EMIntegrateSTEM

Program: EMIntegrateSTEM

This is a utility program that takes the output of a STEM diffraction simulation program (such as EMDispFieldSTEM or EMAtomCoordSTEM) and integrates a selection of the diffracted intensities to form an image.

This program works in the same way as most other programs and uses a name list input file obtained as follows:

EMIntegrateSTEM -t

The resulting EMIntegrateSTEM.template should be renamed to EMIntegrateSTEM.nml and the parameter fields edited as necessary:

 &IntegrateSTEMNamelist
! DO NOT CHANGE THIS LINE
!------------------------
! IO Filenames
!------------------------
! Name of the file containing diffraction data
 inputfilename = 'undefined',
!------------------------
! Detector Parameters
!------------------------
! Size of detector pixels in nm
 pixsize = 9000,
! Inner diameter of the annular detector, if used [mm]
 id = 4,
! Outer diamater of the annular detector, if used [mm]
 od = 10,
! Camera length [cm]
 camlen = 3,
!------------------------
! Operating Parameters
!------------------------
! Operating mode
! 1 = single reflection, 2 = annular detector
! default is annular detector
 mode = 2,
! If using a single reflection integration, specify the reflection here
! Default is the through-beam 0,0,0
 ref = 0,0,0,
! Generate a CBED pattern, only works if mode = 2
 CBED = .False.,
/

There are several parameters to control the integration behavior of the program: the mode parameter controls if integration will be performed using a model of an annular detector, or if a single reflection will be integrated. If single reflection mode is desired, the reflection must be specified using the ref paramter.

There are detector parameters which can be changed to model a particular detector, such as the pixel size (pixsize), inner and outer diameters of an annular detector (id and od respectively), and the camera length (camlen). These parameters are only used if mode = 2, for an annular detector.

After the parameters in the namelist file have been set, call

EMIntegrateSTEM

with no flags to perform the integration. The resulting image will be saved in the directory where the program is called and named according to the mode: if mode = 1, the file name will be 'h k l.tif', where hkl is the reflection used for integration; if mode = 2, the file name will be 'id od camlen.tif', where id, od, and camlen are the respective parameters set in the namelist file.