We present a detailed error analysis of a Rydberg blockade mediated controlled-NOT quantum gate between two neutral atoms as demonstrated recently in Phys. Rev. Lett. 104, 010503 (2010) and Phys. Rev. A 82, 030306 (2010). Numerical solutions of a master equation for the gate dynamics, including all known sources of technical error, are shown to be in good agreement with experiments. The primary sources of gate error are identified and suggestions given for future improvements. We also present numerical simulations of quantum process tomography to find the intrinsic fidelity, neglecting technical errors, of a Rydberg blockade controlled phase gate. The gate fidelity is characterized using trace overlap and trace distance measures. We show that the trace distance is linearly sensitive to errors arising from the finite Rydberg blockade shift and introduce a modified pulse sequence which corrects the linear errors. Our analysis shows that the intrinsic gate error extracted from simulated quantum process tomography can be under 0.002 for specific states of $^{87}$Rb or Cs atoms. The relation between the process fidelity and the gate error probability used in calculations of fault tolerance thresholds is discussed.
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