[Ifeffit] Ru input file - a question and a problem
bravel at anl.gov
Wed May 2 16:50:19 CDT 2007
On Wednesday 02 May 2007, Vivek Murthi wrote:
> The problem:_
> 1. I got the crystallographic data for Ru from
> "database.iem.ac.ru/*mincryst*/" which I used inside atoms to generate
> FEFF a input file. However, FEFF returns an error saying that my atoms
> list might be wrong and that two atoms are separated by less than an
> 0.93 angstroms. I also checked the 5 digit precision in the input file
> to make sure that wasn't creating the problem. The FEFF input file
> generated by atoms definitely has atoms bizarrely close to each other.
> I do not understand why a standard crystallographic data would give such
> results. I have attached the "Ru.inp" input file I used and the error
> buffer from FEFF below for your convenience.
> ! This atoms input file was generated by Artemis 0.8.007
> ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
> title = ...
> space = P63/MMC
> a = 2.7040 b = 2.7040 c = 4.2820
> alpha = 90.0 beta = 90.0 gamma = 120.0
> core = Ru edge = K rmax = 3.0
> shift 0.00000 0.00000 0.00000
> ! elem x y z tag occ.
> Ru 0.33330 0.66670 0.25000 Ru 1.00000
I suppose that I have used confusing language in the past. In this
context, "five digits" means "five digits to the right of the decimal
One way of avoiding this problem in Artemis is to use simple
fractions. Instead of "0.33333", you can just enter "1/3".
P.S. The next version of Artemis checks for numbers that are close to
1/3 and 2/3 and prompts you to choose between the number you entered
and the fraction. It's a bit annoying to have to answer a bunch of
dialog boxes, but it should help avoid this problem.
Bruce Ravel ---------------------------------------------- bravel at anl.gov
Molecular Environmental Science Group, Building 203, Room E-165
MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033
Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/
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