Molecular Arrangement and Fringe Identification and Analysis from Molecular Dynamics (MAFIA-MD): A Tool for Analyzing the Molecular Structures Formed during Reactive Molecular Dynamics Simulation of Hydrocarbons

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Computer Physics Communications

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DOI: 10.1016/j.cpc.2022.108325


Reactive molecular dynamics (RMD) simulations are becoming popular, with the recent developments in high-performance and efficient computing architecture, for investigating fundamental physico-chemical behaviors of reacting species. Due to the complexity of hydrocarbon systems, characterization of molecules formed during RMD simulations of hydrocarbons can be very challenging for simulations involving a large number of molecules. The novel post-processing utility “MAFIA-MD” – an acronym for “Molecular Arrangement and Fringe Identification and Analysis from Molecular Dynamics” – presented in this manuscript can analyze and perform molecular characterization of a large number of RMD trajectory files (.XYZ files) simultaneously. The utility will be useful for analysis and chemical characterization of trajectories without the large bond information files. A graphical user interface (GUI) is developed for easy operation. The utility analyzes the existing cyclic structures in the domain and generates statistics of alicyclic and aromatic hydrocarbons based on the number of carbon atoms. Alongside the statistical analysis, the program also separates the constituent molecules and extracts their chemical information in terms of Simplified Molecular-Input Line-Entry System (SMILES) and Spatial Data File (.SDF)”. A methodology for calculating fringe spacing is also implemented in the code for validation of RMD simulation with High-Resolution Transmission Electron Microscopy (HRTEM) images.

Program summary

Program title: MAFIA-MD

CPC Library link to program files: https://doi.org/10.17632/s7dsk553fh.1

Developer's repository link: https://github.com/kmmukut/MAFIA-MD.git

Licensing provisions: MIT

Programming language: Python 3.7

Supplementary material: Bash script for splitting long continuous trajectory files with multiple timestep into trajectory files for individual timestep and some example input trajectory files for testing.

Nature of problem: Reactive molecular dynamics (RMD) simulations of hydrocarbons allow chemical reactions between different hydrocarbon molecules through bond breaking and new bond formation. The information about the chemical changes is stored in the bond information files and trajectory of individual atoms are stored in trajectory files. While the bond files can become very large for large simulations, trajectory files remain quite small. MAFIA-MD will be useful for practitioners interested in analyzing the chemical structures of emerging molecular clusters from small individual trajectory files without requiring the large, memory-intensive bond information files. Identification of chemical characteristics, particularly aromatic and alicyclic ring structures and molecular fringes, are important for gaining insights from RMD simulations of hydrocarbons, especially in exploration of soot formation during combustion. The capability of isolating the cyclic and non-cyclic molecules from trajectory files is the novel part of MAFIA-MD.

Solution method: The coordinates of individual atoms are taken as the input for the program. The coordinates are then analyzed to create an adjacency matrix [1] based on the bond distance between carbon atoms. This adjacency matrix is then converted into a directed graph and the cyclic structures are extracted from the graph by implementing an efficient depth-first-search algorithm [2] developed by Johnson [3]. Apart from the ability to isolate cyclic and non-cyclic components by chemical structural analysis, a methodology to calculate fringe spacing is also implemented by calculating the distances between cyclic structures. The utility uses a Python interface for easy management of the input and output parameters. The detailed solution methodology has been discussed in the manuscript.

Additional comments including restrictions and unusual features: In the current version, the utility can analyze only carbon and hydrogen atoms. The future versions will implement the addition of other common atoms found in aromatic molecules, e.g. nitrogen, oxygen, sulfur, etc. MAFIA-MD can be run on Linux, macOS, and Windows operating systems.


Computer Physics Communications, Vol. 276 (July 2022): 108325. DOI.