Parallel optimization method of large-scale molecular dynamics in nanofabrication
A molecular dynamics and nanofabrication technology, used in special data processing applications, instruments, electrical digital data processing, etc.
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[0022] The present invention will be described in detail below with reference to the accompanying drawings.
[0023] Theoretically, when calculating the interatomic force, the interaction between each atom and all other atoms in the system needs to be calculated; however, since the force between atoms decreases rapidly with distance, it is not necessary Computes the interactions of each atom with all other atoms in the system. The invention proposes a serial algorithm that reduces unnecessary calculation amount, and at the same time optimizes data storage, saves memory, and improves the efficiency of serial MD calculation. Through parallel computing, the scale of MD simulation can be greatly improved. The invention divides all the atoms in the system into three-dimensional small grids according to the physical positions of the atoms, and determines the range of interaction between the atoms according to the movement of the system atoms in the simulation process. In the grid ...
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