Strategies for non-uniform sampling of molecular dynamics phase space trajectories of relaxation phenomena
Non-uniform phase space trajectory sampling schedules were developed for time-domain analysis of molecular dynamics simulations of transient processes to reduce the data storage costs to record the trajectory for post-processing and permanent archival. Sampling periods are defined as functions of time such that the spacing between sampled points is either exactly or approximately constant in the logarithmic-time domain. A non-uniform sampling schedule was applied to uniformly sampled time histories of translational kinetic energy for translationally excited molecules in a crystal. Direct comparison of the non-uniformly sampled time history to the uniform one reveals that the non-uniform time history accurately captures the relaxation process with a 93% reduction in data storage cost for the conditions studied. Implications for frequency-domain analysis are discussed. A sampling schedule for simulations of supported shock waves is presented that provides an approximate 60% reduction in data storage cost.
non-uniform sampling molecular dynamics relaxation phenomena shock waves time-series analysis particle methods