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 ------------------------------------ [EMAIL PROTECTED] 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/
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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