ReaxFF MD模拟的物种和化学反应自动分类及可视化  

Automatic classification and visualization of species and reactions obtained from ReaxFF MD simulations

作　　者：韩君易[1,2] 李晓霞[1] 郭力[1] 郑默[1,2] 乔显杰[1] 刘晓龙[1,2] 高明杰[1,2] 张婷婷[1,2] 韩嵩[1,2] 

机构地区：[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,北京100049

出　　处：《计算机与应用化学》2015年第5期519-526,共8页Computers and Applied Chemistry

基　　金：国家自然科学基金资助项目(21373227;91434105;21073195;21103196);多相复杂系统国家重点实验室自由探索项目基金(MPCS-2012-A-05)

摘　　要：反应分子动力学(ReaxFF MD)是一种可模拟大规模反应分子体系(>1000原子)的方法,已获得大量应用。本文针对国际上现有的ReaxFF MD模拟平台缺乏从模拟结果中分析反应机理能力的现状,为国际上首个ReaxFF MD模拟结果化学反应分析及可视化工具VARxMD进一步扩展建立了模拟体系的物种自动分类和反应分类能力。本文阐述基于化学结构特征等多种分类规则对ReaxFF MD模拟体系中化学结构复杂、数量众多的物种和化学反应进行自动分类和可视化的策略和方法。通过建立一套灵活的分类规则构建机制,可帮助研究者自主定义和组合考察对象的特征,以建立满足多重目标的分类规则。实现了基于反应体系的物种组成、化学结构、性质等特征的物种自动分类;以此为基础,进一步实现了基于化学反应的组成物种、反应官能团等特征信息的化学反应自动分类方法。为考察ReaxFF MD反应体系的演变规律和具体的反应行为,将物种分类及反应分类所获的对象集合视作一个整体进行化学计量统计,实现了考察对象集合随时间变化趋势的图形化显示,以及指定原子、键、官能团、分子片段、物种的反应路径细节的2D和3D可视化观察。VARxMD独特的物种分类能力在利用ReaxFF MD模拟煤热解反应机理、揭示煤热解不同类别产物的演变趋势方面发挥了关键作用。ReaxFF molecular dynamics （ReaxFF MD） is widely applied to study large scale reactive molecular systems （〉1000 atoms）. This work further extends the analytical capability of VARxMD, the ftrst and only software in the world that is capable of catching detailed chemical reactions from the ReaxFF MD simulation trajectories. This paper introduces the strategy and applications for automatic classification and visualization of species and reactions based on chemical structure processing and other category rules in order to get enriched information on reaction mechanism from huge simulation trajectory data. A flexible mechanism has been created for VARxMD which helps in creating customized and combined classification rules for species and reaction categorization. With such approach, chemical composition, chemical structure and chemical properties can be employed to define rules for species classification. Chemical reactions can be classified by species composition, reactive functional groups. For investigating the evolution and detailed reactive behaviors of the entire reactive system simulated by ReaxFF MD, visualization modules including for data plotting modules and viewers for 2D and 3D chemical structure viewers of species and reactions have been implemented in VARxMD for the data sets obtained in automated classification of species and reactions. Applications of species category to ReaxFF MD simulation of coal pyrolysis in uncovering product evolution are introduced to demonstrate the new and unique capability of VARxMD.

关 键 词：反应分子动力学 VARxMD 反应分类 物种分类 化学反应机理 

分 类 号：TQ015.9[化学工程] TP391.9[自动化与计算机技术—计算机应用技术]