Collisions of isobar nuclei, those with the same mass number but different structure parameters, provide a new way to probe the initial condition of the heavy ion collisions. Using transport model simulation of 96Ru+96Ru and 96Zr+96Zr collisions at two energies sNN=0.2 TeV and 5.02 TeV, where 96Ru and 96Zr nuclei have significantly different deformations and radial profiles, we identify sources of eccentricities contributing independently to the final state harmonic flow vn. The efficacy for flow generation differs among these sources, and explains the modest energy dependence of the isobar ratios of vn. Additionally, a significant component of vn is found to be uncorrelated with the eccentricity, but is instead generated dynamically during system evoluation. Experimental measurement of these ratios at the LHC energy and comparison with RHIC energy can provide insight into the collision-energy dependence of the initial condition.