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A neural network consists of many neurons connected by synapses. It is able to process information and generate a specific pattern of electrical activity. To analyze its interior structure and exterior properties, one computer simulator was implemented. As the neural network is complicated and the simulation is time consuming, so data structure and computation scheme are critical to the simulation process. In this paper, the data structure is designed to be sharable and reusable, and parallel computation is applied to match the data structure. With the data structure and parallel computation, the simulation is made much more efficient and high performance was achieved.