目前以分子動力學模擬薄膜沈積的研究非常廣泛，但仍然存在1)薄膜能量累積問題與2)總計算量過大或計算效能因粒子數不斷增加而下降之問題。為了解決薄膜能量累積所產生的誤差，在此乃提出三種創新溫度控制演算法來有效維持薄膜溫度，其分別為以精確性主導之KEC (Kinetic Energy Corrector)動能控制方法、運算效率主導之TLM (Thermal control Layer Marching)溫度控制調移演算法及兼具精確性與運算效率之TLMC (Thermal control Layer Marching algorithm with kinetic energy Corrector)整合方法，並提出在不同入射能量之下所適合之自由反應層厚度。而對於總計算過大之處理方法乃引進平行化技巧，其中最佳化之力切割與空間切割法乃分別應用於半導體雙鑲嵌製程與合金薄膜沈積製程中，這兩項應用課題在溫度控制上也一併採用TLM方法來進行加速模擬。
　　於雙鑲嵌製程中探討引洞幾何、入射動能與尺寸大小對於填充形貌的影響，並發現不同的上下引洞寬度比與入射動能會對上下引洞填充率造成不同之交互影響性，且透過導角的引入更明顯改善最終的填充結果；另外，以二維雙鑲嵌系統來討論尺寸效應，發現不同的尺寸大小乃直接反應出填充率與填充型態上的差異，本文預測大約銅導線線寬8nm為幾何效應的分界；其中透過三維模型的模擬後，更發現非對稱結構導致不同方向具有不同的填充行為，且各方向的填充阻礙將互相影響而嚴重放大，故以二維簡化模型來預測三維系統是不太準確的。
　　於合金薄膜中則探討沈積、加熱與退火等過程之結構特性，透過徑向分佈函數與聚集原子數的分析可以發現，合金隨著溫度的變化，薄膜內部會產生不同程度之聚集行為。最後，乃針對目前的平行化分子動力學模擬薄膜沈積課題提出未來展望與理論突破的方向。

Up to now, the research of the thin film deposition using molecular dynamics simulations is very comprehensive, but the queries of 1) thin film energy accumulation and 2) total amount of calculations is too large or particles increasing constantly caused in decay of computational efficiency still exist. In order to correct errors for thin film energy accumulation, we have proposed three kinds of innovative temperature control algorithms to effectively maintain the temperature of thin film. The kinetic energy corrector algorithm (KEC) is relative to accuracy, and the thermal control layer marching algorithm (TLM) is with respect to efficiency. Finally, the thermal control layer marching algorithm with kinetic energy corrector (TLMC) is combined that both accuracy and efficiency. Besides, we address the various suitable thickness of the free reaction layer under different incident energy. On the other hand, the parallel technique applied to treat the problem concerning with vast calculating amount is also introduced. Force Decomposition and Spatial Decomposition Algorithms are applied to dual damascene processing and alloy thin film deposition, respectively. Moreover, both them are adopted to control temperature and accelerate simulation by using TLM algorithm.
For dual damascene processing, the influence of filling morphology are explored under various conditions, such as via-geometry, incident energy and system size. Our significant results show that the different upper/lower via-radius ratio and incident energy caused in different interaction that influence on upper/lower coverage percentage. Furthermore, when beveled angles are introduced, the final filling coverage is obviously improved. In addition, the size effect with the two-dimensional dual damascene system is discussed and results have shown the difference both with the filling rate and filling type in different system size. Thereof, the width of the copper conductor in 8nm with a boundary of the effect of geometry has been predicted. Moreover, the asymmetrical structures caused in different directions with different filling behaviors by means of the simulation for three-dimensional model have also examined. Finally, we found the difference of filling hindering from every direction, indeed, it can affect each other and enlarge seriously, thus it is not very accuracy using simplify two-dimensional model to predict three-dimensional system.
For the thin film of alloy, the structure characteristics in deposition, heating and annealing processing are treated. Our most important result has shown the inner thin film produced various aggregation abilities that accompanied the temperature exchange of alloy through analysis of radial distribution function and aggregation atom. Eventually, we propose the direction of future perspective and theoretical breakthrough to insight into the subjects in relation to thin film deposition by using parallel molecular dynamics simulation.

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