ABSTRACT
New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.
ABSTRACT
Hierarchical, self-assembled structures are ordered on multiple scales, and formed by objects comprised of even smaller elements. Such structures are widely reported for nanoparticles, macromolecules, and peptides, and even in entropy-driven hard particle assembly hierarchical colloidal crystals have been reported. Here we consider the hierarchical self-assembly of a cubic colloidal crystal from congruent hard cube derivatives, and investigate how various ways of slicing and dicing a cube can affect the ability of the pieces to entropically re-assemble the initial colloidal crystal formed from perfect cubes. We present design rules that support heuristics reported for different systems, and present evidence for a previously unreported cubatic phase from 2 : 1 rectangular prisms.
