Structure-model files are formatted text files with the extension MOD.
They 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.
Section
|
Keyword
|
Command in Fortran Format
|
Private
|
CONV
|
( 1X , 'CONV' , 4X ,
I4 ) n
n = 1: conventional structure
model
n = 0: incommensurate modulated
structure model |
TYPE
|
( 1X , 'TYPE' , 4X ,
I4 ) n
n = 0: projected model along
the [100] direction
n = 1: projected model along
the [010] direction
n = 2: projected model along
the [001] direction
n = -1:
3-dimensional model |
XRAY
|
( 1X , 'XRAY' , 4X ,
I4 ) n
n = 0: electron diffraction
will be simulated
n = 1: X-ray diffraction will
be simulated
Omitting this command is equivalent
to set n = 0. |
RECI
|
( 1X , 'RECI' , 4X , 5F8.2 ) Ax ,
Ay , Bx , By , Zoom
( 1X , 'RECI' , 4X , 7F8.2 ) Ax , Ay , Bx , By , Qx ,
Qy , Zoom
The first command is for conventional structures, while
the second is for incommensurate structures. These commands are used to
inform VEC how to display the 2- or 3-dimensional diffraction pattern
in a window.
X and Y are respectively the horizontal and vertical
axes of the window with the origin at the upper-left conner.
A and B are vectors representing two of the three
axes a,
b and c, which define
the crystallographic unit cell.
For [100]
projections, A = c , B = b.
For [010]
projections, A = a , B = c .
For [001]
projections, A = a, B = b.
Ax, Ay: X, Y components (in pixels) of the vector
A
Bx, By: X, Y components (in pixels) of the vector
B
Qx, Qy: X, Y components (in pixels) of the modulation
vector
q
Zoom: linear scale factor of the displayed model |
SIZE
|
( 1X , 'SIZE' , 4X ,
4I8 ) Ox , Oy , W , H
Ox, Oy: X, Y coordinates (in pixels) of
the unit-cell origin in the model window
W, H: width and height (in pixels) of the
model window
------------------------------------
Omitting commands SIZE and RECI does not
affect subsequent operations on the model window. However, in this case
the model image will not display properly. |
Cell
|
CELL
|
( 1X , 'CELL' , 5X , 6F10.4 ) a
,
b , c , a ,
b
, g
This defines the crystallographic unit cell with a
, b and c in Angstroms and a
, b and g
in degrees. |
QVEC
|
( 1X , 'QVEC' , 5X , 3F10.4 ) k1
, k2 , k3
This defines the modulation wave vector q
= k1a* +
k2b*
+ k3c* |
Symmetry
|
SGSY
|
( 1X , 'SGSY' , 5X , 2I4 ) n
, i
n: symmetry order of the space group
- the maximum nember of independent symmetry operations
i = 0: noncentrosymmetric
i = 1: centrosymmetric |
SYOP
|
( 1X , 'SYOP' , 5X , 3 ( 3I2 , F10.7
, 4X ) ) ( ( R ( I , J ) , J = 1 , 3 ) , T ( I ) ) ,
I = 1 , 3
( 1X , 'SYOP' , 5X , 4 ( 4I2 , F10.7 , 2X ) ) ( ( R (
I , J ) , J = 1 , 4 ) , T ( I ) ) , I = 1 , 4
The first command is for conventional structres while
the second is for incommensurate modulated structures.
Each command (a single line) defines one symmetry operation,
which consists of a rotation R ( I , J ) and the associated translation
T ( I ). There will be n SYOP lines for a space group of the order
n. |
ATOM
|
ATCO
|
( 1X , 'ATCO' , 4X , A2 , A6 , 6F8.5
) symbol , code , x , y ,z , B-factor , occupancy , valence
This defines the species (atomic symbol), identify code,
positiion (in fractional coordinates), isotropic temperature factor B =
8p2U
and
valence of an atom. 'valence' is temporarily void. |
UIJ
|
( 1X , 'UIJ' , 4X , A2 , A6 , 6F8.5
) symbol , code , U11
, U22 , U33
, U12 , U23
, U13
This defines coefficients of the anisotropic temperature
factor of the given atom defined by the preceding ATCO command. |
XWAV
|
( 1X , 'XWAV' , 4X , A2 , A6 , 9F8.5
) symbol, code, C0
, C1 , C2
, C3 , C4
, S1 , S2
, S3 , S4
This defines the X component of the positional modulation
of the given atom.
Cn: the nth
order
coefficient for COS functions in the Fourier-series expansion*
Sn: the nth
order
coefficient for SIN functions in the Fourier-series expansion* |
YWAV
|
( 1X , 'YWAV' , 4X , A2 , A6 , 9F8.5
) symbol , code , C0
, C1 , C2
, C3 , C4
, S1 , S2
, S3 , S4
This defines the Y component of the positional modulation
of the given atom.
Cn: the nth
order
coefficient for COS functions in the Fourier-series expansion*
Sn: the nth
order
coefficient for SIN functions in the Fourier-series expansion* |
ZWAV
|
( 1X , 'ZWAV' , 4X , A2 , A6 , 9F8.5
) symbol , code , C0
, C1 , C2
, C3 , C4
, S1 , S2
, S3 , S4
This defines the Z component of the positional modulation
of the given atom.
Cn: the nth
order
coefficient for COS functions in the Fourier-series expansion*
Sn: the nth
order
coefficient for SIN functions in the Fourier-series expansion* |
PWAV
|
( 1X , 'PWAV' , 4X , A2 , A6 , 9F8.5
) symbol , code , C0
, C1 , C2
, C3 , C4
, S1 , S2
, S3 , S4
This defines the occupational modulation of the given
atom.
Cn: the nth
order
coefficient for COS functions in the Fourier-series expansion*
Sn: the nth
order
coefficient for SIN functions in the Fourier-series expansion* |