The canonical ensemble via symplectic integrators using Nosé and Nosé-Poincaré chains.
Simulations that sample from the canonical ensemble can be generated by the addition of a single degree of freedom, provided that the system is ergodic, as described by Nosé with subsequent modifications by Hoover to allow sampling in real time. Nosé-Hoover dynamics is not ergodic for small or stiff systems and the addition of auxiliary thermostats is needed to overcome this deficiency. Nosé-Hoover dynamics, like its derivatives, does not have a Hamiltonian structure, precluding the use of symplectic integrators which are noted for their long term stability and structure preservation. As an alternative to Nosé-Hoover, the Hamiltonian Nosé-Poincaré method was proposed by Bond, Laird, and Leimkuhler [J. Comput. Phys. 151, 114 (1999)], but the straightforward addition of thermostatting chains does not sample from the canonical ensemble. In this paper a method is proposed whereby additional thermostats can be applied to a Hamiltonian system while retaining sampling from the canonical ensemble. This technique has been used to construct thermostatting chains for the Nosé and Nosé-Poincaré methods.
Leimkuhler
Benedict J
BJ
Centre for Mathematical Modelling, University of Leicester, Leicester LE1 7RH, United Kingdom.
Sweet
Christopher R
CR