[Ifeffit] Quick question about atoms.exe and .cif files
Bruce Ravel
bravel at bnl.gov
Tue Aug 26 08:05:31 CDT 2008
On Tuesday 26 August 2008 01:44:03 you wrote:
> Hi Bruce,
>
> I have atoms running well, but whenever I input a simple diamond
> structure .cif file (like the attached silicon.cif file), I get the wrong
> structure. I've tried everything that I could think of, but it doesn't
> work. I'm not sure if it is something I'm doing wrong, or something
> intrinsic in the .cif file. I'm currently running the command line program
> with the command "atoms.exe -u -o "silicon.inf" "Silicon.cif"", with the
> files being appropriately loaded. If you get the chance could you tell me
> if it is an easy problem that I can quickly fix (and the solution), or if
> it is something more in depth: I'd appreciate it.
>
> Zak
I am forwarding this question to the Ifeffit mailing list. This is
the sort of question for which that forum was created. Please make
use of it.
http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest
As the warning message says, "F d -3 m" is one of those space groups
in the International Tables that offers two choices for the position
of the origin. There is no way to correct that from the command line,
so your two options are:
1. Use Artemis to generate your unit cell file and apply the shift
vector given in the warning message
or
2. Edit the cif file to put the Si atom at (1/8,1/8,1/8)
B
--
Bruce Ravel ------------------------------------ bravel at bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
My homepage: http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
-------------- next part --------------
data_global
_chemical_name 'Silicon'
loop_
_publ_author_name
'Wyckoff R W G'
_journal_name_full "Crystal Structures"
_journal_volume 1
_journal_year 1963
_journal_page_first 7
_journal_page_last 83
_publ_section_title
;
Second edition. Interscience Publishers, New York, New York
Sample at T = 300 K
;
_chemical_formula_sum 'Si'
_cell_length_a 5.43070
_cell_length_b 5.43070
_cell_length_c 5.43070
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 160.165
_symmetry_space_group_name_H-M 'F d 3 m'
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'x,1/2+y,1/2+z'
'1/2+x,y,1/2+z'
'1/2+x,1/2+y,z'
'3/4+z,3/4-x,1/4+y'
'3/4+z,1/4-x,3/4+y'
'1/4+z,3/4-x,3/4+y'
'1/4+z,1/4-x,1/4+y'
'-y,1/2+z,1/2-x'
'-y,+z,-x'
'1/2-y,1/2+z,-x'
'1/2-y,+z,1/2-x'
'3/4+x,3/4-y,1/4+z'
'3/4+x,1/4-y,3/4+z'
'1/4+x,3/4-y,3/4+z'
'1/4+x,1/4-y,1/4+z'
'-z,1/2+x,1/2-y'
'-z,+x,-y'
'1/2-z,1/2+x,-y'
'1/2-z,+x,1/2-y'
'3/4+y,3/4-z,1/4+x'
'3/4+y,1/4-z,3/4+x'
'1/4+y,3/4-z,3/4+x'
'1/4+y,1/4-z,1/4+x'
'-x,1/2+y,1/2-z'
'-x,+y,-z'
'1/2-x,1/2+y,-z'
'1/2-x,+y,1/2-z'
'1/2+x,-z,1/2-y'
'1/2+x,1/2-z,-y'
'+x,-z,-y'
'+x,1/2-z,1/2-y'
'3/4-z,3/4+y,1/4+x'
'3/4-z,1/4+y,3/4+x'
'1/4-z,3/4+y,3/4+x'
'1/4-z,1/4+y,1/4+x'
'1/2+y,-x,1/2-z'
'1/2+y,1/2-x,-z'
'+y,-x,-z'
'+y,1/2-x,1/2-z'
'3/4-x,3/4+z,1/4+y'
'3/4-x,1/4+z,3/4+y'
'1/4-x,3/4+z,3/4+y'
'1/4-x,1/4+z,1/4+y'
'1/2+z,-y,1/2-x'
'1/2+z,1/2-y,-x'
'+z,-y,-x'
'+z,1/2-y,1/2-x'
'3/4-y,3/4+x,1/4+z'
'3/4-y,1/4+x,3/4+z'
'1/4-y,3/4+x,3/4+z'
'1/4-y,1/4+x,1/4+z'
'x,1/2+z,1/2+y'
'x,+z,+y'
'1/2+x,1/2+z,+y'
'1/2+x,+z,1/2+y'
'1/4-z,3/4-y,3/4-x'
'1/4-z,1/4-y,1/4-x'
'3/4-z,3/4-y,1/4-x'
'3/4-z,1/4-y,3/4-x'
'y,1/2+x,1/2+z'
'y,+x,+z'
'1/2+y,1/2+x,+z'
'1/2+y,+x,1/2+z'
'1/4-x,3/4-z,3/4-y'
'1/4-x,1/4-z,1/4-y'
'3/4-x,3/4-z,1/4-y'
'3/4-x,1/4-z,3/4-y'
'z,1/2+y,1/2+x'
'z,+y,+x'
'1/2+z,1/2+y,+x'
'1/2+z,+y,1/2+x'
'1/4-y,3/4-x,3/4-z'
'1/4-y,1/4-x,1/4-z'
'3/4-y,3/4-x,1/4-z'
'3/4-y,1/4-x,3/4-z'
'3/4+z,1/4+x,3/4-y'
'3/4+z,3/4+x,1/4-y'
'1/4+z,1/4+x,1/4-y'
'1/4+z,3/4+x,3/4-y'
'-y,1/2-z,1/2+x'
'-y,-z,+x'
'1/2-y,1/2-z,+x'
'1/2-y,-z,1/2+x'
'3/4+x,1/4+y,3/4-z'
'3/4+x,3/4+y,1/4-z'
'1/4+x,1/4+y,1/4-z'
'1/4+x,3/4+y,3/4-z'
'-z,1/2-x,1/2+y'
'-z,-x,+y'
'1/2-z,1/2-x,+y'
'1/2-z,-x,1/2+y'
'3/4+y,1/4+z,3/4-x'
'3/4+y,3/4+z,1/4-x'
'1/4+y,1/4+z,1/4-x'
'1/4+y,3/4+z,3/4-x'
'-x,1/2-y,1/2+z'
'-x,-y,+z'
'1/2-x,1/2-y,+z'
'1/2-x,-y,1/2+z'
'1/4-z,3/4+x,3/4+y'
'1/4-z,1/4+x,1/4+y'
'3/4-z,3/4+x,1/4+y'
'3/4-z,1/4+x,3/4+y'
'y,-z,-x'
'y,1/2-z,1/2-x'
'1/2+y,-z,1/2-x'
'1/2+y,1/2-z,-x'
'1/4-x,3/4+y,3/4+z'
'1/4-x,1/4+y,1/4+z'
'3/4-x,3/4+y,1/4+z'
'3/4-x,1/4+y,3/4+z'
'z,-x,-y'
'z,1/2-x,1/2-y'
'1/2+z,-x,1/2-y'
'1/2+z,1/2-x,-y'
'1/4-y,3/4+z,3/4+x'
'1/4-y,1/4+z,1/4+x'
'3/4-y,3/4+z,1/4+x'
'3/4-y,1/4+z,3/4+x'
'x,-y,-z'
'x,1/2-y,1/2-z'
'1/2+x,-y,1/2-z'
'1/2+x,1/2-y,-z'
'1/2-x,1/2+z,-y'
'1/2-x,+z,1/2-y'
'-x,1/2+z,1/2-y'
'-x,+z,-y'
'1/4+z,3/4-y,3/4+x'
'1/4+z,1/4-y,1/4+x'
'3/4+z,3/4-y,1/4+x'
'3/4+z,1/4-y,3/4+x'
'1/2-y,1/2+x,-z'
'1/2-y,+x,1/2-z'
'-y,1/2+x,1/2-z'
'-y,+x,-z'
'1/4+x,3/4-z,3/4+y'
'1/4+x,1/4-z,1/4+y'
'3/4+x,3/4-z,1/4+y'
'3/4+x,1/4-z,3/4+y'
'1/2-z,1/2+y,-x'
'1/2-z,+y,1/2-x'
'-z,1/2+y,1/2-x'
'-z,+y,-x'
'1/4+y,3/4-x,3/4+z'
'1/4+y,1/4-x,1/4+z'
'3/4+y,3/4-x,1/4+z'
'3/4+y,1/4-x,3/4+z'
'-x,-z,y'
'-x,1/2-z,1/2+y'
'1/2-x,-z,1/2+y'
'1/2-x,1/2-z,y'
'3/4+z,3/4+y,1/4-x'
'3/4+z,1/4+y,3/4-x'
'1/4+z,3/4+y,3/4-x'
'1/4+z,1/4+y,1/4-x'
'-y,-x,z'
'-y,1/2-x,1/2+z'
'1/2-y,-x,1/2+z'
'1/2-y,1/2-x,z'
'3/4+x,3/4+z,1/4-y'
'3/4+x,1/4+z,3/4-y'
'1/4+x,3/4+z,3/4-y'
'1/4+x,1/4+z,1/4-y'
'-z,-y,x'
'-z,1/2-y,1/2+x'
'1/2-z,-y,1/2+x'
'1/2-z,1/2-y,x'
'3/4+y,3/4+x,1/4-z'
'3/4+y,1/4+x,3/4-z'
'1/4+y,3/4+x,3/4-z'
'1/4+y,1/4+x,1/4-z'
'1/4-z,1/4-x,1/4-y'
'1/4-z,3/4-x,3/4-y'
'3/4-z,1/4-x,3/4-y'
'3/4-z,3/4-x,1/4-y'
'y,z,x'
'y,1/2+z,1/2+x'
'1/2+y,z,1/2+x'
'1/2+y,1/2+z,x'
'1/4-x,1/4-y,1/4-z'
'1/4-x,3/4-y,3/4-z'
'3/4-x,1/4-y,3/4-z'
'3/4-x,3/4-y,1/4-z'
'z,x,y'
'z,1/2+x,1/2+y'
'1/2+z,x,1/2+y'
'1/2+z,1/2+x,y'
'1/4-y,1/4-z,1/4-x'
'1/4-y,3/4-z,3/4-x'
'3/4-y,1/4-z,3/4-x'
'3/4-y,3/4-z,1/4-x'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Si 0.00000 0.00000 0.00000
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