Keywords in Structure-factor files

Keywords in
Structure-Factor Files

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 I^th kind of atoms
N ( I ): number of the I^th 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

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.
Cell	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 I^th kind of atoms N ( I ): number of the I^th 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
Symmetry	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