Molecular dynamics boundary condition rapid applying method based on geometric boundary operation

Abstract

The invention discloses a rapid molecular dynamics boundary condition applying method based on geometric boundary operation, which comprises the following steps of: extracting a geometric boundary of a molecular dynamics simulation model according to the molecular dynamics simulation model, finding out boundary particles through geometric boundary operation, and acquiring position information of each boundary particle in a boundary domain; each boundary particle is endowed with reasonable speed and acting force, so that the macroscopic physical quantity of the boundary particle is consistent with the microscopic state, and the complete molecular dynamics boundary condition is obtained. The invention provides a general scheme for quickly applying boundary conditions on a complex molecular dynamics system; smooth transition speed boundary conditions and stress boundary conditions and speed distribution and potential energy distribution of boundary particles are applied and are consistent with a local microdynamics state of a system, state fluctuation near the boundary is limited to a low level, the problem that tasks for applying the boundary conditions are heavy is solved, and meanwhile boundary oscillation is greatly reduced.

Description

technical field [0001] The invention relates to the technical field of molecular dynamics calculation and simulation, in particular to a method for rapidly applying molecular dynamics boundary conditions based on geometric boundary operations. Background technique [0002] With the development of computer technology and numerical simulation theory, molecular dynamics (Molecular Dynamics, MD) method has attracted more and more attention. Molecular dynamics is a numerical simulation method that obtains the phase trajectory of the system by numerically solving the mechanical motion equation of the molecular system, and counts the structural characteristics and properties of the system. It is widely used in the simulation of biological computing, microfluidics and micro-nano engineering problems. [0003] Molecular dynamics is a particle-based computational method, and the imposition of boundary conditions is a very difficult task. In traditional grid-based calculation methods...

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Problems solved by technology

[0008] The purpose of the present invention is to provide a method for quickly applying molecular dynamics boundary conditions based on geometric boundary operations, in order to solve the problem of heavy task of applying boundary conditions in the prior art

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