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Self-assembled quantum dots (QDs) realized by Stranski-Krastanov growth mode often demonstrate polarized transitions in quantized electron (hole) states and non-degeneracy in the first excited state in various spectroscopic analyses. These observations confirm the presence of certain symmetry breaking/lowering mechanisms in these low dimensional QDs which cannot be represented accurately with continuum material representations. Atomistic calculations indeed reveal optical polarization anisotropy and non-degeneracy in the excited states due to underlying crystalline symmetry, atomistic long-range strain and piezoelectric fields. This work presents the use of the comprehensive atomistic simulation package NEMO 3D in the study of competing effects in realistically-sized pyramidal InAs/GaAs quantum dots.