Analysis And Visualization Of The Space-Temporal Properties For Reactive Molecular Dynamics Simulations

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 the unique capability for automated analysis of detailed chemical reactions 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 followingBased 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 exploring 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 analytical methods.The extended capabilities of VARxMD would be applicable in other complicated molecular systems like catalytic reactions and hot spot analysis in energetic materials for a profound understanding the reactions in a picked zone and the dynamic physical properties.