I hope to include all bonds to a nucleus on the unit cell’s surface. With this aim, it seems I need two copies of the nucleus: on a boundary and on its periodic image. Can these be flagged, eg as images of the same nucleus? (For stoichometry, each counts as 1/2 a nucleus.)
Can an accordant crystal structure be correctly optimized?
Is there pertinent documentation?
It is true, an atom on the face is shared between two unit cells and thus counts 1/2. Note face here contributes to surface, because atoms on a ridge or an apex of the parallelepiped are count differently (1/4 and 1/8, respectively).
It is however not clear if your «periodic image» refers to what IUCr defines as asymmetric unit. Nor, what you mean by «optimizing a crystal structure». If you have access to the experimental diffraction data (often referred as *.hkl file because it stores the location of the diffraction peaks (h, k, l)-indices, observed scaled diffraction intensity I**2, and width of the diffraction peak \sigma(I)), you first establish a model to account for the observed diffraction pattern (known as structure solution) which eventually refined (e.g., by moving the atoms within the unit cell assigned). For one sample, there may be multiple models; statistical test values offer a guide to select one of them.
Speculation: In case you aim for conversion of a *.cif file into a *.mol/*.sdf file with a connectivity table for atoms within the same molecule, you might consider cod-tools by the Crystallography Open Database. (For Linux distributions related to Debian, there is a dedicated package to facilitate the installation.)
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