物理化学学报

最新录用 上一篇    下一篇

ReaxFF MD局部区域反应追踪与物理性质可视化分析

唐钰杰1,2,3, 郑默1,3, 任春醒1,2,3, 李晓霞1,2,3, 郭力1,2,3   

  1. 1 中国科学院过程工程研究所多相复杂系统国家重点实验室, 北京 100190;
    2 中国科学院大学化学工程学院, 北京 100049;
    3 中国科学院绿色制造创新研究院, 北京 100190
  • 收稿日期:2020-03-16 修回日期:2020-04-07 录用日期:2020-04-10 发布日期:2020-04-14
  • 通讯作者: 李晓霞 E-mail:xxia@ipe.ac.cn
  • 基金资助:
    国家重点研发计划(2016YFB0600302)、国家自然科学基金委重大计划项目(91641102,91434105)及面上项目(21606231)资助项目

Visualized Reaction Tracking and Physical Property Analysis for a Picked 3D Area in a Reactive Molecular Dynamics Simulation System

Yujie Tang1,2,3, Mo Zheng1,3, Chunxing Ren1,2,3, Xiaoxia Li1,2,3, Li Guo1,2,3   

  1. 1 State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China;
    2 School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
    3 Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, P. R. China
  • Received:2020-03-16 Revised:2020-04-07 Accepted:2020-04-10 Published:2020-04-14
  • Supported by:
    This work was supported by the National Key Research and Development Plan of China (2016YFB0600302) and National Natural Science Foundation of China (91641102, 91434105, 21606231).

摘要: 基于ReaxFF反应力场的反应分子动力学(ReaxFF MD)模拟方法已应用于复杂反应过程如热解、氧化、催化反应等反应机理的研究而备受关注。这类过程不仅化学反应复杂、且伴随物理过程的变化,其模拟结果分析具有挑战性。国际上首个ReaxFF MD化学反应分析及可视化工具VARxMD可在自动分析化学反应位点的基础上获得完整反应列表、反应物和生成物的动态演化、指定反应物与生成物之间的反应网络等多层次化学反应信息,并进行基于2D和3D化学结构的可视化。因VARxMD主要针对完整模拟体系进行全局化学反应信息的挖掘,缺乏针对模拟体系中指定3D局部区域内的化学反应进行追踪和物理性质分析的能力。本工作基于VARxMD对全局化学反应的分析结果和可视化方法,通过动态继承VARxMD的全局反应分析结果,从VARxMD全局反应3D可视化视图入手进行扩展,将VTK可视化框架的观察者模式与命令模式相结合,建立了模拟体系3D局部区域的选择和绘制方法,实现了3D局部区域内化学反应追踪和瞬态结构特性的分析。从模拟体系全局分析到3D局部区域分析能力的扩展已应用于煤热解反应模拟中煤颗粒孔道间的反应追踪以及含能材料热分解过程中富碳团簇形成过程中的瞬态结构表征,也有望应用于催化反应体系表界面反应分析、含能材料爆轰过程中反应热点分析,以及煤、生物质、高分子、碳氢燃料、含能材料等体系的热解与氧化反应的ReaxFF MD模拟。

关键词: ReaxFF MD, 区域反应追踪, 物理性质, 可视化

Abstract: Recently, the application of ReaxFF based reactive molecular dynamics simulation (ReaxFF MD) in complex processes of pyrolysis, oxidation and catalysis has attracted considerable attention. The analysis of the simulation results of these processes is challenging owing to the complex chemical reactions involved, coupled with their dynamic physical properties. VARxMD is a leading tool for the chemical reaction analysis and visualization of ReaxFF MD simulations, which allows the automated analysis of reaction sites to get overall reaction lists, evolution trends of reactants and products, and reaction networks of specified reactants and products. The visualization of the reaction details and dynamic evolution profiles are readily available for each reactant and product. Additionally, the detailed reaction sites of bond breaking and formation are available in 2D chemical structure diagrams and 3D structure views; for specified reactions, they are categorized on the basis of the chemical structures of the bonding sites or function groups in the reacting species. However, the current VARxMD code mainly focuses on global chemical reaction information in the simulation system of the ReaxFF MD, and is incapable of locally tracking the chemical reaction and physical properties in a 3D picked zone. This work extends the VARxMD from global analysis to a focused 3D zone picked interactively from the 3D visualization modules of VARxMD, as well as physical property analysis to complement reaction analysis. The analysis of reactions and physical properties can be implemented in three steps:picking and drawing a 3D zone, identifying molecules in the picked zone, and analyzing the reactions and physical properties of the picked molecules. A 3D zone can be picked by specifying the geometric parameters or drawing on a screen using a mouse. The picking of a cuboid or sphere was implemented using the VTK 3D view libraries by specifying geometric parameters. The interactive 3D zone picking was implemented using a combination of observer and command patterns in the VTK visualization paradigm. The chemical reaction tracking and dynamic radial distribution function (RDF) of the 3D picked zone was efficiently implemented by inheriting data obtained from the global analysis of VARxMD. The reaction tracking between coal particles in coal pyrolysis simulation and dynamic structure characterization of carbon rich cluster formation in the thermal decomposition of an energetic material are presented as application examples. The obtained detailed reactions between the coal particles and comparison of the reaction between the locally and globally picked areas in the cuboid are helpful in understanding the role of micro pores in coal particles. The carbon to carbon RDF analysis and comparison of the spherical region picked for the layered molecular clusters in the pyrolysis system of the TNT crystal model with the standard RDF of the 5-layer graphene demonstrate the extended VARxMD as a chemical structure characteristic tool for detecting the dynamic formation profile of carbon rich clusters in the pyrolysis of TNT. The extended capability of VARxMD for a 3D picked zone of a ReaxFF MD simulation system can be useful for interfacial reaction analysis in a catalysis system, hot spot formation analysis in the detonation of energetic material systems, and particularly the pyrolysis or oxidation processes of coal, biomass, polymers, hydrocarbon fuels, and energetic materials.

Key words: ReaxFF MD, Regional reaction tracking, Physical property, Visualization

MSC2000: 

  • O643