A method of determining an uncertainty in the position of a domain within a self-assembly block copolymer (BCP) feature. The method includes simulating a BCP feature, calculating a minimum energy position of a first domain within the simulated BCP feature, simulating the application of a potential that causes the position of the first domain to be displaced from the minimum energy position, simulating release of the potential back toward the minimum energy, recording a plurality of energies of the BCP feature during the release and recording at each of the plurality of energies a displacement of the first domain from the minimum energy position, calculating, from the recorded energies and recorded displacements, a probability distribution indicating a probability of the first domain being displaced from the minimum energy position, and, from the probability distribution, calculating an uncertainty in the position of the first domain within the BCP feature.