A method of manufacturing a semiconductor device (for a layout diagram stored on a non-transitory computer-readable medium) includes generating the layout diagram. The generating the layout diagram includes: placing standard functional cells to partially fill a logic area of the layout diagram according to at least one corresponding schematic design thereby leaving, as unfilled, a spare region in the logic area; selecting a first pitch for additional cells to be placed in the spare region, wherein use of the first pitch minimizes wasted space in the spare region; selecting standard not-yet-programmed (SNYP) spare cells, which are to become at least some of the additional cells, according to the first pitch; and placing the selected SNYP spare cells into the spare region of the layout diagram.