Atomic Interferometer has two quantum unitary gates that must be realized for quantum sensing purposes from atomic gravimeter and atomic interferometer gyroscope. An optimal cost function which define the distance between two unitary operator is defines and based on it a pulse based stochastic gradient descent algorithm is derived for implementation of atomic mirror and atomic beam-splitter gates. By using numerical optimal control for those gate realization, we achieved to gate fidelity of 0.995 and 0.998 for mirror and beam-splitter gates, respectively. For this research, a two-level atomic clock transitions are employed.