Research And Application Of NanoMD Molecular Dynamics Software Based On OpenGL

As an interdiscipline, nanotechnology has received great attention recently. Nanoscaled science and technology involve several classical disciplines, including physics, chemistry, material science, biology, electronics, mechanics and measurements. It is a product of close cooperation among those modern scientific subjects, such as chaos physics, quantum mechanics, mesoscopic physics, molecular biology and computer technology.NanoMD based on the theory of molecular dynamics is a widely used calculation software in the application of nano-technology. The software, which consists of background calculation and foreground interface display, is a set of self-developed simulation system. The simulation results of dynamic and real-time tracking simulation process can be shown in the interface by calling the background calculation procedure. The program optimizes modeling and simulation in view of the characteristics of nano-material and nano-manipulation. We can study the stability, deformation behavior of nano-material during mechanical process and crystal growth on the surface at atomic level. A series of specific analytical methods were developed, which were based on the periodic arranging characteristics of particles and combined with the Fourier transform theory in the signal processing subjects, These methods include crystalline structure observation, surface morphology analysis, bulk crystallographic analysis, local energy analysis and atomic coordination number analysis. It turns out to be a powerful tool for nano-technology research.NanoMD is a kind of special software for Ultra-large Scale Molecular Dynamics (ULMD) simulation, being developed by Prof. Jianwei Zhao's Group, School of Chemistry and Chemical Engineering, Nanjing University. Focusing on the special need of nanotechnology, an ultra-large scale and high-performance molecular dynamics (MD) simulation program together with a series of analysis tools is being implemented. NanoMD requires the OpenGL display technology, large scale parallel computing technique, special algorithms such as Cell-list and Verlet table. In order to improve the software performance and extent application in nanotechnology, the present thesis is focusing on the improvement of the OpenGL display, the real-time rotation of the simulated system, and the display of surface and defects based on the atomic coordination number. In addition, to achieve a deeper understanding of the atomic details of several nano-processes, I had realized of the new simulation function- mechanically controllable breaking junction (MCBJ). Furthermore, with the assistance of the improved display technique, I have systematically analyzed the strain rate and temperature dependences of the deformation behavior of the single-crystal copper nanowire. The surface atoms with higher energy have been considered to be responsible for the unique deformation process.The improvement and implementation of these algorithms and procedures lay a good foundation for the further development of NanoMD software.