ReaxFF MD反应分子体系时空性质分析与可视化

反应分子动力学(ReaxFF MD)模拟方法已成功应用于复杂反应过程，如热解、氧化、催化反应等的机理研究而备受关注。这类过程不仅化学反应复杂、且伴随物理结构的动态变化，模拟结果的分析极具挑战性。国际上首个ReaxFF MD化学反应分析及可视化工具VARxMD具有独特的分析功能，包括全局唯一化学反应列表的生成、反应位点的突出显示、物种的分类和统计、化学反应的分类、及特定反应物到特定生成物的反应网络构建等，在大规模模拟结果的分析上极具潜力。然而，当前VARxMD主要应用于大规模分子体系模拟结果的全局反应机理揭示，缺乏物理性质的时空演化分析功能和特定局部区域的反应追踪功能。本工作继承VARxMD原有的数据结构和ReaxFF MD模拟结果文件，进一步扩展了VARxMD全局的物理性质和局部区域的化学反应追踪与物理性质分析的能力，可为用户获得更加丰富的反应细节提供便利。本论文工作的主要成果包括： 基于ReaxFF MD模拟复杂过程的全局体系，扩展实现了基本物理性质的分析并完成了程序的嵌入。模拟体系的全局物理性质分析包括可表征模拟体系瞬时物理结构的径向分布函数、度量体系粒子自扩散行为的均方位移函数、体系的范德华和溶剂可及表面积、表面积对应的体积等；并最终运用Qwt框架实现物理性质演化趋势科学绘图。 基于VARxMD模拟盒子的子空间，扩展了3D局部区域的化学反应追踪和物理性质分析的功能。本论文利用VTK可视化流水线渲染3D局部区域，采用Qt的信号与槽机制实现界面交互，构建了模拟体系3D局部区域不同形状的选择和绘制方法，包括通过屏幕绘制矩形以光线投射方法识别分子的交互模式和通过绘制长方体、球体等以边界判断方法识别分子的几何模式，并实现了特定局部区域选定时刻下的向前（向后）化学反应追踪和物理性质分析。本论文实现的物理性质分析功能和体系3D局部区域反应追踪的功能已应用于复杂体系的化学反应分析。通过绘制并选择煤热解反应模拟中煤颗粒孔道之间的局部区域，追踪了该区域内化学反应的演化，揭示了煤颗粒间的孔道对煤热解过程的促进作用；通过输入半径和球心坐标选择了含能材料TNT共晶热分解体系的球体区域，利用RDF计算表征了TNT分解过程中富碳团簇形成过程中的瞬态结构。这些信息是实验或其它模拟结果分析软件难以获得的。 本论文在原有VARxMD功能和ReaxFF MD模拟结果文件的基础上，扩展了基本物理性质和特定局部区域反应追踪的分析能力，为研究复杂体系的时空特征提供了新的手段，有望进一步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等更多ReaxFF MD模拟复杂体系的反应分析中。;The applications of reactive molecular dynamics simulation (ReaxFF MD) in complex processes of pyrolysis, oxidation and catalysis have attracted wide attentions. The analysis of simulation result for these processes is challenging due to the involved complex chemical reactions coupled with the change of dynamic physical properties. As a leading tool for chemical reaction analysis and visualization of ReaxFF MD simulations, VARxMD provides unique capability for automated analysis of detailed chemical reaction and visualization of reaction sites from the ReaxFF MD trajectories. The functions of VARxMD include functional groups searching, substructure searching in reactants and products, reaction categorizing, and reaction network generating from the specified reactants to specified products. The current VARxMD program mainly focuses on analyzing global chemical reactions obtained from ReaxFF MD simulations, but the functions of analyzing space-temporal dynamic physical properties and tracking chemical reactions in a picked zone are still lacking. The thesis enhances the functions in VARxMD for dynamic physical propreties analysis and reaction list generation locally in the picked zone, which complements complex chemical reaction analysis in space-temporal evolution. The main results are summarized as following. Based on ReaxFF MD simulation trajectories, a new function of dynamic physical property analysis has been created and integrated to VARxMD. The physical properties include the radial distribution function of characterizing the instantaneous physical structure, the mean square displacement function of measuring the self-diffusion behaviours, the van der Waals surface area, the solvent accessible surface area and the corresponding volumes. In addition, the Qwt framework was used to display the evolution trends of physical properties. On the basis of original data structures in VARxMD, a strategy was proposed for tracking chemical reactions in a picked 3D zone, and further analyzing their physical properties. The 3D picked zone was rendered by using the visualization pipeline in VTK, and the interface interaction was implemented by using Qt signals and slot mechanisms. The method by combining the interactive and geometric mode to identify molecules was employed to select and draw the picked 3D local zone. Subsequently, the chemical reactions (forward or backward) with the identified molecules involved are tracked and their physical properties are analyzed based on the picked zone. The new features of physical property analysis and reaction tracking in a picked zone have been applied in the exploration the effects of pore sizes in coal pyrolysis simulation and dynamic structure of carbon-rich cluster in the thermolysis of an energetic material. The reaction comparison between the global area and locally picked zone indicates that the micropore play an important role during coal pyrolysis process. The C ~ C RDF analysis for the picked carbon-rich clusters produced from thermolysis process of the TNT crystal provides rich information in dynamic structure characterization. These analysis results can not be accessible by the state-of-the-art experimental techniques and other computational or analysis methods. The extended capabilities of VARxMD would be applicable in other complicated molecular systems like catalysis reactions and hot spot analysis in energetic materials for a profound understanding the chemical reactions a picked zone and dynamic physical properties.