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.
<snip>
! 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 atoms ! elem x y z tag occ. Ru 0.33330 0.66670 0.25000 Ru 1.00000
Vivek, 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 place." One way of avoiding this problem in Artemis is to use simple fractions. Instead of "0.33333", you can just enter "1/3". B 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@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/