Aspherical particle models for molecular dynamics simulation
TD Nguyen and SJ Plimpton, COMPUTER PHYSICS COMMUNICATIONS, 243, 12-24 (2019).
In traditional molecular dynamics (MD) simulations, atoms and coarse- grained particles are modeled as point masses interacting via isotropic potentials. For studies where particle shape plays a vital role, more complex models are required. In this paper we describe a spectrum of approaches for modeling aspherical particles, all of which are now available (some recently) as options within the LAMMPS MD package. Broadly these include two classes of models. In the first, individual particles are aspherical, either via a pairwise anisotropic potential which implicitly assigns a simple geometric shape to each particle, or in a more general way where particles store internal state which can explicitly define a complex geometric shape. In the second class of models, individual particles are simple points or spheres, but rigid body constraints are used to create composite aspherical particles in a variety of complex shapes. We discuss parallel algorithms and associated data structures for both kinds of models, which enable dynamics simulations of aspherical particle systems across a wide range of length and time scales. We also highlight parallel performance and scalability and give a few illustrative examples of aspherical models in different contexts. (C) 2019 Elsevier B.V. All rights reserved.
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