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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. 

Key properties of two-dimensional (2D) layered materials are highly strain tunable, arising from bond modulation and associated reconfiguration of the energy bands around the Fermi level. Approaches to locally controlling and patterning strain have included both active and passive elastic deformation via sustained loading and templating with nanostructures. Here, by float-capturing ultrathin flakes of single-crystal 2H-MoS₂ on amorphous holey silicon nitride substrates, we find that highly symmetric, high-fidelity strain patterns are formed. The hexagonally arranged holes and surface topography combine to generate highly conformal flake-substrate coverage creating patterns that match optimal centroidal Voronoi tessellation in 2D Euclidean space. Using TEM imaging and diffraction, as well as AFM topographic mapping, we determine that the substrate-driven 3D geometry of the flakes over the holes consists of symmetric, out-of-plane bowl-like deformation of up to 35 nm, with in-plane, isotropic tensile strains of up to 1.8% (measured with both selected-area diffraction and AFM). Atomistic and image simulations accurately predict spontaneous formation of the strain patterns, with van der Waals forces and substrate topography as the input parameters. These results show that predictable patterns and 3D topography can be spontaneously induced in 2D materials captured on bare, holey substrates. The method also enables electron scattering studies of precisely aligned, substrate-free strained regions in transmission mode.