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A crystalline structure modeling methodology that is conventionally used to model crystalline matter down to the atomic level is instead used to determine spot placement for radiation treatment. The cross-sectional shape of a treatment target is specified; locations (peaks) in a density field inside the shape are determined using the crystalline structure model; locations of spots in the treatment target for spot scanning are determined, where the locations correspond to the locations (peaks) inside the shape determined using the crystalline structure model; and the locations of the spots are stored as candidates for potential inclusion in a radiation treatment plan.