1. A method of designing a guiding pattern opening in a layer on a substrate, the guiding pattern opening yielding a set of self-assembled domains at specified locations within the guiding pattern opening when the guided pattern opening is filled with a self-assembly material that undergoes directed self-assembly, the method comprising: (a) specifying a number and corresponding locations of self-assembled domains; (b) generating a mathematical description of an initial guiding pattern opening based on said specified number and locations of self-assembled domains and designating said initial guiding pattern opening as a current guiding pattern opening; (c) using a computer, computing a mathematical model to generate calculated numbers and calculated high-probability locations of self-assembled domains within said current guiding pattern opening, wherein said function represents the relative probability that said self-assembled domains will form at said specified locations within said current guiding pattern opening; (d) comparing the calculated number of high-probability locations of said mathematical model with said specified number of self-assembled domains and comparing the calculated locations of said high-probability locations with said specified locations of self-assembled domains; (e) adjusting the current guiding pattern opening based on said comparing of step (d); and (f) repeating steps (c) to (e) until both (i) said calculated number of self-assembled domains and said specified number of self-assembled domains is the same and (ii) said high-probability locations of self-assembled domains and said specified locations of self-assembled domains agree within a specified range.