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RMD_Digging: A toolkit for pre_ and post_processing and analyzing the results of reactive molecular dynamics (ReaxFF) simulation
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Prof. Adri C.T. van Duin of Pennsylvania State University and Prof. William A. Goddard, III develop the reactive force field simulation (ReaxFF) to model the reactive events and dynamic behavior of various systems like polymer materials, fuel, energetic materials, catalytic systems, metal materials, etc. ReaxFF simulation is mainly supported by the open source Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), whose primary developers are at Sandia National Labs and Temple University. However, the pre and post processing as well as corresponding analysis are very hard for many beginners due to the lack of specialized knowledge. When I studied at Sichuan University for my doctorate in 2017 2020, I ever investigated the thermolysis of polymer materials by ReaxFF simulations. I also take advantage of this method to study the radiation effects of polymers now in the Institute of Nuclear Physics and Chemistry. I wrote some codes to process the raw data generated during simulations ever since 2019 based on MATLAB language. With the development of the codes, I gradually realize that I should devote myself to developing a toolkit, which is called RMD_Digging. RMD is the abbreviation of Reactive Molecular Dynamics. Digging denotes the main functions of the toolkit, which are to dig out information from a wealth of data for further analysis. The first version of RMD_Digging (V1.0) was finished in 2020.
RMD_Digging can be accessed on the code hoster of GitHub. Since then, I have also kept improving the functions of the toolkit by adding new functions, optimizing codes and debugging with the feedback from users, and this toolkit is updated to the second version (V2.0) in 2022. Now the toolkit is renamed RMD_Digging when I decided to apply for its copyright in China. This toolkit (RMD_Digging on the GitHub) is also an open--source toolkit for researchers, and it can be downloaded and distributed free of charge and rewritten to meet a special need. I will also stick to its development in the future. I hope this toolkit can prosper in this field and contribute to one’s study.
RMD_Digging is developed by the MATLAB language. It is aimed to provide pre-processing and post-processing tools for the reactive molecular dynamics (ReaxFF) simulations performed on the LAMMPS platform. Its functions involve formatting the reactive force field parameters, statistic anasysis of structures, trajectories and mechanisms and output of the visualization files. Besides, extra modelling by other softwares can be performed by preparing corresponding input files. The following softwares are used to realize these goals, including Materials studio, VMD and Gaussian. Let's make it more versatile, powerful and robust together!
(1)ReaxFF_Gen toolkit is used to generate standard file with ReaxFF force field parameters from literatures.
(2)loglammps toolkit is mainly used to extract and process data with statistic average method.
(3)species toolkit can process the simulation generated species files. It sorts out the formed products with time sequence and can further refine them by molecular weight, elements and so on. Moreover, the evolution of number-average molecular weight and weight-average molecular weight can be calculated.
(4)bonds_analysis toolkit can read and handle the bond order (BO) information, further mainly cope with the BO information with the following purpose: a)obtain the BO information of the specific molecule or fragment; b)give the chemical composition of all the molecules and fragments (molecular formula); c)rearrange molecular formula and trace the BO information of the interested species.
(5)lammpstrj2xyz_arc_pdb toolkit can output the *.xyz, *.arc and *.pdb file, which can be be used for visualization by virture of Materials studio and VMD software, both in the form of static image and dynamic trajectory.
(6)chemi_mechanism toolkit can export the products in specific trajectories and analysis the reaction path/channel. More desired functions like orientation analysis will be added in the furture.
(7)structure_analysis toolkit is aimed to analysis the complex molecular structure, such as benzene ring, phenolic hydroxylic group and other specific chemical bonds or groups. However, its function is incomplete. Much work will be carried out in the furture.
(1) Liu, Q.; Liu, S.; Lv, Y.; Hu, P.; Huang, Y.; Kong, M.; Li, G. Atomic-scale insight into the pyrolysis of polycarbonate by ReaxFF-based reactive molecular dynamics simulation. Fuel 2021, 287, 119484, DOI: https://doi.org/10.1016/j.fuel.2020.119484.
(2) Liu, Q.; Huang, W.; Liu, B.; Wang, P.-C.; Chen, H.-B. Gamma Radiation Chemistry of Polydimethylsiloxane Foam in Radiation-Thermal Environments: Experiments and Simulations. ACS Appl. Mat. Interfaces 2021, 13 (34), 41287-41302, DOI: https://doi.org/10.1021/acsami.1c10765.
(3) C. Li, Q. Liu, W. Gong, Z. Zhou, Z. Yao, X. Meng, Study on the atomic scale of thermal and thermo-oxidative degradation of polylactic acid via reactive molecular dynamics simulation, Thermochim. Acta 709 (2022) 179144.
(4) Liu, Q., RMD_Digging ToolKit, 2020, https://github.com/dadaoqiuzhi/RMD_Digging.
(5) Liu, Q.; Huang, W.; Chen, H. Paving the Way to Simulate and Understand the Radiochemical Damage of Porous Polymer Foam. ACS Materials Letters 2023, 2174-2188. DOI: 10.1021/acsmaterialslett.3c00307.