The rapid development in nano-scale fabrication processes and techniques demands efficient CAD tools to facilitate the
design process at nano-scale. Numerous CAD systems are available for constructing molecular structures, atom by atom.
However, these tools are generally developed to assist quantum or molecular analyses and simulations for relatively
small clusters, which typically involve tens to hundreds of atoms for quantum simulations, and hundreds to thousands of
atoms for molecular dynamics simulations. They are not designed for larger structures at the device level, which usually
consist of hundreds of such clusters.
Conventional CAD tools manage the geometry of one device concisely via the boundary of the device, which is the
aggregated shape of the clusters. However, such boundary representations do not provide the association between the
boundary and its underlying atomic clusters. Establishing such association will allow modification of the clusters
thereby reflecting the device geometry in a coherent fashion. Accordingly, we can quickly switch between two different
levels of representation. As a result, one benefits from the concise shape representation at the device level, while
enabling the editing of molecular entities as well. In this paper, we propose a "skeleton" geometry mapping method to
establish the needed association for fast switching between different levels, and an assembly tree "level-of-detail"
architecture which allows to quickly locate and locally update design modifications.
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