The Atomistic-to-Continuum (AtC) package ex-tends a classical molecular dynamics code, pairing atomic-scale simulation with the Finite Element Method (FEM) to model the effects of molecular behavior at a larger scale. Currently, the AtC pack-age supports neither parallel computation nor the desired methodological flexibility. We will profile and optimize AtC, then extend its functionality to include parallelization of computation, more complex element geometries including tetrahedra, and support for higher-order shape functions in the FEM.