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This study focuses on investigating spatial variation of ground motion that has great influence on the dynamic behavior of the large structures located on the surface topography. One of the most effective parameters on the spatial variation of ground motion is the difference between the arrival time of seismic waves in different points located on the abutments. In this research, a three-dimensional model of the Pacoima Dam site is prepared. The time domain 3D boundary element method is used to apply non-uniform excitation at the dam supports. This model is subjected to vertically propagating incident SH and P waves. The time delay can be characterized by calculating the value of the time delay for which the cross-correlation between two records is maximized. Finally, to obtain the time delay in a topographic site, a function considering effective parameters such as the height from the canyon base, wave velocity and predominant frequency, is presented. Furthermore, a code was developed for generating the spatially variation of seismic ground motions. The results show that the proposed functions have an acceptable accuracy in estimating the time delay to generate non-uniform ground motion.