The use of either linear or nonlinear elastic theory in deriving methodolog
ies for atomistic simulations is shown to be based on two very different vi
ews of the interaction of the 'system' with the 'reservoir'. These views ma
y be related through the definition of a phenomenological relaxation time,
which describes how the reservoir responds to changes in stress of the syst
em. A general procedure for introducing a finite relaxation time of the res
ervoir into atomistic simulations is described, and numerical results are p
resented which demonstrate how the linear and nonlinear simulations can be
brought into agreement. A discussion of the underlying thermodynamic assump
tions is given, and the benefits of using Nose-Hoover chains in simulating
structural transformations are demonstrated.