Techniques are provided for calibrating physical directed self-assembly (DSA) models. For example, an experimental DSA process is performed using a block copolymer (BCP) material and a DSA guiding pattern with a predefined defect formed as part of the DSA guiding pattern. A difference in size (e.g., shrinkage) is determined between a size of the predefined defect of the DSA guiding pattern and a remaining size of a morphological defect in the BCP material as assembled at a completion of the experimental DSA process. The difference in size is utilized as calibration data in a DSA simulation system to calibrate a simulated physical DSA model which defines a simulated DSA process that corresponds to the experimental DSA process. The simulated physical DSA model defines a simulated guiding pattern with a programmed defect, which corresponds to the DSA guiding pattern and the predefined defect.