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研究生:林弘凡
研究生(外文):Hong-Fan Lin
論文名稱:應用分子動力學與平行運算於奈米流場分析之研究
論文名稱(外文):The Study of the Appliction
指導教授:張榮語張榮語引用關係
指導教授(外文):Rong-Yen Chang
學位類別:碩士
校院名稱:國立清華大學
系所名稱:化學工程學系
學門:工程學門
學類:化學工程學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:中文
論文頁數:201
中文關鍵詞:分子動力學模擬奈米尺度流動平行運算個人電腦叢集
外文關鍵詞:Molecular dynamicsNanoscale FlowParallel computingPC-Cluster
相關次數:
  • 被引用被引用:8
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  • 下載下載:31
  • 收藏至我的研究室書目清單書目收藏:0
應用分子動力學(MD)搭配平行運算技術,於個人電腦叢集系統進行奈米尺寸之收縮膨脹流場分析,探討不同鏈長之無支鏈烷類分子於流場之基本性值,包括流速分佈、壓力分佈、應力張量以及分子鏈結構性值等。
於固定驅動力下,分別使用不同鏈長的無支鏈分子為基本流體,探討分子鏈鏈長對穩態流動行為之影響;研究結果顯示,奈米系統中流場密度分佈變化相當明顯,尤其在高壓或牆壁分子表面,與連續流場假設的不可壓縮流體有很顯著的差異;除此之外,黏度性質也有明顯的改變,因而使得收縮膨脹流場之速度分佈相當特殊;也因使用無粗糙度的牆壁表面,滑動現象於本系統中相當嚴重。
於相同驅動力下,因鏈長增加導致系統流速變慢,使得流場內系統的壓力與正向應力隨著鏈長下降,但剪切應力則因分子間糾纏、拉伸等作用增加,而有上升的趨勢;分子鏈行為的排向性質也受到流場變化影響,在收縮管處有較大的排向性,且於膨脹管中央因流速過慢,使得多數分子鏈排向幾乎垂直於流場方向,但也因牆壁分子採用強吸附力的金原子分子,使得在牆壁表面有特殊的吸附現象。
平行計算效率會隨著MD計算量多寡而改變,當計算量太小時則無法發揮其效能;而本研究所採用混合原子分散法與力分散法,於少量的平行電腦個數時,有高達九成以上的平行運算效率。
By the use of molecular dynamics and parallel algorithm on PC-cluster, we report a series of properties including velocity distribution, pressure distribution, stress tensor and molecular structure at equilibrium state for nano-scale contraction-expansion flow with different chain length.
There are some interesting effects on chain length of contraction-expansion flow under the same driving force. With the increasing chain length, the density of local system gets more uniform. This is great different form the assumption that the density of fluid is incompressive. For the roughness of wall and the viscosity of fluid, the velocity profile is very special.
Under the same driving force, the flow velocity and shear stress decreases with the chain length while the pressure and normal stress increases with the chain length. The end-to-end distance and orientation factor is large at the contraction flow. Because of the strong attraction of the wall, there is large end-to-end distance and orientation factor in the surface of wall at the expansion flow.
The parallel efficiency changes with the computing data. For small computing data, the parallel method has lower efficiency. We have used the parallel algorithm coupling atomic decomposition and force decomposition parallel method successfully to simulate molecular dynamcis. With the lower number of parallel computer, the efficiency gets much better.
中文摘要 I
Abstract II
目錄 III
圖目錄 VI
表目錄 XII
符號說明 XIII
第一章、緒論 1
1.1研究目的與動機 1
1.2微流體引論 4
1.2.1微流體與巨觀之差異 4
1.2.2微流體之應用 6
1.3分子動力學引論 9
1.4平行運算機制與平台 13
1.4.1平行電腦基本介紹 13
1.4.2個人電腦叢集之發展 16
1.4.3平行程式編輯設計 20
第二章、文獻回顧 23
2.1分子動力學文獻回顧 23
2.1.1分子動力學發展史 23
2.1.2分子動力學模擬流動行為文獻回顧 24
2.2平行分子動力學文獻回顧 35
2.2.1力分散方法於平行分子動力學之文獻回顧 36
2.2.2空間分散方法於平行分子動力學之文獻回顧 39
2.2.3平行分子動力學應用之文獻回顧 40
第三章、研究方法 43
3.1分子動力學理論 43
3.1.1分子動力學基本假設 43
3.1.2分子動力學模擬流程架構 44
3.1.3分子動力學系統初始化 46
3.1.4分子動力學系統控制 49
3.1.5分子動力學求解運動方程式 63
3.1.6分子動力學簡化方法 67
3.1.7分子動力學性質計算 74
3.1.8減縮單位 79
3.2分子勢能模型 80
3.2.1簡單分子勢能模型 81
3.2.2帶電分子勢能模型 86
3.2.3高分子勢能模型 90
3.2.4鍵結勢能方程式 92
3.2.5金屬勢能模型 96
3.3平行方法於分子動力學 98
3.3.1原子分散法(Atom Decomposition Method) 99
3.3.2力分散法(Force Decomposition Method) 101
3.3.3空間分散法(Spatial Decomposition Method)103
3.3.4平行化效能評估 106
第四章、模擬系統與數值方法 107
4.1簡單剪切流場 107
4.2收縮-膨脹流場 111
4.3個人電腦叢集系統 114
4.4 平行計算於分子動力學 117
4.4.1模擬程式平行化分析 117
4.4.2模擬程式平行化方法 118
第五章、結果與討論 119
5.1簡單剪切流場 119
5.1.1不同牆壁參數 119
5.1.2不同牆壁吸引力 123
5.1.3不同的剪切速率 127
5.2 收縮膨脹流場 129
5.2 收縮膨脹流場之模擬結果 129
5.2.1 長鏈分子l = 25之膨脹收縮流場 130
5.2.2 長鏈分子l = 50之膨脹收縮流場 146
5.2.3 長鏈分子l = 100之膨脹收縮流場 157
5.2.4膨脹收縮流場不同鏈長分子之比較 168
5.3 平行化結果與效率探討 186
5.3.1平行計算結果之驗證 186
5.3.2平行計算效率評估 188
第六章、結論與未來展望 193
參考文獻 195
Appendix A 減縮單位轉換 201
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