Hi, One of the most common inquiries that finds its way into my mailbox is why the dopants capability in Atoms does not do what the user expects. Typically, the user expects Atoms to write a magical feff.inp file that correctly accounts for the dopants in the material such that FEFF can be run using this magic input file to generate fitting standards or a XANES calculations for the doped material. I get this question so often, that I want to post a response to both the feff and ifeffit mailing lists with an obvious subject line. Then, in the future, I (or even you!) can just point the curious to this posting. ----------- O ----------- First off, this topic is covered in the Atoms document http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/Atoms/Atoms/At... See section 3.4, Dopants. I also discuss this issue in Chapter 10 of the lecture notes for my course on EXAFS Analysis Using FEFF and FEFFIT. http://leonardo.phys.washington.edu/~ravel/course/notes.pdf The discussion in this posting applies to the old versions (2.50 and earlier) of Atoms as well as to the current version. ----------- O ----------- Atoms is, except in extremely contrived situations, not capable of writing a proper feff.inp file for a doped material. This is not a programming shortcoming of Atoms, but a number theoretic limitation imposed by the physical model used by FEFF. In the feff.inp file, there is a big list of atomic coordinates. The reason that people like using Atoms is because, without Atoms, it is a pain in the ass to generate that list. The virtue of Atoms is that it automates that annoying task for a certain class of matter, i.e. crystals. FEFF expects a point in space to be either unoccupied or occupied by a specific atom. A given point may be occupied neither by a fraction of an atoms nor by two different kinds of atoms. Let's use a very simple example -- gold doped into fcc copper. In fcc copper, there are 12 atoms in the first shell. If the level of doping was, say, 25%, then Atoms could reasonably use a random number generator to choose three of the 12 first neighbor sites and replace them with gold atoms. However, what should Atoms do with the second shell, which contains 6 atoms? 25% of 6 is 1.5. Feff does not allow a site to be half occupied by an atomic species, thus Atoms would have to decide either to over-dope or under-dope the second shell. This problem only gets worse if the doping fraction is not a rational (in the number theory sense) fraction, if the material is non-isotropic, or if the materials has multiple sites that the dopant might want to go to. Because Atoms cannot solve this problem correctly except in the most contrived of situations, I decided that Atoms would not attempt to solve it in any situation. If you specify dopants in Atoms' input data, the list in the feff.inp file will be be made as if there are no dopants. This leads to two big questions: 1. Why are dopants allowed in Atoms? 2. How do one deal with a doped sample? The first question is the easy one. Atoms does many things other besides feff.inp generation. Calculations involving tables of absorption coefficients and simulations of powder diffraction and DAFS spectra can use dopant information quite well. The second question is the tricky one and the answer is somewhat different for EXAFS as for XANES. The chapter in the PDF file mentioned at the beginning of this posting discusses one approach to analyzing EXAFS of doped materials. In this posting http://cars9.uchicago.edu/feff/feffusers/msg00022.html Scott Calvin adds his two cents worth. The bottom line for EXAFS analysis is that most dopant problems require running FEFF many times to deal with the wide variety of local environments one finds in a doping problem. One of my papers, A Combined EXAFS and First Principles Theory Study of Pb(1-x)Ge(x)Te, B. Ravel, E. Cockayne, M. Newville, and K.M. Rabe, Phys. Rev. B 60, #21, pp. 14632-14642 (1999). discusses a very thorough approach to one particular case of a doped material. The best approach to simulating a XANES spectrum on a doped material that I am aware of also involves running FEFF many times. One problem a colleague of mine asked me about some time ago was the situation of oxygen vacancies in Au2O3. After some discussion, the solution we came up with was to use Atoms to generate the feff.inp for the pure material. My friend then wrote a little computer program that would read in the feff.inp file, randomly remove oxygen atoms from the list, write the feff.inp file back out with the missing oxygens, and run FEFF. He would do this repeatedly, each time replacing a different set of randomly selected atoms and each time saving the result. This set of computed spectra was then averaged. New calculations were made and added to the running average until the result stopped changing. If I remember, it took about 10 calculations to converge. This random substitution approach would work just as well for dopants as for vacancies. I hope that is helpful. 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/