On Thursday 11 November 2004 9:11 am, Valmor Mastelaro wrote:
Bruce, I´m using the atoms program to obtain the feff.inp file for a PZT compound. when I introduced the crystallographic informations on the atoms, I obtained only one distance that is too short to be true, Ti-Zr = 0.483
I verify all the crystallographic parameters in the literature and they seens to be correct. (Journal of Physics: condensed matter 10, 6251-6269 (1998).
Hi Valmor. I am taking the liberty of forwarding my answer to the Ifeffit mailing list as well as the feffusers list. Here is the Atoms input file that Valmor sent: space = R 3 c a = 5.78510 c = 14.2880 core = Ti edge = K rmax = 9.0 atoms ! elem x y z tag occ. Pb 0.00000 0.00000 0.27170 1.00000 Ti 0.00000 0.00000 0.03590 1.00000 Zr 0.00000 0.00000 0.00210 1.00000 O 0.16321 0.34281 0.08333 1.00000 Actually, the one very short atom was only the most obvious of a host of problems with this input data. Look also at the Zr/Ti coordination shell. There are far too many atoms and they are much too close (about 0.483 AA apart -- imagine that!) to one another. Reading the paper that he cited, I see that coordinates are given for the anion and cation positions by parameterized deviations from the symmetry positions of the space group. It's really a very clever paper -- the parameters of the structure are things like cation displacement and octahedral tilt. Very cool stuff, all of which is explained abstractly in Table 1. Then in Table 3, the authors give the actual values of the parameters for each of the anions and cations. Among the data in this table are the fractional occupancies of Zr and Ti along with separate displacement parameters for those two cations. Before I go on, you need to read this old entry to the Ifeffit mailing list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2002-July/000092.html That entry actually answers your question about why Atoms isn't working as you anticipated, but I'll expand on a few points here. Feff (and therefore Atoms) presumes that you have one entire atoms at any given site. Feff does not allow you to fractionally occupy a location in space. This may be a shortcoming of Feff, but there are good reasons why Feff behaves that way. Since Feff does not know how to compute a cluster with fractional atoms, Atoms does attempt to write fractional atoms to the cluster. Thus, when you put *both* Ti and Zr in the atoms.inp file, Atoms put six of each in the unit cell. (This crystal has six formula units in each unit cell.) That's obviously incorrect. The paper you cite clearly states that the samples have between 13 and 40% Ti according to the stoichiometry Pb Zr_{1-x} Ti_x O_3. So it is simply incorrect to have both the Ti and Zr entries in your atoms input file. As I explain in the link above, you generally cannot solve a problem like this with a single Feff calculation. You simply must consider an analysis strategy which involves at least 2 and possibly many more Feff calculation. Are you doing EXAFS analysis? If so, then you should consider running Feff once without the Ti site and using the parameter given in the cited paper for the Zr site. Then run Feff again with the Zr site and using the parameters given for the Ti site. Then, when you do your analysis, you will need to multiply the amplitude terms for the paths from the Zr calculation by (to use the example of one end member) 0.87 and multiply the amplitudes of the paths from the Ti calculation by 0.13. Or are you doing XANES calculations? In that case, you will need to run many Feff calculations with the Ti and Zr sites randomly populated following the modle of the Au2O3 that I discuss in the link above. In any case, the bottom line that you have to remember when using Atoms and Feff is that these programs do not and cannot treat occupancy in the same manner as is discussed in a paper on Reitveld refinement. (That is true at least in the context of running a *single* Feff calculation.) You have to understand and think hard about how Atoms works and how Feff works and how they should be used for your specific analysis problem -- this is particularly true in a problem like this, which involves a rather complicated scheme for treating the relationship between stoichiometry and structure. Hope that helps, B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/