Structure-factor files are formatted text files. 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 ,
2I4 ) type , zone
type = 0: file containing
structure factors after image averaging
type = 1: file containing
structure factors after image deconvolution
type = 2: file containing
structure-factor amplitudes measured from a diffraction pattern
type = 3: file containing
simulating dynamical electron diffraction data
zone = 0: [100] zone, i.e.
0kl
reflections
zone = 1: [010] zone, i.e. h0l
reflections
zone = 2: [001] zone, i.e. hk0
reflections
zone = -1:
3-dimensional diffraction data |
XRAY
|
( 1X , 'XRAY' , 4X ,
I4 ) n
n = 0: electron diffraction
data
n = 1: X-ray diffraction data
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 a 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 is at the upper-left conner.
A and B are vectors representing two of the three
reciprocal axes a*,
b* and c*,
which define the reciprocal 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 diffraction
pattern |
FFT3
|
( 1X , 'FFT3' , 4X ,
4I8 ) Nx , Ny , W , H
Nx: number of grid points along X in Fourier
transform
Ny: number of grid points along Y in Fourier
transform
W, H: width and height (in pixels) of the
resultant image (inverse Fourier transform) |
FFT4
|
( 1X , 'FFT3' , 4X ,
5I8 ) Nx , Ny , Nz , W , H
Nx: number of grid points along X
in Fourier transform
Ny: number of grid points along Y
in Fourier transform
Nz: number of grid points along Z
in Fourier transform
W, H: width and height (in pixels)
of the resultant image (inverse Fourier transform) |
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* |
Contents
|
CONT
|
( 1X , 'CONT' , 4X , 6 ( A2 , I4 )
) ( S ( I ) , N ( I ) ) , I = 1 , 6
S ( I ): element symbol of the Ith
kind of atoms
N ( I ): number of the Ith
kind of atoms |
Condition
|
HREM
|
( 1X , 'HREM' , 5X , 3F10.3 ) V ,
Cs , D
V: accelerating voltage (in kilovolts)
Cs: spherical-aberration coefficient (in millimeters)
D: standard deviation of the Gaussian distribution
of defocus due to the chromatic aberration (in Angstroms) |
FOBS
|
( 1X , 'FOBS' , 5X , A80 ) File
File: Full path and file name of the file containing
observed structure-factor amplitudes |
DECO
|
( 1X , 'DECO' , 5X , F10.1 ) Defocus
Defocus: the defocus value in Angstroms used in
deconvolution operation |
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. |
HKL
|
CALC
|
( 1X , 'CALC' , 4X , 3I5 , A1 , 3F10.3
) h , k , l , Flag , F , phase , Fref
( 1X , 'CALC' , 4X , 4I5 , A1 , 3F10.3 ) h , k , l ,
m , Flag , F , phase , Fref
The first command is for conventional structures, while
the second is for incommensurate structures.
h , k , l or h , k , l , m: diffraction indices
of a reflection
Flag: the reflection will be void, if its 'Flag'
is not a space.
F: structure-factor amplitude
phase: structure-factor phase
Fref: reference value of the structure-factor amplitude |
FOBS
|
( 1X , 'CALC' , 4X , 3I5 , A1 , F10.3
, 10X, F10.3 ) h , k , l , Flag , F , Fref
( 1X , 'CALC' , 4X , 4I5 , A1 , F10.3 , 10X, F10.3 )
h , k , l , m , Flag , F , Fref
The first command is for conventional structures, while
the second is for incommensurate structures.
h , k , l or h , k , l , m: diffraction indices
of a reflection
Flag: the reflection will be void, if its 'Flag'
is not a space.
F: structure-factor amplitude
phase: structure-factor phase
Fref: reference value of the structure-factor amplitude |