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In this paper, we study the general spinless quadratic fermion Hamiltonian with interaction matrices given by the symmetric and antisymmetric parts of the adjacency matrix of a directed graph. The correlation matrix and entanglement entropy are provided for the ground state of the Hamiltonian, analytically. We also show that a volume law scaling holds for some scalable sets of nonsymmetric association-scheme graphs. The scaling of the entanglement entropy is then used as a tool for studying the graph isomorphism problem, in particular to distinguish some nonisomorphic pairs of directed strongly regular graphs.