Abstract
Polymeric materials modelling has the potential to rapidly accelerate the discovery of new materials due to the comparative ease of simulations compared to laboratory testing campaigns. High quality molecular dynamics simulation software, such as LAMMPS, are able to facilitate the transition from empirical to digitised chemistry. However, in order to fully benefit from the speed of simulations, tools need to be developed to automate the preprocessing stages required for modelling. AutoMapper is an open-source Python application that automates the generation of files required to use REACTER, a powerful polymer bonding package implemented within LAMMPS. To automate this process, the authors developed an iterative path search algorithm based on chemical graph theory to accurately map pre- and post-reaction polymerisation structures, and hence eliminating the bulk of the human effort previously required to run a simulation. AutoMapper requires minimal user input, is force field independent, and has shown marvellous performance on a wide range of polymerisation types.