Hi! This week I received an interesting question about Atoms whose answer will, I think, be of wide interest to the denizens of this list. The fellow who started the discussion had an atoms.inp file for ammonium tetraoxorhenate, (NH4)ReO4. Here is the input data: space = I 41/a a = 5.995 c = 12.440 rmax=10 core = Re1 atoms # elem. x y z tag Re 0.00000 0.00000 0.00000 Re1 O 0.20450 0.37860 0.17020 O1 N 0.00000 0.00000 0.50000 N1 These data ran atoms to completion, but then Feff stopped after issuing the statement about computing the "muffin tin radii and interstitial parameters" with this error message: WARNING: NO ATOMS CLOSE ENOUGH TO OVERLAP ATOM 10, UNIQUE POT 3!! My correspondant found this message a little cryptic and asked for advice. You will notice that the input data for atoms did not specify the hydrogen positions. Often it is fine with both Atoms and Feff to neglect the positions of the hydrogen atoms. For example, in a mineral phase with water molecules in the crystal structure, one can often just specify the positions of the water oxygens and neglect the water hydrogens. Doing so will still let both Atoms and Feff run to completion and leave you with a Feff calculation that is quite useful in analysis. So what happened here? Apparently my correspondent presumed that ammonium is like water in that specifying the locations of the hydrogens is not essential to the Feff calculation. Like in water, the hydrogens are fairly tightly bound to the nitrogen -- less than an Angstrom away -- so it might be ok. In this case, however, the hydrogens are essential. Adding the hydrogen position H 0.37200 0.45600 0.03300 H1 avoids the problem during the Feff run. Feff finishes and the analysis can proceed. It turns out that, while the N and the H are, indeed, quite close together, the N is quite a long way away from its next nearest neighbor, which is oxygen. The oxygen shell is split into two subshells, the closer of which is at about 2.85 Angstroms from the N. When Feff goes to compute the muffin tin potential, a near neighbor separation of 2.85 Angstroms is too large and it is unable to determine the radii of the atoms. That is the meaning of Feff's slightly cryptic error message. With the intervening hydrogen atoms, Feff's algorithm for constructing the muffin tins is no longer ill-defined -- the separation between atoms is no longer too large. To conclude, while it is probably unlikely that the hydrogen locations can be well measured by the EXAFS experiment, it is quite important to include the hydrogens in the theory. The rule of thumb that says that hydrogens in hydrated crystal structures can be neglected is not a very good general rule. This is certainly a case where the hydrogens cannot be ignored. Well, *I* thought it was interesting. Hopefully you did too! B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/