This paper discusses the control challenges of a parallel evaporator organic Rankine cycle (ORC) waste heat recovery (WHR) system for a diesel engine. A nonlinear model predictive control (NMPC) is proposed to regulate the mixed working fluid outlet temperature of both evaporators, ensuring efficient and safe ORC system operation. The NMPC is designed using a reduced order control model of the moving boundary heat exchanger system. In the NMPC formulation, the temperature difference between evaporator outlets is penalized so that the mixed temperature can be controlled smoothly without exceeding maximum or minimum working fluid temperature limits in either evaporator. The NMPC performance is demonstrated in simulation over an experimentally validated, high fidelity, physics based ORC plant model. NMPC performance is further validated through comparison with a classical PID control for selected high load and low load engine operating conditions. Compared to PID control, NMPC provides significantly improved performance in terms of control response time, overshoot, and temperature regulation.

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