Surface identification, meshing and analysis during large molecular dynamics simulations

Abstract

Techniques are presented for the identification and analysis of surfaces and interfaces in atomistic simulations of solids. Atomistic and other particle-based simulations have no inherent notion of a surface, only atomic positions and interactions. The algorithms we develop here provide an unambiguous means to determine which atoms constitute the surface, and the list of surface atoms and a tessellation (meshing) of the surface are determined simultaneously. The tessellation is then used to calculate various surface integrals such as volume, area and shape (multiple moment). The principle of surface identification and tessellation is closely related to that used in the generation of the r-reduced surface, a step in the visualization of molecular surfaces used in biology. The algorithms have been implemented and demonstrated to run automatically (on the fly) in a large-scale parallel molecular dynamics (MD) code on a supercomputer. We demonstrate the validity of the method in three applications in which the surfaces and interfaces evolve: void surfaces in ductile fracture, the surface morphology due to significant plastic deformation of a nanoscale metal plate, and the interfaces (grain boundaries) and void surfaces in a nanoscale polycrystalline system undergoing ductile failure. The technique is found to be quite robust, even when the topology of the surfaces changes as in the case of void coalescence where two surfaces merge into one. It is found to add negligible computational overhead to an MD code.