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This paper presents structure thermal mechanics analysis of spindle disk assembly used in spinning magnetic data storage hard disk drives (HDDs). With the view toward understanding the underlying physics and to minimize the corresponding repeatable run-out (RRO) of track following position error signal (PES) in high track per inch (TPI) magnetic disk drives, analytical representation of thermal expansion mismatch between disk and spindle hub structure formulated in form of operators and finite element analyses (FEA) are employed in this paper. Parameter studies with analyses taken at different operational temperatures suggest that RRO can be minimized significantly when location of spindle notch, which is can be the internal feature used to position bearings to the hub structure, is properly located. RRO harmonics resulted from the thermal expansion mismatch and structure misalignments having ramping characteristics from disk outer diameter to inner diameter are studied and concluded with simple algebraic expression related to number of fasteners used in disk-spindle assembly.