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The microscopic model of the Si(001) crystal surface was investigated by first principles calculations to clarify the behavior of intrinsic point defects during crystal growth and thermal annealing. A c(4 × 2) structure model was used to describe the crystal surface in contact with vacuum. The calculations show that a vacancy in the first or second atomic layer has about a 2.0 eV lower formation energy than deeper inside the bulk and that there is a diffusion barrier to penetrate into the deeper crystal region. Furthermore, a vacancy in the first or second atomic layer is stabilized by the fact that Si atoms with dangling bonds attract each other due to ionic and/or covalent bonding. There is, however, no barrier for the diffusion of a vacancy from the first layer to the second one. The tetrahedral (T)-site and dumbbell (DB)-site, in which a Si atom is captured from the surface and forms a self-interstitial, are found as stable sites near the third atomic layer. The T-site has a barrier of 0.48 eV, whereas the DB-site has no barrier for the interstitial to penetrate into the crystal from the vacuum. Self-interstitials in both the T- and DB-sites in the third atomic layer have a 1.7 to 2.8 eV lower formation energy than deeper in the bulk and there is a diffusion barrier to penetrate into the deeper crystal region; 32 sites were found as stable sub-surface vacancy positions, whereas only 8 sites were found as stable self-interstitial positions. Using these results, a mechanism for the elimination of crystal-originated pits by thermal annealing is proposed. It is shown that the microscopic model is consistent with and allows to fine-tune existing macroscopic models that are used to calculate the intrinsic point defects behavior during crystal growth from a melt.