This is a valid point, as was Chris's response. When Atoms reads crystal data (which your cif file is -- it has two molecular units in a triclinic P -1 unit cell) it assigns unique potentials, then makes a rhmoboid out of unit cells which is big enough to completely enclose a sphere if radius RMAX. It then keeps only the atoms which are within the sphere. The mistake that Atoms seems to be making is not going through the sphere and verifying that each unique potential is represented. That is, Atoms should be smart enough to do automatically what you have gotten good at doing by hand. I'll put that on the to do list. Thanks, B On 10/30/2013 10:55 AM, Georges Siddiqi wrote:
2) Not critical - I deal with a lot of organometallic compounds whose cif files correspond of only 1 absorbing atom surrounded by a network of non-absorbing atoms. i.e. not a regular, repeating lattice.**When I import the cif file for one of these compounds (*see attachment, schrock 1.cif*), the Atoms page is fine, but in the Feff page, the "potentials" lists the absorbing atom as ipot 0 and 1: POTENTIALS * ipot Z tag 0 74 W 1 74 W 2 8 O 3 7 N 4 6 C 5 1 H while in the atoms list, it only appears once as ipot 0. Naturally, if I just click "run Feff", the program returns an error.
My workaround to this has been to copy the atoms list into notepad, save, import into excel, subtract 1 from the ipot column (besides ipot 0), and replace the old atoms list with the corrected atoms list. then I manually change the potentials to: POTENTIALS * ipot Z tag 0 74 W 1 8 O 2 7 N 3 6 C 4 1 H
after this it works fine.
So this isn't a big burden, after a bit of practice I've gotten pretty fast at editing the Feff file, but if there's some easier solution it would be great.
This problem occurs with any monomeric compounds. If I run the feff on a dimeric organometallic compound, there's no problems.
Please let me know if there's any additional information I can supply that would help with this.
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel