jjr> what is the recommended procedure for lattices with non-integer jjr> occupation? The Atoms documentation seems not very specific on jjr> this point, though it does emphasize the "confusing" aspects of jjr> the problem and the fact that it is easy to generate nonsense jjr> feff.inp. I've tried really hard in my documents and in fora such as this one and FEFFUSERS (see for example http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-July/000092.html) to explain well why I think that translating non-integer crystallographic occupancies into a sensible feff.inp file is too hard of a problem for a computer program. If my explanations remain "unspecific" after all that, then I'll try harder the next time I sit down to write on that topic. jjr> For example I could edit the feff.inp file that is generated and jjr> cut out *arbitrarily* some fraction of the atoms of a given tag, jjr> e.g., 2/3 of the Li1s, 1/2 of the Li2s, etc. That *is* the standard solution, although I would do something a bit more sophisticated that I will explain in a a few paragraphs. The reason that removing arbitrary atoms is the only solution I recommend is because Feff has the requirement that a point in space either be empty or be entirely occupied by a particular atom. Because Feff does not allow a site to fractionally occupied, Atoms cannot do something that is guaranteed to be sensible. Feff could do a wieghted sum of phase shifts of different atom types when it evaluates the elements of its t-matrix. That may work well for stochastic doping, but not for clustering. The best solution I have come up with for a problem like this is to have atoms generate the feff.inp file for the undoped (or unvacated) cluster. Then write yourself a little program that reads in the feff.inp, uses a random number generator to remove the proper number of vacated atoms, writes out the altered feff.inp file, and runs feff. Add up these feff runs until their sum converges. It probably won't take more that about 10 calculations. jjr> But I also must edit the stoichiometry so the potentials come jjr> out right. But this procedure does seem arbitrary. Also, it jjr> appears that the Li atoms in this material are not all jjr> distinguishable so one has to take a linear combination FEFF jjr> runs for the different input Li sites. jjr> can TkAtoms take the occupancy into account in determining the jjr> stoichiometry? I should use the occupancy information to compute better stoichiometries. Good suggestion. Thanks! I'll put that on the list of things to do, but I may not get to it for a while. As for the different Li sites, here is a tidbit from the Atoms doc that may be of value: How do I change the unique potentials assignment in feff.inp files? There are three schemes for assigning unique potentials. They are assignment by atomic species, by user-supplied tag, or by crystallographic site. Change the value of the :ipots argument to the <potentials> token in 'feff.atp' to be one of species, tags, or sites. I welcome suggestions for new assignment schemes. On unix, the `feff.atp' file gets installed in the site_perl space of the perl hierarchy. On my computer, its in: /usr/lib/perl5/site_perl/5.6.0/i586-linux/Xray/atp/ Copy `feff.atp' from there into your ~/.atoms/ directory and edit it as indicated. TkAtoms will use the personal copy rather than the system-wdie copy. You could even call your edited file something like "feff_tags.atp" and that will come up in the output file types menu in TkAtoms. On a windows computer, it'll be at (I don't have windows booted up right now, so this is by memory and may be slightly wrong) C:\Program Files\Ifeffit\perl\Xray\atp\ 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/