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反应分子动力学(ReaxFF MD)是一种很有潜力研究较大体系(>1000个原子)复杂化学反应的方法。国际上现有的ReaxFF MD模拟结果分析工具无法让用户了解所模拟的过程中发生的化学反应细节,对于规模小或简单的反应体系进行人工分析还可以接受,但对于原子规模达到~1000-~10000的大体系模拟,反应分析功能的缺乏,将使研究者对反应机理的分析陷入困境。本文研发的反应分子动力学分析与可视化工具VARxMD(Visualization and Analysis of ReaxFF Molecular Dynamics),它是国际上第一个实现对ReaxFF MD模拟轨迹进行化学反应自动分析的工具。VARxMD是基于Qt/VTK和其它第三方库研发的跨平台图形用户界面程序,借助化学信息学的化学结构处理方法,对ReaxFF MD模拟结果轨迹中的原子、物种、成断键的分析,并结合数据可视化和分子片段结构可视化,实现对ReaxFF MD模拟结果的深度分析,可获得模拟过程中完整的化学反应信息。VARxMD已应用于煤热解和聚乙烯等复杂分子体系热解的化学反应机理探索,且VARxMD具有通用性,有望被应用于更多的体系。
Reactive molecular dynamics (ReaxFF MD) is a promising method for studying complex chemical reactions in larger systems (> 1000 atoms). The existing ReaxFF MD simulation result analysis tool in the world can not let users know the details of the chemical reactions that occur in the simulation process. It is acceptable for manual analysis of small or simple reaction systems. However, for the atomic scale up to ~1000 ~ 10000 system simulation, the lack of reaction analysis capabilities, will enable researchers to analyze the reaction mechanism in trouble. In this paper, the molecular dynamics analysis and visualization tool VARxMD (Visualization and Analysis of ReaxFF Molecular Dynamics), which is the first in the world to achieve ReaxFF MD simulation trajectory chemical reaction automatic analysis tool. VARxMD is a cross-platform graphical user interface program developed based on Qt / VTK and other third-party libraries. With chemical structure processing of chemical informatics, VARxMD analyzes and combines the atoms, species, and broken bonds in the trace of ReaxFF MD simulation results Data visualization and molecular fragment structure visualization allow for in-depth analysis of ReaxFF MD simulation results for complete chemical reaction information during simulation. VARxMD has been applied to the chemical reaction mechanism of pyrolysis of complex molecular systems such as coal pyrolysis and polyethylene, and the versatility of VARxMD is expected to be applied to more systems.