In this paper, we propose a heat jet approach for atomic simulations at finite temperature. Thermal fluctuations are injected into an atomic subsystem from its boundaries, without modifying the governing equations for the interior domain. More precisely, we design a two way local boundary condition, and take the incoming part of a phonon representation for thermal fluctuation input. In this way, non-thermal wave propagation simulations are effectively performed at finite temperature. We further apply this approach to nonlinear chains with the Morse potential. Chains with model parameters fitted to carbon and gold are simulated at room temperature with fidelity.