370953 Polymatic: A General Simulated Polymerization Algorithm
Generating representative structures of amorphous polymers for simulations is a non-trivial task due to their disordered nature. This problem is exacerbated for (a) glassy polymers with bulky structures and slow dynamics, and (b) network polymers with complex connectivity. To this end, we have released an open-source code called Polymatic [1,2] for structure generation of amorphous polymers with a wide range of structures and connectivity. The code implements a general simulated polymerization algorithm, where bonds are formed between repeat units during molecular dynamics simulations according to a set of bonding criteria to construct well-relaxed polymeric structures. It requires only the description of the monomer repeat unit and definition of the bonding criteria, and works in conjunction with the LAMMPS package to perform energy minimization and molecular dynamics simulations.
Here, we will present the basic algorithm of Polymatic and its application to a variety of different examples, including glassy linear polymers, hypercrosslinked polymers, and thermally post-crosslinked copolymers. Definition of the structural connectivity between pairs of "reactive" atoms allows for the construction of copolymers and complex ladder backbones. In addition, networked structures can be built in a single stage, where bonds and crosslinks are formed simultaneously, or in two stages, where linear polymers are first made and then post-crosslinked, which allows different synthetic routes for network polymers to be mimicked. As such, use of the Polymatic algorithm provides not only a realistic model of amorphous polymers, but also a unique view into the evolution of the structure throughout the virtual synthesis.
 Abbott, L. J.; Hart, K. E.; Colina, C. M. Theor. Chem. Acc. 2013, 132, 1334.
 Abbott, L. J. Polymatic: A Simulated Polymerization Algorithm, 2013, https://nanohub.org/resources/17278.
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