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Alternative TitleReaction Analysis and Visualization of ReaxFF Molecular Dynamics Simulations
Thesis Advisor李晓霞
Degree Grantor中国科学院研究生院
Degree Discipline化学工程
Keyword反应分子动力学   varxmd   化学反应分析与可视化   化学反应机理   化学信息学   化学结构处理
Abstract反应分子动力学(ReaxFF MD)是一种可以研究大体系(>1000个原子)复杂化学反应极具前景的方法。但是国际上现有的ReaxFF MD模拟结果分析工具只能从模拟轨迹中获得以化学式表示的分子片段随着时间变化的规律,缺乏直接获取模拟过程中发生的化学反应信息,从而限制了其在探索过程反应机理中应有的作用。本论文的主要目标是建立反应分子动力学分析与可视化工具VARxMD(Visualization and Analysis of ReaxFF Molecular Dynamics),以实现对ReaxFF MD模拟轨迹的详细化学反应分析与可视化。本论文主要介绍建立VARxMD的核心功能——化学反应分析相关算法的实现策略、关键技术细节和在模拟过程中的应用。论文主要内容有: (1)建立了国际上首个对ReaxFF MD模拟结果的化学反应分析和可视化工具VARxMD。VARxMD分析化学反应的输入是ReaxFF MD模拟轨迹文件,包括原子的3D(Three-Dimensional,三维)坐标和键级信息(BO,Bond Order)。VARxMD借助化学信息学的化学结构处理方法,经过原子间连接性判断、连通分子片段判别、周期性边界条件坐标变换、键类型识别、物种全局索引表的创建和检索、化学反应识别等步骤实现ReaxFF MD模拟结果中完整化学反应的分析,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,使得对于所模拟的复杂体系的反应机理分析成为可能。 (2)VARxMD是基于C++/Qt/VTK和其它第三方库研发的跨平台图形用户界面程序。本论文介绍VARxMD中为支持ReaxFF MD模拟结果化学反应分析功能而设计的关键技术,包括化学反应中的反应物和生成物的分子片段可视化、工程树模型、分析工程的工程化管理、帧筛选器、帧序列化、数据缓存机制等技术。 (3)本论文还介绍了VARxMD的功能及其在复杂体系模拟(煤模型热解和聚乙烯热解)分析中的具体应用。VARxMD是第一个能对ReaxFF MD模拟结果进行反应分析和可视化的工具,且具有通用性,有望被应用于更多的体系。; ReaxFF MD(Reactive Force Field Molecular Dynamics)is a promising method for investigating complex chemical reactions in relatively larger scale molecular systems. The existing analysis tools for ReaxFF MD lack the capability of distinguishing isomers and capturing chemical reactions directly by analyzing the simulation trajectory, which is critical in exploring reaction mechanisms. This paper presents algorithms, implementation strategy, features, and applications of VARxMD, a new tool for Visualization and Analysis of ReaxFF Molecular Dynamics. VARxMD is dedicated to detailed chemical reaction analysis and visualization from the trajectories obtained in ReaxFF MD simulations. The interrelationships among the atoms, bonds, fragments, species and reactions are analyzed directly from the three-dimensional (3D) coordinates and bond orders of the atoms in a trajectory, which are accomplished by recognizing connected fragments, bond types, and reactions. Consequently, detailed chemical reactions taking place between two sampled frames can be generated automatically. VARxMD is OS-independent with well-tuned graphical user interfaces (GUI), which was implemented with C++/Qt/VTK and other third-party libraries by using a novel design and algorithms. To support the chemical reaction analyses and visualizations of ReaxFF MD, a number of technical strategies are developed in VARxMD, such as the visualization of the molecular fragments in chemical reactions, the project tree model, the management of analysis project, the frame filter, the serialization of analyzed results, cache mechanism. Applications of VARxMD in ReaxFF MD simulations of coal and HDPE (High-Density PolyEthylene) pyrolysis show that VARxMD provides great conveniences in mechanism exploration for large systems with complex chemical reactions involved which are difficult to access manually. To the best of our knowledge, VARxMD is the first tool specialized for reaction analysis and visualization in ReaxFF MD simulations, and wide application of this tool can surely be expected.
Document Type学位论文
Recommended Citation
GB/T 7714
刘健. 反应分子动力学模拟的化学分析与可视化研究[D]. 中国科学院研究生院,2014.
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