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Active layer nanomorphology is a major factor that determines the efficiency of bulk heterojunction polymer solar cells (PSCs). Synthesizing diblock copolymers in which acceptor and donor materials are the constituent blocks is the most recent method to control the structure of the active layer. In the current work, a computational method is proposed to predict the nanomorphology of the active layer consisting of a diblock copolymer. Diblock copolymers have a tendency to self-organize and form well-defined nanostructures. The shape of the structure depends on the Flory-Huggins interaction parameter (i.e., χ), the total degree of polymerization (N) and volume fractions of the constituent blocks (φi). In this work, molecular dynamics (MD) simulations were used to calculate χ parameters for two different block copolymers used in PSCs: P3HT-b-poly(S8A2)-C60 and P3HT-b-poly(n-butyl acrylate-stat-acrylate perylene) also known as P3HT-b-PPerAcr. Such calculations indicated strong segregation of blocks into cylindrical structure for P3HT-b-poly(S8A2)-C60 and intermediate segregation into cylindrical structure for P3HT-b-PPerAcr. Experimental results of P3HT-b-poly(S8A2)-C60 and P3HT-b-PTP4AP, a diblock copolymer having very similar structure to P3HT-b-PPerAcr, validate our predictions.