5.92904 3 Li4 9.63246 626 -7.47842 -1.30540 -5.92904 3 Li4 9.63246 627 -6.62675 6.10000 3.44983 2 O3 9.64495 628 -6.62675 -6.10000 3.44983 2 O3 9.64495 629 5.69490 4.62990 6.27320 3 Li1 9.65510 630 5.69490 -4.62990 6.27320 3 Li1 9.65510 631 -3.38713 6.10000 -6.70144 3 Li2 9.67429 632 -3.38713 -6.10000 -6.70144 3 Li2 9.67429 633 6.89248 0.00000 -6.79115 3 Li2 9.67605 634 6.65913 0.00000 7.02693 2 O2 9.68100 635 -5.18606 1.31760 -8.07434 3 Li5 9.68640 636 -5.18606 -1.31760 -8.07434 3 Li5 9.68640 637 2.80119 9.15000 1.60795 3 Li2 9.70333 638 2.80119 -9.15000 1.60795 3 Li2 9.70333 639 6.00997 4.39017 -6.22801 2 O1 9.70471 640 6.00997 -4.39017 -6.22801 2 O1 9.70471 641 0.55510 1.47010 -9.58194 3 Li1 9.70994 642 0.55510 -1.47010 -9.58194 3 Li1 9.70994 643 6.65913 6.10000 -3.57307 2 O2 9.71189 644 6.65913 -6.10000 -3.57307 2 O2 9.71189 645 5.09355 1.31760 -8.16405 3 Li5 9.71247 646 5.09355 -1.31760 -8.16405 3 Li5 9.71247 647 -1.45611 1.34017 -9.51033 2 O1 9.71405 648 -1.45611 -1.34017 -9.51033 2 O1 9.71405 649 -8.52694 1.74460 -4.32989 3 Li4 9.72112 650 -8.52694 -1.74460 -4.32989 3 Li4 9.72112 651 3.99877 7.67990 4.44360 3 Li1 9.73225 652 3.99877 -7.67990 4.44360 3 Li1 9.73225 653 0.90101 9.15000 -3.19846 2 O3 9.73470 654 0.90101 -9.15000 -3.19846 2 O3 9.73470 655 -2.33861 3.05000 -8.94719 3 Li2 9.73775 656 -2.33861 -3.05000 -8.94719 3 Li2 9.73775 657 -6.62675 0.00000 -7.15017 2 O3 9.74878 658 -2.10526 3.05000 9.03473 2 O2 9.76530 659 -2.10526 -3.05000 9.03473 2 O2 9.76530 660 3.03454 9.15000 -1.61012 2 O2 9.77361 661 3.03454 -9.15000 -1.61012 2 O2 9.77361 662 -1.13590 9.15000 -3.30259 3 Li 9.79387 663 -1.13590 -9.15000 -3.30259 3 Li 9.79387 664 -2.33861 7.40540 -5.97389 3 Li4 9.79778 665 -2.33861 -7.40540 -5.97389 3 Li4 9.79778 666 -3.38713 0.00000 9.19856 3 Li2 9.80235 667 -4.58471 7.57010 -4.23709 3 Li1 9.81218 668 -4.58471 -7.57010 -4.23709 3 Li1 9.81218 669 9.14371 3.05000 1.90770 3 Li 9.82595 670 9.14371 -3.05000 1.90770 3 Li 9.82595 671 -6.28084 4.52010 -6.06669 3 Li1 9.83285 672 -6.28084 -4.52010 -6.06669 3 Li1 9.83285 673 3.11986 6.10000 7.09703 1 Si 9.86465 674 3.11986 -6.10000 7.09703 1 Si 9.86465 675 0.55510 7.57010 6.31806 3 Li1 9.87585 676 0.55510 -7.57010 6.31806 3 Li1 9.87585 677 -9.72965 0.00000 -1.70119 3 Li 9.87725 678 -1.14104 7.67990 -6.11154 3 Li1 9.88098 679 -1.14104 -7.67990 -6.11154 3 Li1 9.88098 680 -9.72451 1.47010 1.10776 3 Li1 9.89719 681 -9.72451 -1.47010 1.10776 3 Li1 9.89719 682 6.00997 7.80983 -0.92801 2 O1 9.89820 683 6.00997 -7.80983 -0.92801 2 O1 9.89820 684 2.80119 3.05000 -8.99205 3 Li2 9.89980 685 2.80119 -3.05000 -8.99205 3 Li2 9.89980 686 0.87017 1.70983 9.71685 2 O1 9.90443 687 0.87017 -1.70983 9.71685 2 O1 9.90443 688 8.82350 1.34017 -4.30004 2 O1 9.90659 689 8.82350 -1.34017 -4.30004 2 O1 9.90659 690 4.60012 4.36760 -7.61914 3 Li5 9.91405 691 4.60012 -4.36760 -7.61914 3 Li5 9.91405 692 -1.45611 7.44017 6.38967 2 O1 9.91485 693 -1.45611 -7.44017 6.38967 2 O1 9.91485 694 -5.67948 7.83240 -2.22944 3 Li5 9.92841 695 -5.67948 -7.83240 -2.22944 3 Li5 9.92841 696 -4.23880 3.05000 -8.45361 2 O3 9.93647 697 -4.23880 -3.05000 -8.45361 2 O3 9.93647 698 2.80119 7.40540 -6.01875 3 Li4 9.94545 699 2.80119 -7.40540 -6.01875 3 Li4 9.94545 700 -6.28084 7.67990 -0.76669 3 Li1 9.95076 701 -6.28084 -7.67990 -0.76669 3 Li1 9.95076 702 -4.26964 7.80983 4.46170 2 O1 9.95641 703 -4.26964 -7.80983 4.46170 2 O1 9.95641 704 1.43401 9.15000 3.66463 1 Si 9.96034 705 1.43401 -9.15000 3.66463 1 Si 9.96034 706 6.89248 6.10000 3.80885 3 Li2 9.96110 707 6.89248 -6.10000 3.80885 3 Li2 9.96110 708 3.03454 3.05000 8.98988 2 O2 9.96639 709 3.03454 -3.05000 8.98988 2 O2 9.96639 710 -4.58985 0.00000 8.85395 3 Li 9.97292 711 -1.14104 1.57990 9.78846 3 Li1 9.98058 712 -1.14104 -1.57990 9.78846 3 Li1 9.98058 713 6.04081 3.05000 7.35668 2 O3 9.99573 714 6.04081 -3.05000 7.35668 2 O3 9.99573 715 0.87017 7.80983 -6.18315 2 O1 9.99910 716 0.87017 -7.80983 -6.18315 2 O1 9.99910 717 -3.70580 9.15000 -1.59052 1 Si 9.99926 718 -3.70580 -9.15000 -1.59052 1 Si 9.99926 719 END ----- End of forwarded message from John J. Rehr -----

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Re: ifeffit windowfunctions
by Matt Newville 11 Dec '02

11 Dec '02

Hi Daniel, On Wed, 11 Dec 2002, Daniel Grolimund wrote: > In case I am using non-regularly spaced k-chi data, the plot of the > chosen Fourier Transform Window is not represented correctly using the > command plot(group.k, group.win)]. > > Is there a way to get around that (except using interpolated and > therefore regularly spaced) data? Funny you mention this, I just noticed the same problem myself over the weekend. Currently, fftf() writes out the window function assuming the 0.05 Ang-1 grid, regardless of the input k-array. I believe this is fixed (that is, the group.win array corresponds to the group.k array!) in my latest test version. I still need to test other fixes in this version, but hopefully I'll get it out early next week. > Further, in a earlier version one had to use ikwindo = n to specify the > Fourier Transform Window type. In ifeffit the termology kwindow = aaaaa > is used. In addition to 'kaiser' and 'hanning' are there any other > options for kwindow ? Oh right. This is one place where Ifeffit and Feffit are different. Feffit's 'ikwindo = 2' caused some headaches (no one could remember them!) so 'kwindow=hanning' etc seemed better (if english-centric) for ifeffit. Other window functions are 'parzen' (linear sills), 'welch' (quadratic sills), and 'sine' (a sine wave over the whole range), and 'gaussian' (which is really weird: centered at dk2, with full width of 1/dk1, someone asked for it many years ago, it could probably be improved!). The next version of ifeffit will also have a window() command to make window functions without actually doing the FTs. --Matt

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RE: [Ifeffit] Double dipping
by Kelly, Shelly D. 02 Dec '02

02 Dec '02

Hi Matt, I think that your reply sounds reasonable. Lets talk some more about this. > The other side of this is that I think it's more difficult than > generally acknowleged to over-interpret data. Most of the cases > I've seen are due to blatantly ignore the confidence limits or do > completely unfair things like fitting So2 to get 0.9+/-0.1, then > fix So2 to 0.90, fitting N, and claiming N to better than 10%. > Those are serious, but are the normal mistakes in analysis that > can happen with any data. If you fix s02 and then you fit N and get a error lets call it dn. Then the more generous estimation of the uncertainty for N is d(s02*n) = ds02*n + s02*dn. How would you estimate the error for N if you fix s02, R and sigma2? I will try to be more specific to my original problem. lets say that the original data set (s3) gives these results for the Ca shell. Ncas3=3.4+/-0.9 Rcas3=4.01+/-0.01 sigma2cas3=0.006+/-0.3 s02s3=1.05+/-0.10 Now I run another fit and I fix all the parameters except for Nca. This time I fit three data sets s3, s4 and s5 together and I get these results. Ncas3 = 3.2+/-0.1 Ncas4 = 2.5+/-0.4 Ncas5 = 2.0+/-0.4 What would you think would be an "appropriate" uncertainty? Surely 0.1 is too small for Ncas3 but 0.9 seems rather huge. So we have some limits but can I do any better than that? The difference is between these to extremes is quite profound. In one case we see a change in the value for Nca in the other we see nothing. Shelly > -----Original Message----- > From: Newville, Matthew G. > Sent: Friday, November 22, 2002 10:17 AM > To: 'ifeffit(a)millenia.cars.aps.anl.gov' > Subject: Re: [Ifeffit] Double dipping > > > Hi Shelly, > > > I would like to take a bunch of parameters (all of them that do > > not vary significantly from the known, as determined by > > individual fits to each data set) from this "known" data set > > and then fit the series including the "original" to see how a > > particluar parameter (the number of Ca atoms) changes as the > > ratio of U to Ca changes. I would like to hear a discussion on > > the fairness of this approach and how would you calculate the > > number of independent points? > > I think what you propose is fair, but you might need to be a > little more specific.... > > In general, I think it's fair to use parameters from one fit to > to another data set. Once one accepts the fact that there is > limited amount of information, getting hung up on trying to count > or enforce N_idp becomes pointless -- the data and estimated > uncertainties __WILL__ indicate how many parameters can be > determined with any confidence. > > N_idp is one statistic, it should not be construed as an exact > value nor a hard upper limit on how much data can be extracted > from data. Any attempt to use N_idp this way is abuse. > > The classic test is whether 100 very noisy scans (say, because > data was collected for 0.01s per point), has 100x more > 'independent points' as 1 scan that collected for 1.0s per point. > The 100 noisy scans __ARE__ independent, but when added together > with give exactly the same result as using the 1 clean scan. So > independent data does not mean you can determine you can > determine more parameters. > > The other side of this is that I think it's more difficult than > generally acknowleged to over-interpret data. Most of the cases > I've seen are due to blatantly ignore the confidence limits or do > completely unfair things like fitting So2 to get 0.9+/-0.1, then > fix So2 to 0.90, fitting N, and claiming N to better than 10%. > Those are serious, but are the normal mistakes in analysis that > can happen with any data. > > --Matt > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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notes for figures
by Bruce Ravel 22 Nov '02

22 Nov '02

Ning, I trust you will not mind if I respond to the ifeffit mailing list. You question is of general interest. > On Fri, 22 Nov 2002, "Ning Chen" <Ning.Chen(a)lightsource.ca> said: NC> Hi Bruce: I am wondering if it is possible to add note to the NC> figure inside the "Graphic window"? Hmmm.... no one has ever asked for that before. Good question! There is a way. It's not particularly convenient, but it's not particularly difficult either. Here is an example: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/tex… I made this first by clicking on the red "kq" button. Then, in the edit menu, I selected "Ifeffit buffer". At the bottom of the little window that popped up, there is a box with a label that says "Ifeffit>". That text box allows the user to interact directly with ifeffit by typing in explicit commands. Here is a picture: http://leonardo.phys.washington.edu/~ravel/software/exafs/images/athena/ife… To get the text string in the plot, I typed: plot_text(x=7, y=-0.3, text="Hi Ning!") which tells Ifeffit to put the indicated text string at the indicated coordinates. The same thing could be done the same way in Artemis. Obviously, this could be made more user friendly by, for example, having Athena or Artemis prompt you to click on a spot in the plot window and then prompt you for a text string. I'll put that on the TODO list. Please note that using the plot_text command as I describe above will trigger the minor bug described by Matt earlier this week on this list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-November/000177.html 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/

2 2

Double dipping
by Kelly, Shelly D. 22 Nov '02

22 Nov '02

Hello All, I am new to this mailing list, so I hope my question is relevant. I have several EXAFS data sets that I want to simultaneously fit with one model. One of the data sets was modeled first and the results will be published separately from the rest. I would like to take a bunch of parameters (all of them that do not vary significantly from the known, as determined by individual fits to each data set) from this "known" data set and then fit the series including the "original" to see how a particluar parameter (the number of Ca atoms) changes as the ratio of U to Ca changes. I would like to hear a discussion on the fairness of this approach and how would you calculate the number of independent points? Shelly Kelly

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Athena 0.8.007 and Artemis 0.5.003
by Bruce Ravel 22 Nov '02

22 Nov '02

Hi Folks, I just posted new versions of my two programs on my web site. The source tarball for Unix and OSX users as well as newly built windows executables are in their standard places. Most of the changes this time fix bugs that I discovered last week when I was visiting the wonderful folks at the Alberta Synchrotron Institute. The two most important changes fix the problems displaying the normalized background function and reading chi(k) data that is not on a uniform k-grid. Windows user who are new to Ifeffit: You just need to download the new executable files and drop them on top of the old ones in C:\Program Files\Ifeffit (or wherever you installed Ifeffit on your computer). The big installer file has *not* yet been updated to include these new versions. Unix, linux, or Mac OSX users: The source tarball now includes the ifeffit wrapper that comes with the main ifeffit distribution. Now, when you update ifeffit, it is no longer necessary to cd into the "wrappers/perl/" directory and build the perl wrapper. Instead the wrapper is built at the same time as Athena and Artemis. I am fairly confident that the wrapper gets compiled correctly. It works fine on my linux computer and on Mac OSX. Please let me know if you have any troubles with the compilation so I can fix the build scripts. As always, feel free to post questions, bug reports, or feature suggestions to this mailing list. Special thanks this time to Paul Fons and to all the folks at the ASI. 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/

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Re: pgplot question
by Matt Newville 20 Nov '02

20 Nov '02

Hi Paul, On Thu, 21 Nov 2002, Paul Fons wrote: > I noticed (from early on) that although pgplot generated graphics show > all spectra labels on screen, when I save them to a file, that the > lowermost scan of a multiple scan plot always has the label missing. > Is this something that is Mac specific or is everyone suffering from > this problem? I want to try tracking it down a little (perhaps > including sending a note to the pgplot author if helpful). This is my fault -- a bug that's been on the to-do list forever, and never done. I believe this will also cause the same behavior: my.x = range(1,100,1)/10 my.y = sin(my.x) my.z = cos(my.x) newplot my.x, my.y, key='sin' plot my.x, my.z, key='cos' #everything is fine... plot xmax = 8 and the most recent 'key' gets lost. Making a hardcopy simply does a plot() with a different device, and so often tickles this error. Workarounds include adding the last trace twice, as in newplot my.x, my.y, key='sin' plot my.x, my.z, key='cos' #everything is fine... plot my.x, my.z, key='cos', color='red' which will then trick a second plot(). Anyway, it's all my fault, not PGPLOT's. Probably should fix it huh?? --Matt

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Ifeffit 1.0075
by Matt Newville 13 Nov '02

13 Nov '02

Hi Everyone, Ifeffit 1.0075 is now available. There are some bug fixes related to erasing paths, which caused serious problems with artemis. There was also a change in the guts of how the Perl wrapper was built, as the older one failed to compile with gcc3.2 on RedHat 8.0. I have not tried this on Mac OS X, and don't foresee any problems, but if someone is brave enough to try it, please let me know if it fails. The most significant change in 1.0075 is the inclusion of Feff6 in the source tree and a Windows executable of Feff6 in the Windows installer. That right, there is now a free version of Feff6 included with Ifeffit!! The plan is to turn this version of Feff into a library that can be called directly from the perl and python scripts. That is, the 'run feff' button on TkAtoms might actually work someday!! If you're as thrilled about this as I am, don't hesitate to thank John Rehr repeatedly. There are new versions of sixpack, artemis, and athena in the Windows installer. The latest source code for these should be downloaded from Sam's and Bruce's web pages. Special Thanks to John, Sam, and of course Bruce, --Matt

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ifeffit and feff
by Bruce Ravel 06 Nov '02

06 Nov '02

Ahmed, I trust you do not mind that I answer your question on the ifeffit mailing list. It seems of sufficiently broad interest that an answer in that forum is appropriate. You asked: AS> I received a note with the latest version of your software. In my AS> understanding that the latest version includes the Feff6L without AS> a license fee. Does this mean that by downloading the latest AS> version of ifeffit, so that I do not need to buy a license of AS> feff? Well, my answer is ether a qualified yes or a qualified no, depending on what your interests are ;-) *IF* you are interested only in the extended EXAFS features of Feff and *IF* you do not think that you need any of the more recent developments of Feff (most notably, self consistent potentials), then you probably do not need a license for Feff. Feff6L is free in both senses of the word -- it doesn't cost you any money and you may freely use, modify, and redistribute the code under the terms of its license. See this post from John Rehr to the mailing list about the Feff6L license: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-November/000169.html However, if you are interested in computing XANES, partial electronic densities of state, charge transfer or ab initio Fermi energies, you will need to license a copy of the latest version of Feff. If you are interested in the latest developments of such theoretical topics as self-consistent potentials, improved self-energies, S02 calculations, resonant scattering corrections, or a whole host of other features available in the latest Feff and not available in Feff6L, you will need to license a copy of the latest version of Feff. Feff6L is useful code for the extended exafs practitioner. If that were not true than Matt would not have been so effusive in his post yesterday announcing Ifeffit 1.0075. While Feff6L is useful and usable for exafs analysis, you must be aware that it is largely limitted to exafs analysis. If you need XANES calculations, you need a Feff8 license. All clear? 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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FEFF6L - Lite EXAFS only version of FEFF6 source code
by John J. Rehr 05 Nov '02

05 Nov '02

Dear Feff developers, In an effort to facilitate the development of EXAFS analysis software, the FEFF Project has made available the source code for a "lite" subset of the FEFF6 distribution sufficient for EXAFS analysis, named FEFF6L. Thus cross-sections and XANES capabilities of FEFF6 are disabled in FEFF6L. A copy of the FEFF6L distribution can be found (shortly) on the FEFF Developer download pages. The subroutines are distributed with a License that permits redistribution without a license fee; see the LICENSE in the distribution for details. c/////////////////////////////////////////////////////////////////////// c Distribution: FEFF6L c Copyright (c) [2002] University of Washington c c This software was prepared in part with US Government Funding under c DOE contract DE-FG03-97ER45623. c c Redistribution and use of this Distribution in source and binary c formats, with or without modification is permitted, provided the c following conditions are met: c c Redistributions must retain the above notices and the following list c of conditions and disclaimer; c c Modified versions carry the marking c "Based on or developed using Distribution: FEFF6L c Copyright (c) [2002] University of Washington" etc. The distribution FEFF6L should not be confused with the full distribution of FEFF6. Also the FEFF Project will continue to develop advanced versions of the FEFF codes which will be distributed with the UWOTT License and license fee. Comments on this EXAFS version are welcome. Sincerely, FEFF Project PIs J. J. Rehr A. L. Ankudinov

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Re: [Ifeffit] Debye factor and S02 correlation
by Bruce Ravel 05 Nov '02

05 Nov '02

jjr> I don't understand Bruce's remark. Incorporating prior knowledge jjr> into statistics is completely proper according to modern jjr> statistical theory. If two quantities are correlated and one jjr> knows one, then naturally the other is better determined. Well, leaving aside the question of whether one can call a Levenberg- Marquardt fit "modern", I agree that one can set a value and call it part of the model. One does that all the time in any fitting problem. But in that case you are asserting a value with no error bar. There is no situation where you can assert a value AND an error bar. My concern was your statement that you somehow knew the value of the error bar on S02. If it floats, you have to use the error bar the fitting algorithm reports. But the most important thing in my comment and the most important thing in the discussion on the topic of amplitude terms in exafs that we have seen in the last week on this list is that, in a difficult fitting problem (i.e. not copper), one rarely has reliable a priori knowledge of the *product* of S02, coordination, and the systematic uncertainties. Thus one rarely has a reliable prior in the Baysian sense. 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/

1 0

rebinning data
by Carlo U. Segre 05 Nov '02

05 Nov '02

hello All: This is to bring back up a subject that was discussed a few months ago on the list. We have been diligently working on a python algorithm for rebinning XAFS data from high point density slew scans. I have been testing it and I hope that there will be a complete version available shortly. It is in the form of a unix filter which takes a few parameters (edge energy, energy above the edge where rebinning is to begin, step size in k for rebinning) and spits out a modified file for each input file. There are just a couple of small glitches in how it handles data points with the same energy (this causes athena to pop up an annoying dialog) but that should be solved this week. I am more than happy to send it to anyone who would like it. Matt, I remember that you had suggested that we send code. 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] Debye factor and S02 correlation
by John J. Rehr 05 Nov '02

05 Nov '02

Matt's test of fitting the inelastic losses using So2 and an effective mean free path (via a constant imaginary shift Ei in the net lifetime width in FEFFIT) is quite interesting. In particular the results are consistent with our current understanding of the physics, namely that the inelastic losses are generally overestimated by the plasmon-pole self energy. Thus one expects Ei to be negative to compensate for errors in this self-energy model. Also it's particularly encouraging that one can fit *both Ei and So2*. I'm not too worried by the evident correlation between these parameters since they both smoothly affect the overall amplitude; what matters is the value of Ei when So2 is about 0.9. Matt wrote: >This seems like a fine approach to me, and it could be automated, >at least somewhat. Feffit/Ifeffit have Ei as a path parameter, >so setting So2 to 0.9 and floating Ei is possible right now. >Using Ei instead of So2 has a couple possible benefits: > 1. Not completed correlated with N (though see below!) > 2. Can accomodate measurement resolution issues. > 3. Might be a little easier conceptually on the new people. > >For one variation on the canonical 'Cu 10K first shell fit', >with sigma2 varying as well, I get these values: > So2 Ei chi_square r-factor > 0.93(0.03) 0.00(fix) 119. 0.0017 > 1.00(fix) 0.55(0.25) 128. 0.0018 > 0.95(fix) 0.14(0.24) 120. 0.0017 > 0.90(fix) -.29(0.23) 116. 0.0016 > 0.85(fix) -.75(0.23) 116. 0.0016 > > 0.87(0.14) -.58(1.27) 116. 0.0016 > >The last one had both So2 and ei (and sigma2!!) floating. The >correlation between them was 0.98, higher than that between So2 >and sigma2, which was a mere(!) 0.94. So it looks like, for this >data, So2 really does want to be ~0.90 +/ 0.05, and Ei wants to >be 0.00 +/- 0.25. As I read the numbers for the minimum chi_square, I would say that the results suggest Ei = -.52 +/- .3 I don't believe the error bar on So2 of +/- .14. Probably +/- .05 is more like it, so the error bar on Ei will be much smaller than 1.27. Also, I think if you look at plots of the fits, they look better with a slightly negative Ei. We would very much like to see more evidence for the inadequacy of the plasmon pole self energy. Thus I would encourage more fits to include E_i as a fitting parameter, with So2 kept under control (e.g. fixed or floating in a range 0.9 +/- .05, assuming edje jump is well defined). J. Rehr

2 1

Re: [Ifeffit] Debye factor and S02 correlation
by John J. Rehr 04 Nov '02

04 Nov '02

Hi Everyone, I agree with Matt's assessment: > ... my view is that the >errors in the calculated mean-free path may have a much stronger >energy dependence than the errors in the calculated So2. From >the analysis point-of-view, I prefer to think of So2 as >k-independent, and put all k-dependent pieces go into lambda(k) >or F(k). Feff tries to include all loss terms as well as it can. There are two ingredients in the mean free path lambda(k) lambda_k approx k/[Im Sigma(E) + Gamma] 1) The core hole lifetime Gamma - FEFF estimates this by interpolating from tabulated values. This rough estimate should not lead to serious errors, in my view, since a 10% error in the lifetime translates to only few percent error at worst in the loss factor exp(-2 lambda R). 2) The self energy Sigma - FEFF uses an electron gas plasmon pole approximation. which can easily be off by 1-2 eV. This is the most serious error and leads to large energy dependent errors in lambda_k. >So2 _is_ calculated (if crudely in Feff6 and 7 -- I don't know if FEFF6-8 will make an atomic value of So2 if one sets S02 = 0 in the HOLE card. This approximation is unsatisfactory since it can't account well for the valence electron contributions or interference effects which dominate So2. I don't think it can be trusted - at least to better than 10%. >Luke Campbell's work on improved So2 is included in Feff8 yet). >So one might even expect that So2 should be 1, and even find it a Luke Campbell's routines are not in FEFF8 yet as they are not yet fully automated or ready to be integrated. This will us take some months. Moreover, Luke still uses a plasmon-pole self energy, which we want to improve. >little strange that it's usually around 0.9. Clearly, there are >loss terms that are not taken into account well enough in Feff. >My view is that it's not well known whether this is dominated by >an k-dependent term (ie, should be put into F or lambda) or a >k-independent term (So2). The remarkable bit of physics here is that interference terms between extrinsic and intrinsic losses and hence tend to suppress shake-up/shake-off effects. In any case, my suggestion in fits would be to treat the loss terms using a constant and an effective mean free path: a) set So2 = constant approx 0.9 b) fit the mean free path, e.g., by fitting the core-hole effective lifetime. I'd be interested in feedback on this suggestion. Can it be automated within FEFFIT? Cheers, John Rehr

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Debye factor and S02 correlation
by Dr. Paul Fons 04 Nov '02

04 Nov '02

I meant to send this off to the list (instead I sent it to Scott Calvin only). Ahh the wonders of email. I thought I would parrot back something I read in one of Bruce's tutorials (that seemed to work well for me), namely that the Debye factor, sigma has a k dependence while S02 does not. This means that if you can Fourier isolate the first shell (and you can assume a coordination number), you can determine a value for S02 by a fit using different k weights. You simply fit sigma for various fixed values of S02 (e.g. 0.6 - 1.0) and repeat the process for different k weights (e.g. k, k^2, k^3). The resulting plot of sigma vs. S02 will result in a straight line for a given k weighting. The three different k weights will intersect at a single point (or almost so) and the value of S02 at this point will be the value of S02 for the sample. While we are discussing S02, I thought I would ask a little more about it myself. 1. S02, the passive electron reduction factor is a term that encompasses many body effects, in particular the effect of the core hole. It is also as such said to have a "weak energy and path dependence" [J.J. Rehr and R.C. Albers in Reviews of Modern Physics, v. 72, no. 3 (2000)]. The question is how fair is it to assume that S02 is a constant independent of shell, or in other words should S02 be allowed to vary with shell (e.g. with significant multiple scattering contributions?) 2. I don't remember the paper offhand, but as I recall, in a paper by Bruce, the value of S02 was ascribed a value greater than unity. I didn't grok the explanation at the time, and was wondering if Bruce (or anyone else) in his ever-expanding knowledge of exafs has an explanation for when/if S02 can be greater than unity. Certainly if you consider Rehr's definition of the overlap integral of the N-1 electron wavefunction with and without a core hole, the value of S02 cannot be greater than unity[same reference, p. 636]. Any comments?

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Re: [Ifeffit] Re: Amplitude and the EXAFS equation
by John J. Rehr 30 Oct '02

30 Oct '02

Dear FEFF and IFEFFIT users, As Matt notes, >Feff tries to estimate many of the the physical processes >identified as So2. It also estimates lambda, but much more >crudely: it interpolates a fit to the *figures* from Rahkonen and >Krause (1974). Feff definitely does not include the energy >resolution of a Si(111) monochromator at 9keV. One of the biggest problems with the current FEFF calculation is that the mean free path lambda is calculated from the Hedin-Lundqvist electron gas self energy in the plasmon-pole approximation. This often overestimates the inelastic losses (too short mean free paths). The consequence of this is that the effective So2 must often be increased to compensate. For this reason, it is not unusual to see fits of So2 that that can exceed unity. Fortunately improvements are in sight. Luke Campbell's thesis focused in part on calculations of So2, and he was able to explain the So2 for Cu (about 0.9) to within a few percent. Also efforts are being made to improve the self energy. However, at present the theoretical So2 is typically 0.9 +/- 0.1. This of course, does not take into account possible errors in the value of the edge jump and corrections for experimental resolution which can affect fits to So2. John Rehr

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