© 2014 IAEA. A multi-phase simulation that is a combination of classical simulation and hybrid simulation for energetic particles interacting with a magnetohydrodynamic (MHD) fluid is developed to simulate the nonlinear dynamics on the slowing down time scale of the energetic particles. The hybrid simulation code is extended with realistic beam deposition profile, collisions and losses, and is used for both the classical and hybrid phases. The code is run without MHD perturbations in the classical phase, while the interaction between the energetic particles and the MHD fluid is simulated in the hybrid phase. In a multi-phase simulation of DIII-D discharge #142111, the stored beam ion energy is saturated due to Alfvén eigenmodes (AE modes) at a level lower than in the classical simulation. After the stored fast ion energy is saturated, the hybrid simulation is run continuously. It is demonstrated that the fast ion spatial profile is significantly flattened due to the interaction with the multiple AE modes with amplitude v/vA∼ δB/B ∼ O(10-4). The dominant AE modes are toroidal Alfvén eigenmodes (TAE modes), which is consistent with the experimental observation at the simulated moment. The amplitude of the temperature fluctuations brought about by the TAE modes is of the order of 1% of the equilibrium temperature. This is also comparable with electron cyclotron emission measurements in the experiment.