The program MSA calculates the diffraction of fast electrons in an atomic structure with the multislice algorithm. The results can be complex-valued wave functions, STEM images, CBED patterns, or probe intensity distributions.
MSA writes its output to disk in raw binary form as arrays of 32-bit floating point values in case of image intensities and 64-bit complex values in case of wave functions. By using the flag
/3dout, the output for multiple sample thicknesses will be stored together in one file for each detector or other output channel.
In cases where many files are saved, the output file name is extended by an additional suffix. The relation to a certain detector is indicated by a suffix equal to the detector name given in the detector parameter file. The relation to the sample thickness selected for output is indicated by the suffix
### is a slice index in the propagation sequence through the sample. Random frozen-phonon configurations are numbered according to the sequence of calculation and indicated by a suffix
STEM image simulations can be done for a series of sample thicknesses and different detectors in one run. Separate files are created for each detector and for each selected output sample thickness (thickness series). In a second run the raw scan images may be convoluted by an effective finite geometrical source size. Due to the fact that MSA applies different frozen-phonon configurations for each STEM pixel, the source size convolution provides also an efficient way of averaging over lattice configurations, leading to good approximations of thermal diffuse scattering.