On Thursday 10 January 2008 15:00:19 Voegelin Andreas wrote:
Using Atoms (latest version of Artemis), I tried to calculate a Feff input file based on a recently published structure for 6-Line Ferrihydrite (Michel et al, Science, 2007).
Attached: Atoms input file generated with Artemis.
For all three Fe sites as core (Fe1 and Fe2 octahedral, Fe3 tetrahedral), running Atoms yields Feff files with "overlapping atoms" located close to each other. The Artemis error messages after running Feff suggests that a shift vector may be needed in order to obtain correct Feff input files.
As a "non-crystallographer", I would be grateful for advice on how this problem can be solved.
Andreas, I'm pretty sure I don't count as a crystallographer, and after looking into this problem, I'm not sure I am confortable calling myself a programmer either ;-) This atoms.inp file (which you copied verbatim from the Science article) triggers a bug I have never seen before in Atoms. When each unique crystal position is expanded to fill the unit cell, the symmetries of the cell will, in many cases, generate a particular position more than once. Atoms has an algorithm which catches those and throws away the repeats. It attempts to treat numerical precision correctly in the sense that two positions that differ by a very small fraction are considered the same. Typically that algorithm handles the level of numerical precision in cell constants and site coordinates given in the Science article without a problem (with the exception of the high symmetry 1/3 and 2/3 positions). In fact, I have never seen a situation where the algorithm failed as it did here -- and I have looked at a lot of atoms.inp files over the years. There is no work-around short of my fixing the algorithm in the next horae release. The only helpful thing I can think of is to attach three feff.inp files -- one for each Fe site -- to this message which I generated with a specially modified version of my demeter code base. That's not a very gratifying situation for either of us, but it should get you over the immediate hurdle. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/