We have been developing methods for explicating the dominant factors that determine the physical and chemical properties of materials and stacked structures used in human societies. Since the number of element atoms which consists of advanced materials has been increasing, and the crystallographic structure of the materials has become very complicated, both the various properties and reliability of the materials fluctuate significantly in nano-scale, and thus, deteriorate easily due to the local damages of the materials. To design the optimal structure, composition of materials, and the fabrication process of both materials and stacked structures, we are going to develop a method of analyzing the atomic structure of thin film materials based on quantum mechanics and experimental methods for measuring material properties, atomic scale damage or defects in nano-materials.