Molecular enclosures appear broadly throughout many solid-state materials and biological systems alike, whether in nanoporous materials for energy storage or nanolipid particles for drug delivery.  Importantly, the constituent ions and molecules that may be confined within these enclosures can largely determine the properties and performance of the system.  It is critical to have a means of determining the density, relative concentration, arrangement, physical and electronic structure, viscosity, diffusivity, etc. of those constituents for two key reasons: a) the physics under such confinement can vary dramatically from bulk and remain poorly understood; and b) rational design of these enclosed systems is predicated on understanding how they are assembled. Current simulation methods fall short for accurately determining the density and structure of molecules packed inside small-scale enclosures, so there is a need for a new simulation method to address this technology gap.