As previously reported, doping is a key process in achieving high proton conductivities in PCFC oxide electrolytes. More specifically, doping with low-valence elements creates oxygen vacancies that maintain electrical neutrality, and these vacancies can subsequently be filled with hydroxy groups to introduce protons into the system. Previously, the relationship between the conductivity and the doping level has been studied experimentally. However, to understand the mechanism of proton conductivity from a microscopic viewpoint, atomistic simulations based on molecular dynamics are essential, and stable atomistic configurations are required to commence these simulations. At present, determination of the stable atomistic configurations of doped atoms and protons is a difficult and time-consuming task since the initial configurations of the doping atoms and protons can change depending on the size of the simulation cell and the number of doped atoms. In addition, relaxation calculations using the density functional theory (DFT) approach are required for each initial configuration, thereby rendering it impossible to perform relaxation calculations for all possible initial configurations and to find stable structures using such approaches.