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課程來源:MIT
     
10.675J / 5.675J 2004秋季課程:分子與延伸系統的量子力學電腦運算(Computational Quantum Mechanics of Molecular and Extended Systems, Fall 2004)

翻譯:饒立

編輯:馬景文   劉慕華


Tetrahedral H-bonded water pentamer figure.
四面體型的氫鍵鍵合的水的五聚體圖像,鍵長鍵角:O-O 0.282 nm, O--O 0.282 nm, O-O-O 109.47。圖片來源:《水的氫鍵》。(倫敦南岸大學Martin Chaplin教授提供,授權使用。)
Tetrahedral H-bonded water pentamer figure, O-O 0.282 nm, O--O 0.282 nm, O-O-O 109.47&deg. From Hydrogen Bonding in Water. (Image courtesy of Professor Martin Chaplin, London South Bank University. Used with permission.)

課程重點

本課程提供一套完整作業和可下載的 課堂講稿
This course features a complete set of assignments and downloadable lecture notes.

課程描述

本課程介紹用於解決多電子體系問題的近似方法:Hartree-Fock理論和密度泛函理論的理論框架,討論多種加入電子相關項的方法。除了化學過程的熱 力學及動力學,還強調使用這些方法計算化學體系的反映活性與光譜性質。本課程還集中於前沿方法運用於複雜超曲面取樣,求出液相反應、催化劑和生物體系。

The theoretical frameworks of Hartree-Fock theory and density functional theory are presented in this course as approximate methods to solve the many-electron problem. A variety of ways to incorporate electron correlation are discussed. The application of these techniques to calculate the reactivity and spectroscopic properties of chemical systems, in addition to the thermodynamics and kinetics of chemical processes, is emphasized. This course also focuses on cutting edge methods to sample complex hypersurfaces, for reactions in liquids, catalysts and biological systems.
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概述

本課程教授從化學與物理的角度進行量子力學計算的藝術。這門課處於實驗課與理論課之間。實驗課靠動 手來學習,學會如何好好操縱儀器和解析資料,比懂得儀器的精確結構和外蓋之內有什麼更加重要。同樣,在課程中學習如何正確應用各種量子計算程式和如何解讀 程式的輸出,但不必知道100行與1000行程式的每一運算是如何工作。另一方面要學會程式背後的理論,以解讀程式輸出的資料。也會學習量子力學計算方法 的應用,以理解其能力和應用範圍。最後,深入理解目前有關這些方法的研究和發展,以瞭解這個領域發展的方向和未來的期望。

課程目標

學習另一種解決科學和工程問題的方法:應用量子力學計算,瞭解其應用範圍、可能性和局限。

在麻省理工學院的研究期間,在實習學校和未來的工作能夠進行量化計算。(這課程有幾個學生已經在主流期刊發表基他們專題的論文)。

增加(至少部分)對文獻的熟悉,並能夠批判性閱讀。

瞭解當前的研究方向和可能性。

必備先修要求

沒有特別先修要求,只需要講師許可。期望生能盡快適應數學和物理的高級概念。

課本

Szabo, Attila和Neil S. Ostlund《現代量子化學:高級電子結構理論導讀》Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, New York: McGraw-Hill, Inc., 1989. ISBN: 0070627398.

課程沒有合適的課本。最好的仍然是Szabo和Ostlund的《現代量子化學》,是本課程“必備”。Frank Jensen的《量子化學導論》有類似內容,還包括密度泛函的討論以及很有用的第12章:〈過渡態理論和統計力學〉。同時有描述許多Gaussian程式使用的方法,頗為有用。“推薦” 在本課程使用。最後,其他參考書參見相關閱讀資料部分。

軟體

Gaussian03:用於進行量子力學計算。calculations.

GaussView:圖形用戶介面,用於建立和運行作業檔案,工作運行和視覺化輸出。

CPMD:分子動力學網站。

硬體

Sun and Linux®電腦

NCSA(美國計算科學協會):SGI Origin 2000 (796處理器)

作業和期末專題

本課程共有五套習題。學生一定要完成期末專題。

Grading

Table of Grading 項目 百分比
作業 30%
參與 20%
期末專題 50%

Overview

The course teaches the art of quantum mechanical calculations from both the chemistry and physics point of view. It, thus, falls somewhere between a laboratory course and a lecture course. In a laboratory course, you must learn by doing, and it is more important that you learn how to run the equipment well and how to interpret the data than that you learn how a piece of equipment is constructed and what exactly is under its cover. Similarly, in this course, you will learn how to run various quantum codes correctly and how to interpret the output of the codes, but you will not necessarily need to know how each algorithm in the 100's of 1000's of lines of code works. On the other hand, you will learn the theories behind the computer codes, so that you will be able to interpret the output of the codes. You will also learn about applications of computational quantum mechanical methods, in order to understand their potential and scope. Finally, you will gain insight into the current research and development of these methods to know where the field is going and what to expect in the future.

Course Objectives

Learn a different approach to solving scientific and engineering problems: performing quantum mechanical calculations and understanding their scope, possibilities and limitations.

Be able to perform calculations during your research at MIT, in Practice School, and in your future work. (Several students of this class have published papers in major journals based on their projects.)

Gain a (partial) familiarity with the literature and be able to read it critically.

Understand current research directions and possibilities.

Pre-requisites

There are no specific prerequisites, just permission of the instructor. It is expected that students should be able relatively quickly to become comfortable with advanced concepts from mathematics and physics.

Textbook

Szabo, Attila, and Neil S. Ostlund. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory. New York: McGraw-Hill, Inc., 1989. ISBN: 0070627398.

There is no suitable textbook for this course. The best one still seems to be Modern Quantum Chemistry by Szabo and Ostlund, which is "required" for the course. Introduction to Quantum Chemistry by Frank Jensen has similar material, but also includes a discussion of density functional theory and has a useful chapter, 12 "Transition State Theory and Statistical Mechanics." It also has helpful descriptions of many of the methods that Gaussian uses. It is "recommended" for the course. Finally, see the References document for other helpful books.

Software

Gaussian03: Used to perform quantum mechanical calculations.

GaussView: GUI, used to create job files, run jobs, and visualize output.

CPMD: Car-Parrinello Molecular Dynamics Web site.

Hardware

Sun and Linux® machines

NCSA (National Computational Science Alliance): SGI Origin 2000 (796 processors)

Homeworks and Final Project

There are five problem sets in this course. Each student is required to complete a final project.

Grading

Table of Grading ACTIVITIES PERCENTAGES
Homework 30%
Participation 20%
Final Project 50%

 
 
Table for Calendar Section 課 課程單元 重要日期
1 導言,課本和筆記,多質點薛定諤方程,密度泛函理論,舉例和啟發
Introduction, Textbook and Notes, Many Body Schrödinger Equation, Density Functional Theory, Examples and Inspiration
 
2 電子自旋,自旋軌道,分子軌道理論,價鍵理論
Electronic Spin, Spin Orbitals, Molecular Orbital Theory, Valence Bond Theory
 
3 Hartree-Fock理論,矩陣操作
Hartree-Fock Theory, Matrix Manipulations
 
4 數學基礎,迪拉克符號,G03計算
Mathematical Underpinnings, Dirac Notation, G03 Calculations
 
5 電子教室導課
Electronic Classroom Tutorial
 
6 Hartree-Fock方程解,變分法原理,均勻場理論
Solution of Hartree-Fock Equations, Variational Principle, Mean Field Theory
習題一上交
Problem set 1 due
7 H-F方程解(續),特徵值的意義,基組導論
Solution of H-F Equations (cont.), Meaning of Eigenvalues, Basis Sets Introduction
 
8 高斯基組
Gaussian Basis Sets
習題二上交
Problem set 2 due
9 相關項,組態相互作用,MP微擾理論
Correlation, CI, MP Perturbation Theories
 
10 密度泛函理論:導論
Density Functional Theory (DFT) - Introduction
習題三上交
Problem set 3 due
11 密度泛函理論:Kohn-Sham方程的解和交換-相關泛函
DFT: Solution of Kohn-Sham Equations and Exchange-Correlation Functionals
 
12 耦合簇理論,QCISD, G1, G2
Coupled-Cluster Theories, QCISD, G1, G2
習題四上交
Problem set 4 due
13 G1,G2(續),比較,美國計算科學協會團隊,專題
G1, G2 (cont.), Comparison, NCSA Teams, Projects
專題初選和文獻搜索上交
Initial choice of project and literature search due
14 平面波贗勢方法(PWPP)
The Plane-wave Pseudopotential Method (PWPP)
 
15 平面波贗勢方法(續),經典分子動力學(MD)導論
PWPP (cont.), Introduction to Classical Molecular Dynamics (MD)
 
16 Car-Parrinello分子力學:方法
Car-Parrinello Molecular Dynamics - Method
 
17 運行Car-Parrinello計算
Running the Car-Parrinello Code
專題進展報告上交
Project status report due
18 Car-Parrinello分子力學:應用
Car-Parrinello Molecular Dynamics - Applications
 
19 嵌入,反應場方法,溶劑化,聯合QM/MM(量子力學/分子力學)
Embedding, Reaction Field Methods, Solvation, Combined QM/MM
習題五上交
Problem set 5 due
20 探索聯合體自由能的前景,反應性
Exploring Complex Free Energy Landscapes - Reactivity
 
21 計算反應速率常數
Computing Reaction Rate Constants
專題定案
Project finalized
22 學生期末專題報告I
Student Final Project Presentations I
 
23 學生期末專題報告II
Student Final Project Presentations II
 
24 選擇性抗硫化自推動氧化催化劑設計(助教講授)
Design of Selective, Sulfur Resistant, Oxidation Automotive Catalysts (Presented by Course Teaching Assistant)
 

 


下表包含指定閱讀的期刊文獻和課本章節:
Assigned readings of journal articles are included in the table below as well as readings from the required text:

Szabo, Attila和Neil S. Ostlund《現代量子化學:高級電子結構理論導讀》Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, New York:McGraw-Hill, Inc.,989. ISBN:0070627398。
Szabo, Attila, and Neil S. Ostlund. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory. New York: McGraw-Hill, Inc., 1989. ISBN: 0070627398.

在表下還列出推薦參考書目。
A bibliography of recommended reference texts are listed below the table.

Table for Readings lec # 課程單元 閱讀資料
1 導言,課本和筆記,多質點薛定諤方程,密度泛函理論,舉例和啟發
Introduction, Textbook and Notes, Many Body Schrödinger Equation, Density Functional Theory, Examples and Inspiration
 
2 電子自旋,自旋軌道,分子軌道理論,價鍵理論
Electronic Spin, Spin Orbitals, Molecular Orbital Theory, Valence Bond Theory
復習量子力學,氫原子的解答。
Review quantum mechanics, Solution of hydrogen atom.
3 Hartree-Fock理論,矩陣操作
Hartree-Fock Theory, Matrix Manipulations
 
4 數學基礎,迪拉克符號,G03計算
Mathematical Underpinnings, Dirac Notation, G03 Calculations
閱讀SO 1-30頁
Read SO, pp. 1-30.
5 電子教室導課
Electronic Classroom Tutorial
 
6 Hartree-Fock方程解,變分法原理,均勻場理論
Solution of Hartree-Fock Equations, Variational Principle, Mean Field Theory
 
7 H-F方程解(續),特徵值的意義,基組導論
Solution of H-F Equations (cont.), Meaning of Eigenvalues, Basis Sets Introduction
閱讀SO 108-122,131-149頁
SO, pp. 108-122, 131-149.
8 高斯基組
Gaussian Basis Sets
 
9 相關項,組態相互作用,MP微擾理論
Correlation, CI, MP Perturbation Theories
閱讀SO 60-64,320-326,350-353頁;學習圖表375-376;速讀SO第四章。
SO, pp. 60-64, 320-326, 350-353; study graphs 375-376; skim SO chapter 4.
10 密度泛函理論:導論
Density Functional Theory (DFT) - Introduction
閱讀密度泛函理論的講義。
Read handout on DFT.

密度泛函理論文獻一:: Hohenberg, P.和W. Kohn. 〈非均勻電子氣Inhomogeneous Electron Gas〉《物理評論Physical Review》136卷, 3B期(1964年11月9日): B864-B871。
DFT paper 1: Hohenberg, P., and W. Kohn. "Inhomogeneous Electron Gas." Physical Review 136, no. 3B (9 November, 1964): B864-B871.

密度泛函理論文獻二: Kohn, W.和L. J. Sham.〈包含交換與關聯效應的自洽方程組Self-Consistent Equations Including Exchange and Correlation Effects〉《物理評論Physical Review》140卷4A-15期(1965年11月): A1133-A1138。
DFT paper 2: Kohn, W., and L. J. Sham. "Self-Consistent Equations Including Exchange and Correlation Effects." Physical Review 140, no. 4A – 15 (November 1965): A1133-A1138.
11 密度泛函理論:導論
DFT: Solution of Kohn-Sham Equations and Exchange-Correlation Functionals
 
12 耦合簇理論,QCISD, G1, G2
Coupled-Cluster Theories, QCISD, G1, G2
速讀SO第5章
Skim SO, chapter 5.
13 G1,G2(續),比較,美國計算科學協會團隊,專題
G1, G2 (cont.), Comparison, NCSA Teams, Projects
閱讀講義
Read handouts

G2理論評價:Curtiss, Larry A., Krishnan Raghavachari, Paul C. Redfern和John A. Pople. 〈計算生成焓的G2和密度泛函理論的評價Assessment of Gaussian-2 and Density Functional Theories for the Computation of Enthalpies of Formation〉《化學物理期刊The Journal of Chemical Physics》106卷3期 (1997年1月15日): 1063-1079。
G2 Assessment: Curtiss, Larry A., Krishnan Raghavachari, Paul C. Redfern, and John A. Pople. "Assessment of Gaussian-2 and Density Functional Theories for the Computation of Enthalpies of Formation." The Journal of Chemical Physics 106, no. 3 (15 January 1997): 1063-1079.

G3理論:Curtiss, Larry A., Krishnan Raghavachari, Paul C. Redfern, Vitaly Rassolov和John A. Pople. 〈包含第一和第二排原子的分子的G3理論Gaussian-3 (G3) Theory for Molecules Containing First and Second-row Atoms〉《化學物理期刊The Journal of Chemical Physics》109卷18期 (1998年11月8日): 7764-7776 begin_of_the_skype_highlighting              7764-7776      end_of_the_skype_highlighting。
G3 Theory: Curtiss, Larry A., Krishnan Raghavachari, Paul C. Redfern, Vitaly Rassolov, and John A. Pople. "Gaussian-3 (G3) Theory for Molecules Containing First and Second-row Atoms." The Journal of Chemical Physics 109, no. 18 (8 November 1998): 7764-7776 begin_of_the_skype_highlighting              7764-7776      end_of_the_skype_highlighting.
14 平面波贗勢方法(PWPP)
The Plane-wave Pseudopotential Method (PWPP)
 
15 平面波贗勢方法(續),經典分子動力學(MD)導論
PWPP (cont.), Introduction to Classical Molecular Dynamics (MD)
 
16 Car-Parrinello分子力學:方法
Car-Parrinello Molecular Dynamics - Method
Car-Parrinello方法的原始文獻:Car, R.和M. Parrinello.〈分子動力學和密度泛函理論的統一方法Unified Approach for Molecular Dynamics and Density-Functional Theory〉,《物理評論通訊Physical Review Letter》55, 卷22–25期 (1985年11月): 2471-2474 begin_of_the_skype_highlighting              2471-2474      end_of_the_skype_highlighting。
Original Car-Parrinello Paper: Car, R., and M. Parrinello. "Unified Approach for Molecular Dynamics and Density-Functional Theory." Physical Review Letter 55, no. 22–25 (November 1985): 2471-2474 begin_of_the_skype_highlighting              2471-2474      end_of_the_skype_highlighting.
17 運行Car-Parrinello計算
Running the Car-Parrinello Code
復習15講和16講的分子動力學
Review molecular dynamics from lecture 15 and 16.
18 Car-Parrinello分子力學:應用
Car-Parrinello Molecular Dynamics - Applications
 
19 嵌入,反應場方法,溶劑化,聯合QM/MM(量子力學/分子力學)
Embedding, Reaction Field Methods, Solvation, Combined QM/MM
 
20 探索聯合體自由能的前景,反應性
Exploring Complex Free Energy Landscapes - Reactivity
 
21 計算反應速率常數
Computing Reaction Rate Constants
 
22 學生期末專題報告I
Student Final Project Presentations I
 
23 學生期末專題報告II
Student Final Project Presentations II
 
24 選擇性抗硫化自推動氧化催化劑設計(課程助教講授)
Design of Selective, Sulfur Resistant, Oxidation Automotive Catalysts (Presented by Course Teaching Assistant)
 

推薦的閱讀資料
Recommended Readings

Jensen, Frank. 《計算化學導論》 Introduction to Computational Chemistry. New York: John Wiley and Sons, 1999. ISBN: 0471980854.
Jensen, Frank. Introduction to Computational Chemistry. New York: John Wiley and Sons, 1999. ISBN: 0471980854.

Hehre, Warren J., Leo Radom, Paul v.R. Schleyer, 和J. A. Pople. 《從頭算分子軌道理論》 Ab initio Molecular Orbital Theory. New York: John Wiley and Sons, 1986. ISBN: 0471812412. [經典課本,有大量數據,主要是使用高斯程式計算。] [This is a classic text with a great amount of data, focussing on calculations performed with Gaussian.]
Hehre, Warren J., Leo Radom, Paul v.R. Schleyer, and J. A. Pople. Ab initio Molecular Orbital Theory. New York: John Wiley and Sons, 1986. ISBN: 0471812412. [This is a classic text with a great amount of data, focussing on calculations performed with Gaussian.]

Parr, Robert G., 和楊偉濤Weitao Yang. 《原子與分子的密度泛函理論》 Density-Functional Theory of Atoms and Molecules. New York: Oxford University Press, 1989. ISBN: 0195042794. [密度泛函理論的經典課本] [Classic book on density functional theory.]
Parr, Robert G., and Weitao Yang. Density-Functional Theory of Atoms and Molecules. New York: Oxford University Press, 1989. ISBN: 0195042794. [Classic book on density functional theory.]

Levine, Ira N. 《量子化學》第五版Quantum Chemistry. 5th ed. Upper Saddle River, NJ: Prentice Hall, 2000. ISBN: 0136855121. [量子力學的入門書,關於電子結構計算的幾章寫得很好。] [Introductory book on quantum mechanics with several good chapters on electronic structure calculations.]
Levine, Ira N. Quantum Chemistry. 5th ed. Upper Saddle River, NJ: Prentice Hall, 2000. ISBN: 0136855121. [Introductory book on quantum mechanics with several good chapters on electronic structure calculations.]

Martin, Richard M. 《電子結構:基本理論和實用方法》Electronic Structure: Basic Theory and Practical Methods. Cambridge, UK: Cambridge University Press, 2004. ISBN: 0521782856. [近期一本從物理角度論述電子結構計算的好書,主要關注密度泛函理論。] [Good recent book on electronic structure calculations from the physics standpoint, with a focus on density functional theory.]
Martin, Richard M. Electronic Structure: Basic Theory and Practical Methods. Cambridge, UK: Cambridge University Press, 2004. ISBN: 0521782856. [Good recent book on electronic structure calculations from the physics standpoint, with a focus on density functional theory.]

Cohen-Tannoudji, Claude, Bernard Diu, 和Franck Laloë. 《量子力學》 Quantum Mechanics. New York: John Wiley and Sons, 1977. ISBN: 0471164321. [許多關於量子力學的書本的一本] [One of the many books on quantum mechanics.]
Cohen-Tannoudji, Claude, Bernard Diu, and Franck Laloë. Quantum Mechanics. New York: John Wiley and Sons, 1977. ISBN: 0471164321. [One of the many books on quantum mechanics.]

Hill, Terrell L. 《統計熱力學導論》An Introduction to Statistical Thermodynamics. Reading, MA: Addison-Wesley Publishing Company, 1962. [有高斯程式使用的基本統計力學公式。有Dover版本。] [Has basic statistical mechanical formulas used in Gaussian. A Dover edition is also available.]
Hill, Terrell L. An Introduction to Statistical Thermodynamics. Reading, MA: Addison-Wesley Publishing Company, 1962. [Has basic statistical mechanical formulas used in Gaussian. A Dover edition is also available.]

McQuarrie, Donald A. 《統計力學》Statistical Mechanics. New York: Harper Collins Publishers, Inc., 1976. ISBN: 0060443669. [比Hill的書更詳細。] [A more elaborate presentation than Hill's book.]
McQuarrie, Donald A. Statistical Mechanics. New York: Harper Collins Publishers, Inc., 1976. ISBN: 0060443669. [A more elaborate presentation than Hill's book.]

Ashcroft, Neil W., 和N. David Mermin. 《固體物理》Solid-State Physics. Fort Worth: Harcourt Brace College Publishers, 1976. ISBN: 0030493463[經典文本][A classic text.]
Ashcroft, Neil W., and N. David Mermin. Solid-State Physics. Fort Worth: Harcourt Brace College Publishers, 1976. ISBN: 0030493463. [A classic text.]


以下是學生記錄的課堂講稿樣板。由Rick Rajter提供,授權使用。
An example set of lecture notes taken by a student in the course are available in the table below. Courtesy of Rick Rajter. Used with permission.

Lecture notes files. 課 課程單元
1 導言,課本和筆記,多質點薛定諤方程,密度泛函理論,舉例和啟發(PDF)
Introduction, Textbook and Notes, Many Body Schrödinger Equation, Density Functional Theory, Examples and Inspiration (PDF)
2 電子自旋,自旋軌道,分子軌道理論,價鍵理論(PDF)
Electronic Spin, Spin Orbitals, Molecular Orbital Theory, Valence Bond Theory (PDF)
3 Hartree-Fock理論,矩陣操作(PDF)
Hartree-Fock Theory, Matrix Manipulations (PDF)
4 數學基礎,迪拉克符號,G03計算 (PDF)
Mathematical Underpinnings, Dirac Notation, G03 Calculations (PDF)
5 電子教室導課
Electronic Classroom Tutorial
6 Hartree-Fock方程解,變分法原理,均勻場理論 (PDF)
Solution of Hartree-Fock Equations, Variational Principle, Mean Field Theory (PDF)
7 H-F方程解(續),特徵值的意義,基組導論(PDF)
Solution of H-F Equations (cont.), Meaning of Eigenvalues, Basis Sets Introduction (PDF)
8 高斯基組(PDF)
Gaussian Basis Sets (PDF)
9 相關項,組態相互作用,MP微擾理論(PDF)
Correlation, CI, MP Perturbation Theories (PDF)
10 密度泛函理論:導論(PDF)
Density Functional Theory (DFT) - Introduction (PDF)
11 密度泛函理論:Kohn-Sham方程的解和交換-相關泛函 (PDF)
DFT: Solution of Kohn-Sham Equations and Exchange-Correlation Functionals (PDF)
12 耦合簇理論,QCISD, G1, G2 (PDF)
Coupled-Cluster Theories, QCISD, G1, G2 (PDF)
13 G1,G2(續),比較,美國計算科學協會團隊,專題 (PDF)
G1, G2 (cont.), Comparison, NCSA Teams, Projects (PDF)
14 平面波贗勢方法(PWPP) (PDF)
The Plane-wave Pseudopotential Method (PWPP) (PDF)
15 平面波贗勢方法(續),經典分子動力學(MD)導論
PWPP (cont.), Introduction to Classical Molecular Dynamics (MD)
16 Car-Parrinello分子力學:方法(PDF)
Car-Parrinello Molecular Dynamics - Method (PDF)
17 運行Car-Parrinello計算(PDF)
Running the Car-Parrinello Code (PDF)
18 Car-Parrinello分子力學:應用 (PDF)
Car-Parrinello Molecular Dynamics - Applications (PDF)
19 嵌入,反應場方法,溶劑化,聯合QM/MM(量子力學/分子力學)(PDF)
Embedding, Reaction Field Methods, Solvation, Combined QM/MM (PDF)
20 探索聯合體自由能的前景,反應性 (PDF)
Exploring Complex Free Energy Landscapes - Reactivity (PDF)
21 計算反應速率常數 (PDF)
Computing Reaction Rate Constants (PDF)
22 學生期末專題報告I
Student Final Project Presentations I
23 學生期末專題報告II
Student Final Project Presentations II
24 選擇性抗硫化自推動氧化催化劑設計(助教講授)(PDF)
Design of Selective, Sulfur Resistant, Oxidation Automotive Catalysts (Presented by Course Teaching Assistant) (PDF)

 
Assignment files. 作業 解答
作業一 (PDF)
Homework 1 (PDF)
(PDF)
作業二(PDF)
Homework 2 (PDF)
(PDF)
作業三 (PDF)
Homework 3 (PDF)
(PDF)

問題二第一步 (TXT)
Problem 2 Step 1 (TXT)
問題二第二步(TXT)
Problem 2 Step 2 (TXT)
問題二第三步(TXT)
Problem 2 Step 3 (TXT)
作業四(PDF)
Homework 4 (PDF)
(PDF)
作業五 (PDF)
Homework 5 (PDF)

Car-Parrinello分子動力學輸入檔(TXT)
CPMD Input File (TXT)
(PDF)

 

每位學生要完成一項期末專題。

學生專題題目:

第22課

蛋氨酸經由自由基途徑氧化的計算處理

多環芳烴(PAHs)的溶劑化能量

氣相中羥基自由基與丙酮地反應

含時密度泛函理論研究釕配合物的吸收光譜-與線性回應的比較

現有相對論數學方法計算重金屬雙原子分子性質的精確度

電子結構計算的可能偏差

ONOO-/CO2加合物結構和熱力學的量子化學研究

應用Car-Parrinello分子動力學加贗動力學方法模擬酮-稀醇的互變現象

分子激勵的補償離子效應:有六氟磷酸酯存在下的一個低聚噻吩激勵分子

羥基遷移的動力學

羥基遷移的動力學

第23課

增加多面低聚Silsesquioxane (POSS)聚合物濃度的修飾

弱結合簇Ar-HCCCN的從頭計算

MgO表面性質w/XL方向

由第一原理計算得到的甲胺轉置-內轉動光譜

量子化學得到的乙基精確熱力學資料

Each student is required to complete a final project.

Student Project Titles

Session 22

Computational Approach to Study Methionine Oxidation by Free Radicals

Solvation Energies of Polycyclic Aromatic Hydrocarbons (PAHs)

Reactions of OH Radicals with Acetone in the Atmosphere

Absorption Spectrum of Ruthenium Complexes by Time Dependent Density Functional Theory - A Comparison with Linear Response

Accuracy of Existing Relativistic Numerical Methods in Predicting the Properties of Heavy Metal Diatomic Molecules

Potential Biases in Electronic Structure Calculations

Quantum Chemical Study of the Structure and Thermodynamics of the ONOO-/CO2 Adduct

Simulation of Keto-enol Tautomerism using CPMD Plus Metadynamics

The Effect of Counterions on Molecular Actuators: An Oligothiophene Actuator in the Presence of Hexafluorophosphate

Kinetics of OH Radical Transfer

Estimation of Solution Phase Thermochemistry

Session 23

Modifications of Polyhedral Oligomeric Silsesquioxane (POSS) to Increase Polymer Strength

ab Inito Calculations of the Weakly Bound Cluster Ar-HCCCN

MgO Surface Properties w/XL Orientation

Inversion-internal Rotational Spectra of Methylamine from First Principles

Accurate Thermodynamic Bulk Data of Ethyl Radical from Quantum Chemistry

 

電腦說明和指南

高斯程式

本課程使用高斯的目的,是除了熱化學計算,更好瞭解化學反應和過渡態理論。記住這點,我們的目的是給你們簡單、說明性的計算,為了簡單和速度犧牲精確度。

額外資訊可在高斯的一般高斯網站找到

這個網站可以下載或連接線上高斯03手冊。高斯98和高斯03的語法差別不大。

在個人電腦運行G03基礎的課堂筆記 (PDF)

Car-Parrinello分子動力學(CPMD)

除了如何下載CPMD(Car-Parrinello分子動力學)和線上手冊,還可以得到廣泛資訊。

CPMD手冊 (3.9.1)

Computer Instructions and Tutorials

Gaussian

The objective of using Gaussian in this course is to understand better chemical reactions and transition state theory, in addition to the computations of thermochemistry. With this in mind, our objective is to give you simple, illustrative calculations, and to sacrifice accuracy for speed and simplicity.

Additional information can be found at the General Gaussian Web site.

At this site, you can download or access the on line Gaussian03 manual. The syntax should not be too much different for Gaussian98 and Gaussian03.

Class notes on Basics of Running G03 on a PC (PDF)

Car-Parrinello Molecular Dynamics (CPMD)

You can get extensive information, in addition to instructions on how to download CPMD and the online manual.

CPMD Manual (3.9.1)

對「課程10.675J:分子與延伸系統的量子力學電腦運算」這門課有興趣的教育家、學生和自學者們,歡迎來和其他應用這個教材學習或教課的人在這個討論群組上互動。

這個服務是由麻省理工學院開放式課程提供,由猶他州立大學教育科技系的「開放持續學習機會研究群」所管理。世界各地的獨立學員可以互相連繫、協同合作、組織學習小組,及就利用麻省理工「開放式課程網頁」教材資源於他們正規或非正規教育學習時得到支援。

「開放式學習支援網」(Open Learning Support, 簡稱OLS)是一個著眼著眼於建立「社群軟體」的研究計劃,讓非正規學習社群利用現存公開的教材而組織起來。OLS基本前提是完整的教育機會必須讓使用者 能夠與能解答其問題或提供支援的其他人建立起溝通管道。贊助者一般只能提供免費開放的網頁教材,但很難提供這樣的社群管道。社群支援必須由其他使用者提 供。因此,OLS是:

在麻省理工「開放式課程網頁」以外獨立運作的。
需要使用者註冊並登入才能參與的
並不頒授任何學位或文憑的計劃
不提供與麻省理工或猶他州立大學教職人員直接連繫的管道
馬上來本課程《10.675J 分子與延伸系統的量子力學電腦運算》的討論群組看看吧。

「開放式學習支援網」是由The William and Flora Hewlett 基金會贊助提供。


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