[Wien] Importing .cif files in Wien2k
Peter Blaha
pblaha at theochem.tuwien.ac.at
Wed Jan 31 11:08:14 CET 2007
This is because it is a "bad" cif file.
It lists the atomic positions as:
Zn 0.33333 0.66667 0.00000
O 0.33333 0.66667 0.38200
These are only 5 significant digits and of course when you apply the
symmetry operations they will produce "more" equivalent sites, because
0.33333 is NOT 1/3. (Wien works internally with a much higher precision.
Just edit the cif file and increase the number of digits to 9.
E B Lombardi schrieb:
> Dear Wien users and authors
>
> When converting the attached .cif file of wurtzite ZnO (attached) using
> cif2struct, the .struct file contains 4 equivalent positions per atom,
> instead of the 2 equivalent sites per atom required for a wurtzite
> structure.
>
> When the .cif file is imported using the w2web interface, the .struct
> file contains 6 equivalent positions per atom!
>
> Attached are
> 1. zincite.cif (downloaded from American Mineralogist Crystal Structure
> Database; http://rruff.geo.arizona.edu/AMS/amcsd.php)
> 2. zincite-cif2struct.struct - created using cif2struct
> 3. zincite-structgen.struct - created from the .cif file using w2web
> 4. zincite.struct - correct struct file.
>
> Thank you in advance
> Regards
> Enrico
>
>
> ------------------------------------------------------------------------
>
>
> data_global
> _chemical_name 'Zincite'
> loop_
> _publ_author_name
> 'Kihara K'
> 'Donnay G'
> _journal_name_full "The Canadian Mineralogist"
> _journal_volume 23
> _journal_year 1985
> _journal_page_first 647
> _journal_page_last 654
> _publ_section_title
> ;
> Anharmonic thermal vibrations in ZnO
> Model: 2-c, at T = 473 K
> ;
> _chemical_formula_sum 'Zn O'
> _cell_length_a 3.2533
> _cell_length_b 3.2533
> _cell_length_c 5.2073
> _cell_angle_alpha 90
> _cell_angle_beta 90
> _cell_angle_gamma 120
> _cell_volume 47.730
> _symmetry_space_group_name_H-M 'P 63 m c'
> loop_
> _symmetry_equiv_pos_as_xyz
> 'x,y,z'
> '-x,-x+y,1/2+z'
> 'x-y,x,1/2+z'
> '-y,-x,z'
> '-y,x-y,z'
> 'x-y,-y,1/2+z'
> '-x,-y,1/2+z'
> 'x,x-y,z'
> '-x+y,-x,z'
> 'y,x,1/2+z'
> 'y,-x+y,1/2+z'
> '-x+y,y,z'
> loop_
> _atom_site_label
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> Zn 0.33333 0.66667 0.00000
> O 0.33333 0.66667 0.38200
> loop_
> _atom_site_aniso_label
> _atom_site_aniso_U_11
> _atom_site_aniso_U_22
> _atom_site_aniso_U_33
> _atom_site_aniso_U_12
> _atom_site_aniso_U_13
> _atom_site_aniso_U_23
> Zn 0.02800 0.02800 0.00830 0.01400 0.00000 0.00000
> O 0.02610 0.02610 0.00760 0.01305 0.00000 0.00000
>
>
> ------------------------------------------------------------------------
>
> blebleble
> H LATTICE,NONEQUIV.ATOMS: 2186_P63mc
> MODE OF CALC=RELA unit=bohr
> 6.147846 6.147846 9.840371 90.000000 90.000000120.000000
> ATOM -1: X=0.33333000 Y=0.66667000 Z=0.00000000
> MULT= 6 ISPLIT= 8
> ATOM -1:X= 0.66666000 Y=0.33333000 Z=0.50000000
> ATOM -1:X= 0.66667000 Y=0.33333000 Z=0.50000000
> ATOM -1:X= 0.33333000 Y=0.66666000 Z=0.00000000
> ATOM -1:X= 0.33334000 Y=0.66667000 Z=0.00000000
> ATOM -1:X= 0.66667000 Y=0.33334000 Z=0.50000000
> Zn NPT= 781 R0=0.00005000 RMT= 2.0000 Z: 30.0
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> ATOM -2: X=0.33333000 Y=0.66667000 Z=0.38200000
> MULT= 6 ISPLIT= 8
> ATOM -2:X= 0.66666000 Y=0.33333000 Z=0.88200000
> ATOM -2:X= 0.66667000 Y=0.33333000 Z=0.88200000
> ATOM -2:X= 0.33333000 Y=0.66666000 Z=0.38200000
> ATOM -2:X= 0.33334000 Y=0.66667000 Z=0.38200000
> ATOM -2:X= 0.66667000 Y=0.33334000 Z=0.88200000
> O NPT= 781 R0=0.00010000 RMT= 2.0000 Z: 8.0
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> 0 NUMBER OF SYMMETRY OPERATIONS
>
>
> ------------------------------------------------------------------------
>
> blebleble
> H LATTICE,NONEQUIV.ATOMS 2 186 P63mc
> MODE OF CALC=RELA unit=bohr
> 6.147846 6.147846 9.840371 90.000000 90.000000120.000000
> ATOM -1: X=0.33333333 Y=0.66666667 Z=0.00000000
> MULT= 2 ISPLIT=15
> -1: X=0.66666667 Y=0.33333333 Z=0.50000000
> Zn NPT= 781 R0=.000050000 RMT= 2.00000 Z: 30.00000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> ATOM -2: X=0.33333333 Y=0.66666667 Z=0.38200000
> MULT= 2 ISPLIT=15
> -2: X=0.66666667 Y=0.33333333 Z=0.88200000
> O NPT= 781 R0=.000100000 RMT= 2.00000 Z: 8.00000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> 0 NUMBER OF SYMMETRY OPERATIONS
>
>
> ------------------------------------------------------------------------
>
> blebleble
> H LATTICE,NONEQUIV.ATOMS 2 186 P63mc
> MODE OF CALC=RELA unit=bohr
> 6.147846 6.147846 9.840371 90.000000 90.000000120.000000
> ATOM -1: X=0.33333000 Y=0.66667000 Z=0.00000000
> MULT= 4 ISPLIT=15
> -1: X=0.66667000 Y=0.33334000 Z=0.50000000
> -1: X=0.66666000 Y=0.33333000 Z=0.50000000
> -1: X=0.33334000 Y=0.66667000 Z=0.00000000
> Zn NPT= 781 R0=.000050000 RMT= 2.00000 Z: 30.00000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> ATOM -2: X=0.33333000 Y=0.66667000 Z=0.38200000
> MULT= 4 ISPLIT=15
> -2: X=0.66667000 Y=0.33334000 Z=0.88200000
> -2: X=0.66666000 Y=0.33333000 Z=0.88200000
> -2: X=0.33334000 Y=0.66667000 Z=0.38200000
> O NPT= 781 R0=.000100000 RMT= 2.00000 Z: 8.00000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> 0 NUMBER OF SYMMETRY OPERATIONS
>
>
> ------------------------------------------------------------------------
>
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--
P.Blaha
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Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-15671 FAX: +43-1-58801-15698
Email: blaha at theochem.tuwien.ac.at WWW:
http://info.tuwien.ac.at/theochem/
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