Ru input file - a question and a problem
Hi Bruce/Matt/Scott I am trying to fit some Ru based catalysts using Ifeffit - 0.8.007. 1. Does anyone have an atoms input file for Ruthenium that they can share with me? _ 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. 2. So I tried playing around with the atoms input file. I set all the xyz co-ordinates to 0, then the FEFF runs without any error but that however gives me 2 Ru paths with two separate R eff ( 2.14 and 2.70 A) but very close to each other in the first shell. Is this a possible scenario? Thank you for your time/comments/solutions. Vivek # Artemis version 0.8.007 # This file created at 16:41:31 on 2 May, 2007 # using Windows XP, perl 5.006001, Tk 800.024, and Ifeffit 1.2.9 # IFEFFIT_DIR is C:\Program Files\Ifeffit # Workspace: C:\Program Files\Ifeffit\horae\stash\artemis.project.1\ Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 1 2 1 0.00000 0.00000 0.00000 2 0.00000 0.00018 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 3 9 3 -1.56108 0.00014 2.14100 9 -1.56116 0.00009 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 4 5 4 0.78066 -1.35186 2.14100 5 0.78058 -1.35191 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 6 10 6 -1.56108 0.00014 -2.14100 10 -1.56116 0.00009 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 7 8 7 0.78066 -1.35186 -2.14100 8 0.78058 -1.35191 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 13 11 0.78058 1.35209 2.14100 13 0.78066 1.35214 2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 12 14 12 0.78058 1.35209 -2.14100 14 0.78066 1.35214 -2.14100 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 15 23 15 0.00000 -2.70382 0.00000 23 0.00000 -2.70400 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 16 21 16 2.34173 -1.35182 0.00000 21 2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 17 22 17 -2.34173 -1.35182 0.00000 22 -2.34173 -1.35200 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 18 24 18 2.34173 1.35200 0.00000 24 2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 19 25 19 -2.34173 1.35200 0.00000 25 -2.34173 1.35218 0.00000 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 20 26 20 0.00000 2.70400 0.00000 26 0.00000 2.70418 0.00000 Run continues... ... Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 muffin tin radii and interstitial parameters phase shifts for unique potential 0 This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ! 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
Hi Vivek, This one's easy: atoms works to five figures past the decimal point. You've written 1/3 as 0.33330, and 2/3 as 0.66670. Try 0.33333 and 0.66667 and I think your problem will be solved... --Scott Calvin Sarah Lawrence College At 05:15 PM 5/2/2007, you wrote:
! 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
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/
participants (3)
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Bruce Ravel -
Scott Calvin -
Vivek Murthi