Strategies for non-uniform sampling of molecular dynamics phase space trajectories of relaxation phenomena

MP Kroonblawd and TD Sewell, COMPUTER PHYSICS COMMUNICATIONS, 196, 143-148 (2015).

DOI: 10.1016/j.cpc.2015.05.026

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. (C) 2015 Elsevier B.V. All rights reserved.

Return to Publications page