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

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.