MOD Files

Structure-model files *.MOD are formatted text files containing information of the structure model. MOD files consist of a number of sections begining with a comment line and ended with the *EOS (end of section) line. In between these two lines, there are command lines begining with a space followed by a keyword and parameters. Examples of MOD files and detailed description of keywords are given.

          (i) 2-dimensional model of copper chlorinated phthalocynine
          (ii) 3-dimensional model of YBaCuO
          (iii) 4-dimensional model of the incommensurate modulated structure g - Na2CO3
          (iv) Keywords in MOD files

Example 1
2-dimensional model of copper chlorinated phthalocynine

On the right there is seen the MOD file created by VEC when it was used to build a structure model from a 2-dimensional enhanced electron microscopy image of copper chlorinated phthalocynine (see model building for phthalocynine). Below is shown the same file opened in graphic mode.

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Phthalocynine.mod
PRIVATE     The item must be at the beginning of the file
 CONV        1
 TYPE        2
 RECI        1.70  171.80  253.45   -1.70    1.00
 SIZE          40     240     342     256
*EOS

CELL DIMension  a         b         c       alpha     beta      gamma
 CELL        19.6200   26.0400    3.7600   90.0000  116.5000   90.0000
*EOS

SYMMETRY
 SGSY     8   1   c 2 m m
 SYOP      1 0 0 0.0000000     0 1 0 0.0000000     0 0 1 0.0000000
 SYOP     -1 0 0 0.0000000     0 1 0 0.0000000     0 0 1 0.0000000
 SYOP      1 0 0 0.0000000     0-1 0 0.0000000     0 0 1 0.0000000
 SYOP     -1 0 0 0.0000000     0-1 0 0.0000000     0 0 1 0.0000000
 SYOP      1 0 0 0.5000000     0 1 0 0.5000000     0 0 1 0.0000000
 SYOP     -1 0 0 0.5000000     0 1 0 0.5000000     0 0 1 0.0000000
 SYOP      1 0 0 0.5000000     0-1 0 0.5000000     0 0 1 0.0000000
 SYOP     -1 0 0 0.5000000     0-1 0 0.5000000     0 0 1 0.0000000
*EOS

ATOMS 
 ATCO    Cu       0.50000 0.50000 0.00000 0.00000 1.00000 0.00000
 UIJ     Cu       0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    N        0.59870 0.50000 0.00000 0.00000 1.00000 0.00000
 UIJ     N        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    N        0.50000 0.41490 0.00000 0.00000 1.00000 0.00000
 UIJ     N        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    N        0.61520 0.40230 0.00000 0.00000 1.00000 0.00000
 UIJ     N        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.44050 0.39550 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.77280 0.44860 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.83700 0.46790 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    Cl       0.90660 0.43980 0.00000 0.00000 1.00000 0.00000
 UIJ     Cl       0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    Cl       0.77210 0.38540 0.00000 0.00000 1.00000 0.00000
 UIJ     Cl       0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.53880 0.33570 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.57340 0.29600 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.54960 0.24490 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    Cl       0.64900 0.29160 0.00000 0.00000 1.00000 0.00000
 UIJ     Cl       0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    Cl       0.57820 0.19730 0.00000 0.00000 1.00000 0.00000
 UIJ     Cl       0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.71000 0.47260 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 ATCO    C        0.64000 0.46120 0.00000 0.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
*EOS

END
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Example 2: 3-dimensional model of YBaCuO

Since keywords RECI and SIZE are absent in the PRIVATE section, when open this file in graphic mode, the model will not display properly. However this would not affects VEC in performing any sorts of calculation available to a 3D conventional structure models.

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YBaCuO.mod
PRIVATE     The item must be at the beginning of the file
 CONV       1
 TYPE       -1
*EOS

CELL DIMension  a         b         c      alpha     beta      gamma
 CELL         3.8177    3.8836   11.6827   90.0000   90.0000   90.0000
*EOS

SYMMETRY
 SGSY     8   1   p m m m
 SYOP      1 0 0 0.0000000     0 1 0 0.0000000     0 0 1 0.0000000
 SYOP     -1 0 0 0.0000000     0 1 0 0.0000000     0 0 1 0.0000000
 SYOP      1 0 0 0.0000000     0-1 0 0.0000000     0 0 1 0.0000000
 SYOP     -1 0 0 0.0000000     0-1 0 0.0000000     0 0 1 0.0000000
 SYOP      1 0 0 0.0000000     0 1 0 0.0000000     0 0-1 0.0000000
 SYOP     -1 0 0 0.0000000     0 1 0 0.0000000     0 0-1 0.0000000
 SYOP      1 0 0 0.0000000     0-1 0 0.0000000     0 0-1 0.0000000
 SYOP     -1 0 0 0.0000000     0-1 0 0.0000000     0 0-1 0.0000000
*EOS

ATOMS                x        y       z      B      Occ
 ATCO    Y        0.50000 0.50000 0.50000 3.00000 1.00000 0.00000
 ATCO    Ba       0.50000 0.50000 0.18440 3.00000 1.00000 0.00000
 ATCO    Cu1      0.00000 0.00000 0.00000 3.00000 1.00000 0.00000
 ATCO    Cu2      0.00000 0.00000 0.35520 3.00000 1.00000 0.00000
 ATCO    O 1      0.00000 0.00000 0.15580 3.00000 1.00000 0.00000
 ATCO    O 2      0.50000 0.00000 0.37790 3.00000 1.00000 0.00000
 ATCO    O 3      0.00000 0.50000 0.37800 3.00000 1.00000 0.00000
 ATCO    O 4      0.00000 0.50000 0.00000 3.00000 1.00000 0.00000
*EOS

END
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Example 3: 4-dimensional model of the incommensurate modulated structure g -Na2CO3

This file was created by the program MIMS when it was used to interpret the 4-dimensional Fourier map calculated by VEC with phases from the program DIMS (see 4D modeling of g-Na2CO3).

Opening the file Na2CO3.mod in graphic mode a table instead of the model image will apear, which contains all the structural parameters

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Na2CO3.mod
PRIVATE     The item must be at the beginning of the file
 CONV       0
 TYPE      -1
 XRAY       1
*EOS

CELL DIMension  a         b         c      alpha     beta      gamma
 CELL         8.9040    5.2390    6.0420   90.0000  101.3500   90.0000
 QVEC         0.1820    0.0000    0.3180
*EOS

SYMMETRY
 SGSY     8   1   P[C 2/m]  -1 s   :B
 SYOP      1 0 0 0 0.0000   0 1 0 0 0.0000   0 0 1 0 0.0000   0 0 0 1 0.0000
 SYOP     -1 0 0 0 0.0000   0-1 0 0 0.0000   0 0-1 0 0.0000   0 0 0-1 0.0000
 SYOP      1 0 0 0 0.0000   0-1 0 0 0.0000   0 0 1 0 0.0000   0 0 0 1 0.5000
 SYOP     -1 0 0 0 0.0000   0 1 0 0 0.0000   0 0-1 0 0.0000   0 0 0-1 0.5000
 SYOP      1 0 0 0 0.5000   0 1 0 0 0.5000   0 0 1 0 0.0000   0 0 0 1 0.0000
 SYOP     -1 0 0 0 0.5000   0-1 0 0 0.5000   0 0-1 0 0.0000   0 0 0-1 0.0000
 SYOP      1 0 0 0 0.5000   0-1 0 0 0.5000   0 0 1 0 0.0000   0 0 0 1 0.5000
 SYOP     -1 0 0 0 0.5000   0 1 0 0 0.5000   0 0-1 0 0.0000   0 0 0-1 0.5000
*EOS

ATOMS 
 ATCO    Na1      0.00000 0.00000 0.00000 1.00000 1.00000 0.00000
 UIJ     Na1      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 XWAV    Na1      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00072-0.00001-0.00017
 YWAV    Na1      0.00000 0.00000 0.00000 0.00000 0.00000 0.05843 0.00000-0.00341 0.00000
 ZWAV    Na1      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00071 0.00000-0.00053
 PWAV    Na1      1.00000 0.00000-0.04302 0.00000 0.03136 0.00000 0.00000 0.00000 0.00000

 ATCO    Na2      0.00000 0.00000 0.50000 1.00000 1.00000 0.00000
 UIJ     Na2      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 XWAV    Na2      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 YWAV    Na2      0.00000 0.05154 0.00000 0.00000 0.00000 0.03271 0.00000 0.00000 0.00000
 ZWAV    Na2      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 PWAV    Na2      1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

 ATCO    Na3      0.33066 0.00000 0.25099 1.00000 1.00000 0.00000
 UIJ     Na3      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 XWAV    Na3      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 YWAV    Na3      0.00000 0.04667 0.00000 0.00000 0.00000 0.03308 0.00000 0.00000 0.00000
 ZWAV    Na3      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 PWAV    Na3      1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

 ATCO    O 2      0.28727 0.50000 0.17667 1.00000 1.00000 0.00000
 UIJ     O 2      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 XWAV    O 2      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 YWAV    O 2      0.00000 0.00000 0.00000 0.00000 0.00000 0.01999 0.00000 0.00000 0.00000
 ZWAV    O 2      0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 PWAV    O 2      1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

 ATCO    C        0.16657 0.50000 0.24848 1.00000 1.00000 0.00000
 UIJ     C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 XWAV    C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00080 0.00000 0.00000
 YWAV    C        0.00000 0.03907 0.00000 0.00000 0.00000 0.04946 0.00000 0.00000 0.00000
 ZWAV    C        0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 PWAV    C        1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

 ATCO    O 13     0.09790 0.29763 0.28185 1.00000 1.00000 0.00000
 UIJ     O 13     0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 XWAV    O 13     0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 YWAV    O 13     0.00000 0.04127 0.00000 0.00000 0.00000 0.04144 0.00000 0.00000 0.00000
 ZWAV    O 13     0.00000-0.03124 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
 PWAV    O 13     1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

*EOS

END

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