The Research Of Large-scale Molecular Dynamics System Based On Spatial-Decomposition Parallel Algorithm

Molecular dynamics(MD),a computer simulation method,can be used to study numerous molecular interaction in nanomaterial.MD method can provide more detailed information about the transformation of the nanomaterial at the microscopic scale.Nano MD is a simulation software developed by Professor Zhao of Nanjing University,which is based on molecular dynamic,and widely used in the nano-simulation field.Because of the special needs of nanotechnology with larger temporal-spatial scale,we have used spatial partitioning algorithm and MPI messaging scheme to realize the large-scale molecular dynamics parallel computation.Each distributed node has be attached exclusive memory,and the virtual process and Cartesian topology are used to improve the operating performance and expandability.The simulation results that the simulation of large-scale system has higher efficiency in spatial decomposition algorithm.However,for the computation of the same system,the proportion of communication increases,and the acceleration ratio gradually becomes flat with the increase of calculation cores.We combined the method of statistical physical chemistry and the concepts of big data in computer science to achieve concurrent operation of large-scale molecular molecular dynamics simulation.In this thesis,we have studied systematically the relationship among the initial structure,the initial deformation and the distribution of breaking positions by using molecular dynamics simulation.The main research content includes three aspects: the effect of the convex and concave microstructures on the initial deformation;statistical analysis of the breaking characteristics and the correlation with the initial microstructure;and,the influence of the initial structure like twin boundary,dislocation in silver nanowire on the deformation.1,The convex nanowire has the similar deformation behavior as the single crystal nanowire does.There is no obvious difference in the potential and stress-strain curves between the convex nanowire and the single nanowire.The stress distribution along the z-axis exhibits a decrease around the convex nanostructure,it cannot induce any initial dislocation and slip.On the country,the concave nanostructure process stress concentration,the structure here is unstable and induce dislocation easier.2,An occasional event which breaking position is located at the nanowire center has been focused.A series of initial configurations have been established corresponding to eight different stretching stages,the distributions of the breaking position and fracture strain have been detailed.For the configuration in the yielding region,the distribution feature is very similar with that of the single crystal nanowire in spite of some dislocations generated in the system.For the configuration in the early stage of the plastic deformation,most of thedistribution features remain,but obvious shift of the distribution wave appears.For the configuration in the middle stage of the plastic deformation,new distribution wave emerges close to the breaking position of the occasional sample,demonstrating that the occasional event changes to the probability event.For the configuration in the late stage of the plastic deformation,the original distribution vanishes,and a sharp distribution wave appears.3,Finally,The tensile behaviors of the silver nanowires with four typical initial structures along with the [111] direction have been investigated by using molecular dynamics simulation.The effects of initial structures like dislocation and twin boundary on the generation and propagation of the dislocations have been analyzed systematically,and the relationship between the initial structures and the distribution of the final breaking positions has been discussed.The research in this thesis not only provides reference for the design of nanodevice,the analysis method is also used to build foundation for the study of nanomaterials,the improvement of algorithm and program has laid a good foundation for the further promotion of Nano MD software.