Abstract: Using the Majorana zero modes of one-dimensional systems as topological qubits has recently generated considerable interest, with experimental efforts progressing rapidly, necessitating increasingly intricate qubit encoding schemes and layouts. Moving from a sketch of a complex design to a physical layout is a daunting engineering challenge, as small details of the design can have large impacts on device operation. Here, we present a computational tool chain that simulates the physics of these devices from the CAD schematics used for fabrication. By systematically varying the designs, we perform high-throughput computations to probe vast swaths of design space. Our simulations take into account the physical effects of self-consistent screening and superconductivity, while also including the detailed geometric configurations and fringing fields that are critical to device performance. Finally, we show validation comparisons with recent experiments in nanowire systems.