TPMD toolkit: A toolkit for studying rate processes using molecular dynamics trajectories and performing temperature programmed molecular dynamics calculations

A set of basic components needed for the analysis of state-to-state transitions in molecular dynamics (MD) trajectories is provided in the form of a toolkit. The toolkit can be used to (a) determine long-lived states of the system, (b) identify mechanism for transition from one state to another by listing atoms that participate in the transition, and (c) calculate kinetic parameters associated with the rate process, e.g., rate constants and Arrhenius parameters. Additionally, the toolkit enables the study of rare kinetic events using the temperature programmed MD (TPMD) method. Results obtained with two prototype systems, namely, Ag trimer diffusion, and Li diffusion in LiFePO_4, are discussed to illustrate the application of the toolkit.