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This paper considers the optimal control problem for realizing logical gates in a closed quantum system. The quantum state is governed by Schrodinger's equation, which we formulate as a time-dependent Hamiltonian system in terms of the real and imaginary parts of the state vector. The system is discretized with the Stormer-Verlet scheme, which is a symplectic partitioned Runge-Kutta method. Our main theoretical contribution is the derivation of a compatible time-discretization of the adjoint state equation, such that the gradient of the discrete objective function can be calculated exactly, at a computational cost of solving two Schrödinger systems, independently of the number of parameters in the control functions. A parameterization of the control functions based on B-splines with built-in carrier waves is also introduced. The carrier waves are used to specify the frequency spectra of the control functions, while the B-spline functions specify their envelope and phase. This approach allows the number of control parameters to be independent of, and significantly smaller than, the number of time steps for integrating Schrodinger's equation. We consider Hamiltonians that model the dynamics of a superconducting multi-level qudit and present numerical examples of how the proposed technique can be combined with the interior point L-BFGS algorithm from the IPOPT package for realizing quantum gates. In a set of test cases, the proposed algorithm is shown to compare favorably with QuTiP/pulse_optim and Grape-Tensorflow.