Measure-preserving and time-reversible integration algorithms for constant temperature molecular dynamics.

• Main Author: Obaga, Emmanuel Omboga.
• Other Authors: Sergi, Alessandro.
• Language: en
• Published: 2013
• Subjects: Molecular dynamics.; Mathematical physics.; Physics > Computer simulation.; Theses > Physics.
• Online Access: http://hdl.handle.net/10413/8896

This thesis concerns the formulation of integration algorithms for non-Hamiltonian molecular dynamics simulation at constant temperature. In particular, the constant temperature dynamics of the Nosé-Hoover, Nosé-Hoover chain, and Bulgac-Kusnezov thermostats are studied. In all cases, the equilibrium statistical mechanics and the integration algorithms have been formulated using non-Hamiltonian brackets in phase space. A systematic approach has been followed in deriving numerically stable and efficient algorithms. Starting from a set of equations of motion, time-reversible algorithms have been formulated through the time-symmetric Trotter factorization of the Liouville propagator. Such a time-symmetric factorization can be combined with the underlying non- Hamiltonian bracket-structure of the Liouville operator, preserving the measure of phase space. In this latter case, algorithms that are both time-reversible and measure-preserving can be obtained. Constant temperature simulations of low-dimensional harmonic systems have been performed in order to illustrate the accuracy and the efficiency of the algorithms presented in this thesis. === Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.