Distributed implementation of the adaptive kinetic Monte Carlo method

摘要

The program EON2 is a distributed implementation of the adaptive kinetic Monte Carlo method for long time scale simulations of atomistic systems. The method is based on the transition state theory approach within the harmonic approximation and the key step is the identification of relevant saddle points on the potential energy rim surrounding the energy minimum corresponding to a state of the system. The saddle point searches are carried out in a distributed fashion starting with random initial displacements of the atoms in regions where atoms have less than optimal coordination. The main priorities of this implementation have been to (1) make the code transparent, (2) decouple the master and slaves, and (3) have a well defined interface to the energy and force evaluation. The computationally intensive parts are implemented in C++, whereas the less compute intensive server-side software is written in Python. The platform for distributed computing is BOINC. A simulation of the annealing of a twist and tilt grain boundary in a copper crystal is described as an example application.