A method of modeling a diesel engine that is capable of multiple combustion modes and equipped with a turbocharger and EGR loop. The model comprises a set of equations, each equation representing one of the following as a time derivative: pressure at the intake manifold, pressure between the turbine and an intake manifold throttle, pressure at the exhaust manifold, the compressor power, and the fresh air fraction (the ratio of fresh air to EGR). The model is used to determine what engine conditions (such as throttle positions and turbocharger output) will result in desired pressures and fresh air fraction.