Parallelization of a Dissipative Particle Dynamics Application in a Partitioned Global Address Space Environment
Karthik Raj Saanthalingam · OhioLink ETD Center (Ohio Library and Information Network) · 2012
Molecular dynamics simulation provides the methodology for detailed microscopic modeling on the molecular scale.The nature of matter is to be found in the structure and motion of its constituent building blocks, and the dynamics is contained in the solution to the N-body problem.Given that the classical N-body problem lacks a general analytical solution, the only path open is the numerical one.Scientists engaged in studying matter at this level require computational tools to allow them to follow the movement of individual molecules and it is this need that the molecular dynamics approach aims to fulfill.The Molecular Dynamics method follows a constructive approach by trying to reproduce the microscopic behavior of matter using model systems rather than deduce the behavior directly from experiment.Dissipative particle dynamics (DPD) is a stochastic simulation method for soft materials and has been applied to a variety of simulations.Doubts about its adequacy due to upper coarse-graining limitations, which could prevent the method from being applicable to the whole mesoscopic range has led to the proposal for a modified coarse-grained level tunable DPD method that demonstrates its performance for linear polymeric systems.The proposed method models the system through the interaction between the particles as a result of interparticle forces.The calculation region size is non-trivial and can vary depending on the simulation strategy adopted and hence greatly affects the performance of the application.Simulations of very large systems, approaching a cubic micron for milliseconds, are