--------------------------- Shelly Kelly Argonne National Laboratory Bldg 203, RM E113
On Saturday 06 January 2007 10:53, Kelly, Shelly D. wrote:
Hello Artemis users,
I found an interesting feature in Artemis when generating a list of atoms from the attached cif file worth sharing on the list. In the
cif
file for Pd2Si the position of the Si2 atoms are at x,y,z = 0.3333, 0.6667, 0 with a space group of p -6 2 m. Using this cif file and choosing either Pd1 or Pd2 as the core atom results in errors in the atom list. For example for the Pd2 site there are 4 Si neighbors with the 1st and 3rd and the 2nd and 4th on top of each other. If you edit the atomic
so
that the Si2 atoms are correct to an additional digit x,y,z = 0.33333, 0.66667,0 then the atom list is fixed with only two Pd2-Si neighbors at each of the unique positions. The interesting feature is that the coordinates on the atoms page need to be correct to the 5 decimal
attached positions place.
This has been discussed many, many times on the mailing list and is explained in question 3 at http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff
The version of Feff that ships with Ifeffit (and, I believe, all others) uses 5 significant figures in the path finder. Since Atoms main purpose is to interact with Feff, it interprets the 5 digit thing quite strictly.
B
[sdk] Hi Bruce, Well, I thought that I had skipped your "here is a link describing that response" by searching the Ifeffit wiki. I didn't run FEFF, so I missed the description of the problem under the FEFF error message of overlapping atoms. I think that it would be helpful for the ATOMS page within Artemis to contain a note of some sort indicating that the 5th digit is significant. Now that I have had additional time to ponder this problem, I realize that I have learned it several times only to forget it again....:) Cheers, Shelly