The simulated annealing algorithm was modified and realized on a home-made parallel super computer system THNPSC-1. The program was applied to the data analyses of two different physical domains: Convergent Beam Electron Diffraction and Auger Electron Spectroscopy. The good results obtained from these two domains indicated that the program is of high-performance and is applicable to various research regions. The source code is available free of charge from the authors.