Molecular Dynamics Problem Initialization and Statistics Collection for Arbitrary Geometries

Molecular dynamics (MD) simulations have been extensively used for analysis of thermophysical properties of a variety of nanoscale systems. The majority of MD codes are developed for a specific system or application type, and thus their use in a wide variety of systems is limited. In addition, these codes can contain a steep learning curve for new users. Therefore, we have developed the Molecular Dynamics in Arbitrary Geometries (MDAG) code package for the explicit purposes of adaptability and ease of use. We describe various standard programming techniques we employed to allow for these goals to be achieved. We also discuss the approaches used for problem initialization based on arbitrary zone placement, and for statistics collection based on the mapping of Cartesian grid-based results onto arbitrary zones. We finally provide example applications of this code on nanoscale thermophysical systems.